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copy and missing data
This commit is contained in:
Max Zwiessele
parent
0082acad63
commit
c4f6b0dbe7
10 changed files with 179 additions and 97 deletions
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@ -3,7 +3,7 @@
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import itertools
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import numpy
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from parameter_core import Constrainable, Gradcheckable, Indexable, Parameterizable, adjust_name_for_printing
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from parameter_core import Constrainable, Gradcheckable, Indexable, Parentable, adjust_name_for_printing
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from array_core import ObservableArray, ParamList
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###### printing
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@ -15,7 +15,7 @@ __precision__ = numpy.get_printoptions()['precision'] # numpy printing precision
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__print_threshold__ = 5
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######
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class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameterizable):
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class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parentable):
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"""
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Parameter object for GPy models.
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@ -114,7 +114,14 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
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self._parent_index_ = state.pop()
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self._direct_parent_ = state.pop()
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self.name = state.pop()
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def copy(self, *args):
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constr = self.constraints.copy()
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priors = self.priors.copy()
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p = Param(self.name, self.view(numpy.ndarray).copy(), self._default_constraint_)
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p.constraints = constr
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p.priors = priors
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return p
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#===========================================================================
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# get/set parameters
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#===========================================================================
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@ -68,6 +68,10 @@ class Parentable(object):
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return self
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return self._direct_parent_._highest_parent_
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def _notify_parameters_changed(self):
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if self.has_parent():
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self._direct_parent_._notify_parameters_changed()
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class Nameable(Parentable):
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_name = None
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def __init__(self, name, direct_parent=None, parent_index=None):
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@ -80,22 +84,47 @@ class Nameable(Parentable):
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@name.setter
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def name(self, name):
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from_name = self.name
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assert isinstance(name, str)
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self._name = name
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if self.has_parent():
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self._direct_parent_._name_changed(self, from_name)
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self._direct_parent_._name_changed(self, from_name)
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class Parameterizable(Parentable):
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def __init__(self, *args, **kwargs):
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super(Parameterizable, self).__init__(*args, **kwargs)
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from GPy.core.parameterization.array_core import ParamList
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_parameters_ = ParamList()
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self._added_names_ = set()
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def parameter_names(self, add_name=False):
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if add_name:
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return [adjust_name_for_printing(self.name) + "." + xi for x in self._parameters_ for xi in x.parameter_names(add_name=True)]
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return [xi for x in self._parameters_ for xi in x.parameter_names(add_name=True)]
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def _add_parameter_name(self, param):
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pname = adjust_name_for_printing(param.name)
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# and makes sure to not delete programmatically added parameters
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if pname in self.__dict__:
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if not (param is self.__dict__[pname]):
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if pname in self._added_names_:
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del self.__dict__[pname]
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self._add_parameter_name(param)
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else:
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self.__dict__[pname] = param
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self._added_names_.add(pname)
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def _remove_parameter_name(self, param=None, pname=None):
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assert param is None or pname is None, "can only delete either param by name, or the name of a param"
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pname = adjust_name_for_printing(pname) or adjust_name_for_printing(param.name)
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if pname in self._added_names_:
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del self.__dict__[pname]
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self._added_names_.remove(pname)
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self._connect_parameters()
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def _name_changed(self, param, old_name):
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self._remove_parameter_name(None, old_name)
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self._add_parameter_name(param)
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def _collect_gradient(self, target):
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import itertools
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[p._collect_gradient(target[s]) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
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@ -113,6 +142,38 @@ class Parameterizable(Parentable):
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[p._set_params(params[s], update=update) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
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self.parameters_changed()
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def copy(self):
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"""Returns a (deep) copy of the current model"""
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import copy
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from .index_operations import ParameterIndexOperations, ParameterIndexOperationsView
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from .array_core import ParamList
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dc = dict()
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for k, v in self.__dict__.iteritems():
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if k not in ['_direct_parent_', '_parameters_', '_parent_index_'] + self.parameter_names():
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if isinstance(v, (Constrainable, ParameterIndexOperations, ParameterIndexOperationsView)):
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dc[k] = v.copy()
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else:
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dc[k] = copy.deepcopy(v)
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if k == '_parameters_':
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params = [p.copy() for p in v]
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#dc = copy.deepcopy(self.__dict__)
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dc['_direct_parent_'] = None
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dc['_parent_index_'] = None
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dc['_parameters_'] = ParamList()
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s = self.__new__(self.__class__)
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s.__dict__ = dc
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#import ipdb;ipdb.set_trace()
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for p in params:
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s.add_parameter(p)
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#dc._notify_parent_change()
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return s
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#return copy.deepcopy(self)
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def _notify_parameters_changed(self):
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self.parameters_changed()
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if self.has_parent():
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self._direct_parent_._notify_parameters_changed()
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def parameters_changed(self):
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"""
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This method gets called when parameters have changed.
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@ -122,11 +183,6 @@ class Parameterizable(Parentable):
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"""
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pass
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def _notify_parameters_changed(self):
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self.parameters_changed()
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if self.has_parent():
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self._direct_parent_._notify_parameters_changed()
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class Gradcheckable(Parentable):
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#===========================================================================
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@ -157,7 +213,7 @@ class Indexable(object):
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"""
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raise NotImplementedError, "shouldnt happen, raveld index transformation required from non parameterization object?"
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class Constrainable(Nameable, Indexable, Parameterizable):
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class Constrainable(Nameable, Indexable, Parentable):
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def __init__(self, name, default_constraint=None):
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super(Constrainable,self).__init__(name)
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self._default_constraint_ = default_constraint
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@ -167,6 +223,16 @@ class Constrainable(Nameable, Indexable, Parameterizable):
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if self._default_constraint_ is not None:
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self.constrain(self._default_constraint_)
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def _disconnect_parent(self, constr=None):
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if constr is None:
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constr = self.constraints.copy()
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self.constraints.clear()
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self.constraints = constr
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self._direct_parent_ = None
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self._parent_index_ = None
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self._connect_fixes()
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self._notify_parent_change()
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#===========================================================================
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# Fixing Parameters:
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#===========================================================================
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@ -3,16 +3,15 @@
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import numpy; np = numpy
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import copy
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import cPickle
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import itertools
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from re import compile, _pattern_type
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from param import ParamConcatenation, Param
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from parameter_core import Constrainable, Pickleable, Observable, adjust_name_for_printing, Gradcheckable
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from transformations import __fixed__, FIXED, UNFIXED
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from param import ParamConcatenation
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from parameter_core import Constrainable, Pickleable, Observable, Parameterizable, adjust_name_for_printing, Gradcheckable
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from transformations import __fixed__
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from array_core import ParamList
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class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable, Parameterizable):
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"""
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Parameterized class
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@ -63,7 +62,6 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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self._fixes_ = None
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self._param_slices_ = []
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self._connect_parameters()
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self._added_names_ = set()
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del self._in_init_
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def add_parameter(self, param, index=None):
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@ -117,17 +115,10 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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raise RuntimeError, "Parameter {} does not belong to this object, remove parameters directly from their respective parents".format(param._short())
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del self._parameters_[param._parent_index_]
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self.size -= param.size
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constr = param.constraints.copy()
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param.constraints.clear()
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param.constraints = constr
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param._direct_parent_ = None
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param._parent_index_ = None
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param._connect_fixes()
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param._notify_parent_change()
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pname = adjust_name_for_printing(param.name)
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if pname in self._added_names_:
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del self.__dict__[pname]
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self._connect_parameters()
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param._disconnect_parent()
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self._remove_parameter_name(param)
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#self._notify_parent_change()
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self._connect_fixes()
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@ -145,19 +136,9 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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for i, p in enumerate(self._parameters_):
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p._direct_parent_ = self
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p._parent_index_ = i
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not_unique = []
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sizes.append(p.size + sizes[-1])
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self._param_slices_.append(slice(sizes[-2], sizes[-1]))
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pname = adjust_name_for_printing(p.name)
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# and makes sure to not delete programmatically added parameters
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if pname in self.__dict__:
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if isinstance(self.__dict__[pname], (Parameterized, Param)):
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if not p is self.__dict__[pname]:
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not_unique.append(pname)
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del self.__dict__[pname]
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elif not (pname in not_unique):
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self.__dict__[pname] = p
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self._added_names_.add(pname)
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self._add_parameter_name(p)
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#===========================================================================
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# Pickling operations
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@ -174,19 +155,7 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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cPickle.dump(self, f, protocol)
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else:
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cPickle.dump(self, f, protocol)
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def copy(self):
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"""Returns a (deep) copy of the current model """
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# dc = dict()
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# for k, v in self.__dict__.iteritems():
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# if k not in ['_highest_parent_', '_direct_parent_']:
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# dc[k] = copy.deepcopy(v)
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# dc = copy.deepcopy(self.__dict__)
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# dc['_highest_parent_'] = None
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# dc['_direct_parent_'] = None
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# s = self.__class__.new()
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# s.__dict__ = dc
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return copy.deepcopy(self)
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def __getstate__(self):
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if self._has_get_set_state():
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return self._getstate()
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@ -265,14 +234,6 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
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if self._has_fixes(): tmp = self._get_params(); tmp[self._fixes_] = p; p = tmp; del tmp
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[numpy.put(p, ind, c.f(p[ind])) for c, ind in self.constraints.iteritems() if c != __fixed__]
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return p
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def _name_changed(self, param, old_name):
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if hasattr(self, old_name) and old_name in self._added_names_:
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delattr(self, old_name)
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self._added_names_.remove(old_name)
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pname = adjust_name_for_printing(param.name)
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if pname not in self.__dict__:
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self._added_names_.add(pname)
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self.__dict__[pname] = param
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#===========================================================================
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# Indexable Handling
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#===========================================================================
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