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

GPy/__init__.py

@@ -4,6 +4,7 @@ import warnings
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 import core
+from core.parameterization import transformations
 import models
 import mappings
 import inference

GPy/core/model.py

@@ -403,17 +403,34 @@ class Model(Parameterized):
         x = self._get_params_transformed().copy()
 
         if not verbose:
+            # make sure only to test the selected parameters
+            if target_param is None:
+                transformed_index = range(len(x))
+            else:
+                transformed_index = self._raveled_index_for(target_param)
+                if self._has_fixes():
+                    indices = np.r_[:self.size]
+                    which = (transformed_index[:,None]==indices[self._fixes_][None,:]).nonzero()
+                    transformed_index = (indices-(~self._fixes_).cumsum())[transformed_index[which[0]]]
+                    
+                if transformed_index.size == 0:
+                    print "No free parameters to check"
+                    return
+            
             # just check the global ratio
-            dx = step * np.sign(np.random.uniform(-1, 1, x.size))
+            dx = np.zeros_like(x)
+            dx[transformed_index] = step * np.sign(np.random.uniform(-1, 1, transformed_index.size))
             
             # evaulate around the point x
             f1 = self.objective_function(x + dx)
             f2 = self.objective_function(x - dx)
             gradient = self.objective_function_gradients(x)
 
+            dx = dx[transformed_index]
+            gradient = gradient[transformed_index]
+            
             numerical_gradient = (f1 - f2) / (2 * dx)
             global_ratio = (f1 - f2) / (2 * np.dot(dx, np.where(gradient == 0, 1e-32, gradient)))
-
             return (np.abs(1. - global_ratio) < tolerance) or (np.abs(gradient - numerical_gradient).mean() < tolerance)
         else:
             # check the gradient of each parameter individually, and do some pretty printing
@@ -433,43 +450,50 @@ class Model(Parameterized):
             separator = '-' * len(header_string[0])
             print '\n'.join([header_string[0], separator])
             if target_param is None:
-                param_list = range(len(x))
+                param_index = range(len(x))
+                transformed_index = param_index
             else:
-                param_list = self._raveled_index_for(target_param)
+                param_index = self._raveled_index_for(target_param)
                 if self._has_fixes():
-                    param_list = np.intersect1d(np.r_[:self.size][self._fixes_], param_list, True)
+                    indices = np.r_[:self.size]
+                    which = (param_index[:,None]==indices[self._fixes_][None,:]).nonzero()
+                    param_index = param_index[which[0]]
+                    transformed_index = (indices-(~self._fixes_).cumsum())[param_index]
+                    #print param_index, transformed_index
+                else:
+                    transformed_index = param_index
                     
-                if param_list.size == 0:
+                if param_index.size == 0:
                     print "No free parameters to check"
                     return
 
             gradient = self.objective_function_gradients(x)
             np.where(gradient == 0, 1e-312, gradient)
             ret = True
-            for i, ind in enumerate(param_list):
+            for nind, xind in itertools.izip(param_index, transformed_index):
                 xx = x.copy()
-                xx[i] += step
+                xx[xind] += step
                 f1 = self.objective_function(xx)
-                xx[i] -= 2.*step
+                xx[xind] -= 2.*step
                 f2 = self.objective_function(xx)
-                
                 numerical_gradient = (f1 - f2) / (2 * step)
-                ratio = (f1 - f2) / (2 * step * gradient[i])
-                difference = np.abs((f1 - f2) / 2 / step - gradient[i])
+                ratio = (f1 - f2) / (2 * step * gradient[xind])
+                difference = np.abs((f1 - f2) / 2 / step - gradient[xind])
 
                 if (np.abs(1. - ratio) < tolerance) or np.abs(difference) < tolerance:
-                    formatted_name = "\033[92m {0} \033[0m".format(names[ind])
+                    formatted_name = "\033[92m {0} \033[0m".format(names[nind])
                     ret &= True
                 else:
-                    formatted_name = "\033[91m {0} \033[0m".format(names[ind])
+                    formatted_name = "\033[91m {0} \033[0m".format(names[nind])
                     ret &= False
 
                 r = '%.6f' % float(ratio)
                 d = '%.6f' % float(difference)
-                g = '%.6f' % gradient[i]
+                g = '%.6f' % gradient[xind]
                 ng = '%.6f' % float(numerical_gradient)
                 grad_string = "{0:<{c0}}|{1:^{c1}}|{2:^{c2}}|{3:^{c3}}|{4:^{c4}}".format(formatted_name, r, d, g, ng, c0=cols[0] + 9, c1=cols[1], c2=cols[2], c3=cols[3], c4=cols[4])
                 print grad_string
+            self._set_params_transformed(x)
             return ret
         
     def input_sensitivity(self):

GPy/core/parameterization/array_core.py

@@ -28,8 +28,8 @@ class ObservableArray(np.ndarray, Observable):
     """
     __array_priority__ = -1 # Never give back ObservableArray
     def __new__(cls, input_array):
-        cls.__name__ = "ObservableArray\n     "
         obj = np.atleast_1d(input_array).view(cls)
+        cls.__name__ = "ObservableArray\n     "
         obj._observers_ = {}
         return obj
     def __array_finalize__(self, obj):

GPy/core/parameterization/index_operations.py

@@ -57,9 +57,12 @@ class ParameterIndexOperations(object):
     You can give an offset to set an offset for the given indices in the
     index array, for multi-param handling.
     '''
-    def __init__(self):
+    _offset = 0
+    def __init__(self, constraints=None):
         self._properties = IntArrayDict()
-        #self._reverse = collections.defaultdict(list)
+        if constraints is not None:
+            for t, i in constraints.iteritems():
+                self.add(t, i)
         
     def __getstate__(self):
         return self._properties#, self._reverse
@@ -118,6 +121,14 @@ class ParameterIndexOperations(object):
             return removed.astype(int)
         return numpy.array([]).astype(int)
     
+    def update(self, parameter_index_view, offset=0):
+        for i, v in parameter_index_view.iteritems():
+            self.add(i, v+offset)
+
+    
+    def copy(self):
+        return ParameterIndexOperations(dict(self.iteritems()))
+    
     def __getitem__(self, prop):
         return self._properties[prop]
     
@@ -191,7 +202,7 @@ class ParameterIndexOperationsView(object):
 
 
     def indices(self):
-        [ind for ind in self.iterindices()]
+        return [ind for ind in self.iterindices()]
 
 
     def properties_for(self, index):
@@ -206,6 +217,8 @@ class ParameterIndexOperationsView(object):
         removed = self._param_index_ops.remove(prop, indices+self._offset)
         if removed.size > 0:
             return removed - self._size + 1
+        if self[prop].size == 0:
+            del self[prop]
         return removed
 
 
@@ -219,9 +232,12 @@ class ParameterIndexOperationsView(object):
         import pprint
         return pprint.pformat(dict(self.iteritems()))
 
-    def update(self, parameter_index_view):
+    def update(self, parameter_index_view, offset=0):
         for i, v in parameter_index_view.iteritems():
-            self.add(i, v)
+            self.add(i, v+offset)
     
+    
+    def copy(self):
+        return ParameterIndexOperations(dict(self.iteritems()))
     pass
 

GPy/core/parameterization/param.py

@@ -43,6 +43,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
     _parameters_ = []
     def __new__(cls, name, input_array, default_constraint=None):
         obj = numpy.atleast_1d(super(Param, cls).__new__(cls, input_array=input_array))
+        cls.__name__ = "Param"
         obj._current_slice_ = (slice(obj.shape[0]),)
         obj._realshape_ = obj.shape
         obj._realsize_ = obj.size
@@ -75,6 +76,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
         self._original_ = getattr(obj, '_original_', None)
         self._name = getattr(obj, 'name', None)
         self.gradient = getattr(obj, 'gradient', None)
+        self.constraints = getattr(obj, 'constraints', None)
 
     def __array_wrap__(self, out_arr, context=None):
         return out_arr.view(numpy.ndarray)
@@ -348,7 +350,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
     def _description_str(self):
         if self.size <= 1: return ["%f" % self]
         else: return [str(self.shape)]
-    def _parameter_names(self, add_name):
+    def parameter_names(self, add_name=False):
         return [self.name]
     @property
     def flattened_parameters(self):
@@ -391,6 +393,9 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
             slice_index = self._current_slice_
         if isinstance(slice_index, (tuple, list)):
             clean_curr_slice = [s for s in slice_index if numpy.any(s != Ellipsis)]
+            for i in range(self._realndim_-len(clean_curr_slice)):
+                i+=len(clean_curr_slice)
+                clean_curr_slice += range(self._realshape_[i]) 
             if (all(isinstance(n, (numpy.ndarray, list, tuple)) for n in clean_curr_slice)
                 and len(set(map(len, clean_curr_slice))) <= 1):
                 return numpy.fromiter(itertools.izip(*clean_curr_slice),

GPy/core/parameterization/parameter_core.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2012, GPy authors (see AUTHORS.txt).
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 
-from transformations import Transformation, Logexp, NegativeLogexp, Logistic
+from transformations import Transformation, Logexp, NegativeLogexp, Logistic, __fixed__, FIXED, UNFIXED
 
 __updated__ = '2013-12-16'
 
@@ -10,11 +10,6 @@ def adjust_name_for_printing(name):
         return name.replace(" ", "_").replace(".", "_").replace("-","").replace("+","").replace("!","").replace("*","").replace("/","")
     return ''
 
-#===============================================================================
-# Printing:
-__fixed__ = "fixed"
-#===============================================================================
-
 class Observable(object):
     _observers_ = {}
     def add_observer(self, observer, callble):
@@ -30,8 +25,10 @@ class Parameterizable(object):
         from GPy.core.parameterization.array_core import ParamList
         _parameters_ = ParamList()
     
-    def parameter_names(self):
-        return [p.name for p in self._parameters_]
+    def parameter_names(self, add_name=False):
+        if add_name:
+            return [adjust_name_for_printing(self.name) + "." + xi for x in self._parameters_ for xi in x.parameter_names(add_name=True)]
+        return [xi for x in self._parameters_ for xi in x.parameter_names(add_name=True)]
     
     def parameters_changed(self):
         """
@@ -77,6 +74,13 @@ class Parentable(object):
     def has_parent(self):
         return self._direct_parent_ is not None
 
+    def _notify_parent_change(self):
+        for p in self._parameters_:
+            p._parent_changed(self)
+
+    def _parent_changed(self):
+        raise NotImplementedError, "shouldnt happen, Parentable objects need to be able to change their parent"
+
     @property
     def _highest_parent_(self):
         if self._direct_parent_ is None:
@@ -120,12 +124,23 @@ class Indexable(object):
     def _offset_for(self, param):
         raise NotImplementedError, "shouldnt happen, offset required from non parameterization object?"
     
+    def _raveled_index_for(self, param):
+        """
+        get the raveled index for a param
+        that is an int array, containing the indexes for the flattened
+        param inside this parameterized logic.
+        """
+        raise NotImplementedError, "shouldnt happen, raveld index transformation required from non parameterization object?"
+
 class Constrainable(Nameable, Indexable, Parameterizable):
     def __init__(self, name, default_constraint=None):
         super(Constrainable,self).__init__(name)
         self._default_constraint_ = default_constraint
         from index_operations import ParameterIndexOperations
         self.constraints = ParameterIndexOperations()
+        if self._default_constraint_ is not None:
+            self.constrain(self._default_constraint_)
+        
     #===========================================================================
     # Fixing Parameters:
     #===========================================================================
@@ -138,26 +153,47 @@ class Constrainable(Nameable, Indexable, Parameterizable):
         if value is not None:
             self[:] = value
         self.constrain(__fixed__, warning=warning)
-        self._highest_parent_._set_fixed(self._raveled_index())
+        rav_i = self._highest_parent_._raveled_index_for(self)
+        self._highest_parent_._set_fixed(rav_i)
     fix = constrain_fixed
+    
     def unconstrain_fixed(self):
         """
         This parameter will no longer be fixed.
         """
         unconstrained = self.unconstrain(__fixed__)
-        import ipdb;ipdb.set_trace()
         self._highest_parent_._set_unfixed(unconstrained)    
-        
     unfix = unconstrain_fixed
+    
+    def _set_fixed(self, index):
+        import numpy as np
+        if not self._has_fixes(): self._fixes_ = np.ones(self.size, dtype=bool)
+        self._fixes_[index] = FIXED
+        if np.all(self._fixes_): self._fixes_ = None  # ==UNFIXED
+    
+    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]
+        self._fixes_[index] = UNFIXED
+        if np.all(self._fixes_): self._fixes_ = None  # ==UNFIXED
+
+    def _connect_fixes(self):
+        import numpy as np
+        fixed_indices = self.constraints[__fixed__]
+        if fixed_indices.size > 0:
+            self._fixes_ = np.ones(self.size, dtype=bool) * UNFIXED
+            self._fixes_[fixed_indices] = FIXED
+        else:
+            self._fixes_ = None
+
     #===========================================================================
     # Constrain operations -> done
     #===========================================================================
     def _parent_changed(self, parent):
-        c = self.constraints
         from index_operations import ParameterIndexOperationsView
         self.constraints = ParameterIndexOperationsView(parent.constraints, parent._offset_for(self), self.size)
-        self.constraints.update(c)
-        del c
+        self._fixes_ = None
         for p in self._parameters_:
             p._parent_changed(parent)
 
@@ -174,17 +210,28 @@ class Constrainable(Nameable, Indexable, Parameterizable):
             self._set_params(transform.initialize(self._get_params()), update=False)
         reconstrained = self.unconstrain()
         self.constraints.add(transform, self._raveled_index())
-        if reconstrained.size > 0:
-            print "WARNING: reconstraining parameters {}".format(self.parameter_names)
+        if warning and reconstrained.size > 0:
+            print "WARNING: reconstraining parameters {}".format(self.parameter_names() or self.name)
         if update:
             self._highest_parent_.parameters_changed()
-        # if self.has_parent():
-        #     self._highest_parent_._add_constrain(self, transform, warning)
-        # else:
-        #     for p in self._parameters_:
-        #         self._add_constrain(p, transform, warning)
-        #     if update:
-        #         self.parameters_changed()
+
+    def unconstrain(self, *transforms):
+        """
+        :param transforms: The transformations to unconstrain from.
+
+        remove all :py:class:`GPy.core.transformations.Transformation`
+        transformats of this parameter object.
+        """
+        if len(transforms) == 0:
+            transforms = self.constraints.properties()
+        import numpy as np
+        removed = np.empty((0,),dtype=int)
+        for t in transforms:
+            unconstrained = self.constraints.remove(t, self._raveled_index())
+            removed = np.union1d(removed, unconstrained)
+            if t is __fixed__:
+                self._highest_parent_._set_unfixed(unconstrained)
+        return removed
     
     def constrain_positive(self, warning=True, update=True):
         """
@@ -211,21 +258,6 @@ class Constrainable(Nameable, Indexable, Parameterizable):
         """
         self.constrain(Logistic(lower, upper), warning=warning, update=update)
 
-    def unconstrain(self, *transforms):
-        """
-        :param transforms: The transformations to unconstrain from.
-
-        remove all :py:class:`GPy.core.transformations.Transformation`
-        transformats of this parameter object.
-        """
-        if len(transforms) == 0:
-            transforms = self.constraints.properties()
-        import numpy as np
-        removed = np.empty((0,),dtype=int)
-        for t in transforms:
-            removed = np.union1d(removed, self.constraints.remove(t, self._raveled_index()))
-        return removed
-    
     def unconstrain_positive(self):
         """
         Remove positive constraint of this parameter.

GPy/core/parameterization/parameterized.py

@@ -8,15 +8,10 @@ import cPickle
 import itertools
 from re import compile, _pattern_type
 from param import ParamConcatenation, Param
-from parameter_core import Constrainable, Pickleable, Observable, adjust_name_for_printing, Gradcheckable, __fixed__
+from parameter_core import Constrainable, Pickleable, Observable, adjust_name_for_printing, Gradcheckable
+from transformations import __fixed__, FIXED, UNFIXED
 from array_core import ParamList
 
-#===============================================================================
-# constants
-FIXED = False
-UNFIXED = True
-#===============================================================================
-
 class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
     """
     Parameterized class
@@ -71,37 +66,6 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
         self._added_names_ = set()
         del self._in_init_
 
-    #===========================================================================
-    # Parameter connection for model creation:
-    #===========================================================================
-#     def set_as_parameter(self, name, array, gradient, index=None, gradient_parent=None):
-#         """
-#         :param name:     name of the param (in print and plots), can be callable without parameters
-#         :type name:      str, callable
-#         :param array:    array which the param consists of
-#         :type array:     array-like
-#         :param gradient: gradient method of the param
-#         :type gradient:  callable
-#         :param index:    (optional) index of the param when printing
-#
-#         (:param gradient_parent:  connect these parameters to this class, but tell
-#                         updates to highest_parent, this is needed when parameterized classes
-#                         contain parameterized classes, but want to access the parameters
-#                         of their children)
-#
-#
-#         Set array (e.g. self.X) as param with name and gradient.
-#         I.e: self.set_as_parameter('curvature', self.lengthscale, self.dK_dlengthscale)
-#
-#         Note: the order in which parameters are added can be adjusted by
-#               giving an index, of where to put this param in printing
-#         """
-#         if index is None:
-#             self._parameters_.append(Param(name, array, gradient))
-#         else:
-#             self._parameters_.insert(index, Param(name, array, gradient))
-#         self._connect_parameters(gradient_parent=gradient_parent)
-
     def _has_fixes(self):
         return hasattr(self, "_fixes_") and self._fixes_ is not None
 
@@ -118,53 +82,25 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
         # if param.has_parent():
         #    raise AttributeError, "parameter {} already in another model, create new object (or copy) for adding".format(param._short())
         if param in self._parameters_ and index is not None:
-            # make sure fixes and constraints are indexed right
-            if self._has_fixes():
-                param_slice = slice(self._offset_for(param), self._offset_for(param) + param.size)
-                dest_index = sum((p.size for p in self._parameters_[:index]))
-                dest_slice = slice(dest_index, dest_index + param.size)
-                fixes_param = self._fixes_[param_slice].copy()
-                self._fixes_[param_slice] = self._fixes_[dest_slice]
-                self._fixes_[dest_slice] = fixes_param
-
-            del self._parameters_[param._parent_index_]
-            self._parameters_.insert(index, param)
+            self.remove_parameter(param)
+            self.add_parameter(param, index)
         elif param not in self._parameters_:
             # make sure the size is set
-            if not hasattr(self, 'size'):
-                self.size = sum(p.size for p in self._parameters_)
             if index is None:
+                self.constraints.update(param.constraints, self.size)
                 self._parameters_.append(param)
-
-                # make sure fixes and constraints are indexed right
-                if param._has_fixes(): fixes_param = param._fixes_.copy()
-                else: fixes_param = numpy.ones(param.size, dtype=bool)
-                if self._has_fixes(): self._fixes_ = np.r_[self._fixes_, fixes_param]
-                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.constraints.update(param.constraints, start)
                 self._parameters_.insert(index, param)
-
-                # make sure fixes and constraints are indexed right
-                if param._has_fixes(): fixes_param = param._fixes_.copy()
-                else: fixes_param = numpy.ones(param.size, dtype=bool)
-                ins = sum((p.size for p in self._parameters_[:index]))
-                if self._has_fixes(): self._fixes_ = np.r_[self._fixes_[:ins], fixes_param, self._fixes[ins:]]
-                elif not np.all(fixes_param):
-                    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()
-        for p in self._parameters_:
-            p._parent_changed(self)
-        if param._default_constraint_ is not None:
-            param.constrain(param._default_constraint_, False)
-        if self._has_fixes() and np.all(self._fixes_):  # ==UNFIXED
-            self._fixes_ = None
+        self._notify_parent_change()
+        self._connect_fixes()
+
 
     def add_parameters(self, *parameters):
         """
@@ -173,19 +109,27 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
         """
         [self.add_parameter(p) for p in parameters]
 
-    def remove_parameter(self, *names_params_indices):
+    def remove_parameter(self, param):
         """
-        :param names_params_indices: mix of parameter_names, param objects, or indices
-            to remove from being a param of this parameterized object.
-
-            note: if it is a string object it will not (!) be regexp-matched
-                  automatically.
+        :param param: param object to remove from being a parameter of this parameterized object.
         """
-        self._parameters_ = ParamList([p for p in self._parameters_
-                        if not (p._parent_index_ in names_params_indices
-                                or p.name in names_params_indices
-                                or p in names_params_indices)])
+        if not param in self._parameters_:
+            raise RuntimeError, "Parameter {} does not belong to this object, remove parameters directly from their respective parents".format(param._short())
+        del self._parameters_[param._parent_index_]
+        self.size -= param.size
+        constr = param.constraints.copy()
+        param.constraints.clear()
+        param.constraints = constr
+        param._direct_parent_ = None
+        param._parent_index_ = None
+        param._connect_fixes()
+        param._notify_parent_change()
+        pname = adjust_name_for_printing(param.name)
+        if pname in self._added_names_:
+            del self.__dict__[pname]
         self._connect_parameters()
+        #self._notify_parent_change()
+        self._connect_fixes()
 
     def _connect_parameters(self):
         # connect parameterlist to this parameterized object
@@ -214,6 +158,7 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
             elif not (pname in not_unique):
                 self.__dict__[pname] = p
                 self._added_names_.add(pname)
+
     #===========================================================================
     # Pickling operations
     #===========================================================================
@@ -337,7 +282,7 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
             self._added_names_.add(pname)
             self.__dict__[pname] = param
     #===========================================================================
-    # Index Handling
+    # Indexable Handling
     #===========================================================================
     def _backtranslate_index(self, param, ind):
         # translate an index in parameterized indexing into the index of param
@@ -373,36 +318,10 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
     #===========================================================================
     # Fixing parameters:
     #===========================================================================
-    def _set_fixed(self, param_or_index):
-        if not self._has_fixes(): self._fixes_ = numpy.ones(self.size, dtype=bool)
-        try:
-            param_or_index = self._raveled_index_for(param_or_index)
-        except AttributeError:
-            pass
-        self._fixes_[param_or_index] = FIXED
-        if numpy.all(self._fixes_): self._fixes_ = None  # ==UNFIXED
-    def _set_unfixed(self, param_or_index):
-        if not self._has_fixes(): self._fixes_ = numpy.ones(self.size, dtype=bool)
-        try:
-            param_or_index = self._raveled_index_for(param_or_index)
-        except AttributeError:
-            pass
-        self._fixes_[param_or_index] = UNFIXED
-        for constr, ind in self.constraints.iteritems():
-            if constr is __fixed__:
-                self._fixes_[ind] = FIXED
-        if numpy.all(self._fixes_): self._fixes_ = None  # ==UNFIXED
     def _fixes_for(self, param):
         if self._has_fixes():
             return self._fixes_[self._raveled_index_for(param)]
         return numpy.ones(self.size, dtype=bool)[self._raveled_index_for(param)]
-    # def _fix(self, param, warning=True):
-    #     f = self._add_constrain(param, __fixed__, warning)
-    #     self._set_fixed(f)
-    # def _unfix(self, param):
-    #     if self._has_fixes():
-    #         f = self._remove_constrain(param, __fixed__)
-    #         self._set_unfixed(f)
     #===========================================================================
     # Convenience for fixed, tied checking of param:
     #===========================================================================
@@ -515,11 +434,7 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
             return self._direct_parent_.hirarchy_name() + adjust_name_for_printing(self.name)
         else:
             return adjust_name_for_printing(self.name)
-    def _parameter_names(self, add_name=False):
-        if add_name:
-            return [adjust_name_for_printing(self.name) + "." + xi for x in self._parameters_ for xi in x._parameter_names(add_name=True)]
-        return [xi for x in self._parameters_ for xi in x._parameter_names(add_name=True)]
-    parameter_names = property(_parameter_names, doc="Names for all parameters handled by this parameterization object -- will add hirarchy name entries for printing")
+    #parameter_names = property(parameter_names, doc="Names for all parameters handled by this parameterization object -- will add hirarchy name entries for printing")
     def _collect_gradient(self, target):
         [p._collect_gradient(target[s]) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
     @property
@@ -549,7 +464,7 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
 
         name = adjust_name_for_printing(self.name) + "."
         constrs = self._constraints_str; ts = self._ties_str
-        desc = self._description_str; names = self.parameter_names
+        desc = self._description_str; names = self.parameter_names()
         nl = max([len(str(x)) for x in names + [name]])
         sl = max([len(str(x)) for x in desc + ["Value"]])
         cl = max([len(str(x)) if x else 0 for x in constrs + ["Constraint"]])

GPy/core/parameterization/transformations.py

@@ -6,8 +6,17 @@ import numpy as np
 from domains import _POSITIVE,_NEGATIVE, _BOUNDED
 import sys
 import weakref
+
 _lim_val = -np.log(sys.float_info.epsilon)
 
+#===============================================================================
+# Fixing constants
+__fixed__ = "fixed"
+FIXED = False
+UNFIXED = True
+#===============================================================================
+
+
 class Transformation(object):
     domain = None
     _instance = None

GPy/examples/regression.py

@@ -473,7 +473,6 @@ def uncertain_inputs_sparse_regression(max_iters=200, optimize=True, plot=True):
     Z = np.random.uniform(-3., 3., (7, 1))
 
     k = GPy.kern.rbf(1)
-    import ipdb;ipdb.set_trace()
     # create simple GP Model - no input uncertainty on this one
     m = GPy.models.SparseGPRegression(X, Y, kernel=GPy.kern.rbf(1), Z=Z)
 

GPy/plotting/matplot_dep/visualize.py

@@ -4,7 +4,6 @@ import GPy
 import numpy as np
 import matplotlib as mpl
 import time
-import Image
 try:
     import visual
     visual_available = True
@@ -324,6 +323,7 @@ class image_show(matplotlib_show):
         else:
             self.vals = 255*(self.vals - self.vals.min())/(self.vals.max() - self.vals.min())
         if not self.palette == []: # applying using an image palette (e.g. if the image has been quantized)
+            from PIL import Image
             self.vals = Image.fromarray(self.vals.astype('uint8'))
             self.vals.putpalette(self.palette) # palette is a list, must be loaded before calling this function
 

GPy/testing/parameterized_tests.py

@@ -0,0 +1,93 @@
+'''
+Created on Feb 13, 2014
+
+@author: maxzwiessele
+'''
+import unittest
+import GPy
+import numpy as np
+
+class Test(unittest.TestCase):
+
+    def setUp(self):
+        self.rbf = GPy.kern.rbf(1)
+        self.white = GPy.kern.white(1)
+        from GPy.core.parameterization import Param
+        from GPy.core.parameterization.transformations import Logistic
+        self.param = Param('param', np.random.rand(25,2), Logistic(0, 1))
+        
+        self.test1 = GPy.core.Parameterized("test model")
+        self.test1.add_parameter(self.white)
+        self.test1.add_parameter(self.rbf, 0)
+        self.test1.add_parameter(self.param)
+        
+    def test_add_parameter(self):
+        self.assertEquals(self.rbf._parent_index_, 0)
+        self.assertEquals(self.white._parent_index_, 1)
+        pass
+    
+    def test_fixes(self):
+        self.white.fix(warning=False)
+        self.test1.remove_parameter(self.test1.param)
+        self.assertTrue(self.test1._has_fixes())
+
+        from GPy.core.parameterization.transformations import FIXED, UNFIXED
+        self.assertListEqual(self.test1._fixes_.tolist(),[UNFIXED,UNFIXED,FIXED])
+
+        self.test1.add_parameter(self.white, 0)
+        self.assertListEqual(self.test1._fixes_.tolist(),[FIXED,UNFIXED,UNFIXED])
+        
+        
+    def test_remove_parameter(self):
+        from GPy.core.parameterization.transformations import FIXED, UNFIXED, __fixed__
+        self.white.fix()
+        self.test1.remove_parameter(self.white)
+        self.assertIs(self.test1._fixes_,None)
+        
+        self.assertListEqual(self.white._fixes_.tolist(), [FIXED])
+        self.assertIs(self.white.constraints,self.white.white.constraints._param_index_ops)
+        self.assertEquals(self.white.white.constraints._offset, 0)
+        self.assertIs(self.test1.constraints, self.rbf.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.param.constraints._param_index_ops)        
+        
+        self.test1.add_parameter(self.white, 0)
+        self.assertIs(self.test1.constraints, self.white.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.rbf.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.param.constraints._param_index_ops)        
+        self.assertListEqual(self.test1.constraints[__fixed__].tolist(), [0])
+        self.assertIs(self.white._fixes_,None)
+        self.assertListEqual(self.test1._fixes_.tolist(),[FIXED] + [UNFIXED] * 52)
+        self.test1.remove_parameter(self.white)
+        self.assertIs(self.test1._fixes_,None)
+        self.assertListEqual(self.white._fixes_.tolist(), [FIXED])
+        self.assertIs(self.white.constraints,self.white.white.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.rbf.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.param.constraints._param_index_ops)        
+        
+    def test_add_parameter_already_in_hirarchy(self):
+        self.test1.add_parameter(self.white._parameters_[0])
+        
+    def test_default_constraints(self):
+        self.assertIs(self.rbf.rbf.variance.constraints._param_index_ops, self.rbf.constraints._param_index_ops)
+        self.assertIs(self.test1.constraints, self.rbf.constraints._param_index_ops)
+        self.assertListEqual(self.rbf.constraints.indices()[0].tolist(), range(2))
+        from GPy.core.parameterization.transformations import Logexp
+        kern = self.rbf+self.white
+        self.assertListEqual(kern.constraints[Logexp()].tolist(), range(3))
+
+    def test_constraints(self):
+        self.rbf.constrain(GPy.transformations.Square(), False)
+        self.assertListEqual(self.test1.constraints[GPy.transformations.Square()].tolist(), range(2))
+        self.assertListEqual(self.test1.constraints[GPy.transformations.Logexp()].tolist(), [2])
+        
+        self.test1.remove_parameter(self.rbf)
+        self.assertListEqual(self.test1.constraints[GPy.transformations.Square()].tolist(), [])
+
+    def test_constraints_views(self):
+        self.assertEqual(self.white.constraints._offset, 2)
+        self.assertEqual(self.rbf.constraints._offset, 0)
+        self.assertEqual(self.param.constraints._offset, 3)
+
+if __name__ == "__main__":
+    #import sys;sys.argv = ['', 'Test.test_add_parameter']
+    unittest.main()