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everything is broken

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This commit is contained in:
James Hensman 2014-02-20 14:04:16 +00:00
parent de51ad638a
commit d636c8c30c
13 changed files with 325 additions and 323 deletions
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10
GPy/core/parameterization/param.py
View file

@ -23,7 +23,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
:param input_array: array which this parameter handles
:type input_array: numpy.ndarray
:param default_constraint: The default constraint for this parameter
:type default_constraint:
:type default_constraint:
You can add/remove constraints by calling constrain on the parameter itself, e.g:
@ -59,7 +59,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
def __init__(self, name, input_array, default_constraint=None):
super(Param, self).__init__(name=name, default_constraint=default_constraint)
def __array_finalize__(self, obj):
# see InfoArray.__array_finalize__ for comments
if obj is None: return
@ -192,7 +192,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
return numpy.r_[a]
return numpy.r_[:b]
return itertools.imap(f, itertools.izip_longest(slice_index[:self._realndim_], self._realshape_, fillvalue=slice(self.size)))
#===========================================================================
# Convenience
#===========================================================================
@ -260,7 +260,7 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parameteri
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])
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),
@ -426,4 +426,4 @@ class ParamConcatenation(object):
start = False
return "\n".join(strings)
def __repr__(self):
return "\n".join(map(repr,self.params))
return "\n".join(map(repr,self.params))

46
GPy/core/parameterization/parameter_core.py
View file

@ -18,8 +18,8 @@ class Observable(object):
def remove_observer(self, observer):
del self._observers_[observer]
def _notify_observers(self):
[callble(self) for callble in self._observers_.itervalues()]
[callble(self) for callble in self._observers_.values()]
class Pickleable(object):
def _getstate(self):
"""
@ -51,7 +51,7 @@ class Parentable(object):
super(Parentable,self).__init__()
self._direct_parent_ = direct_parent
self._parent_index_ = parent_index
def has_parent(self):
return self._direct_parent_ is not None
@ -82,7 +82,7 @@ class Nameable(Parentable):
from_name = self.name
self._name = name
if self.has_parent():
self._direct_parent_._name_changed(self, from_name)
self._direct_parent_._name_changed(self, from_name)
class Parameterizable(Parentable):
@ -90,7 +90,7 @@ class Parameterizable(Parentable):
super(Parameterizable, self).__init__(*args, **kwargs)
from GPy.core.parameterization.array_core import ParamList
_parameters_ = ParamList()
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)]
@ -142,21 +142,21 @@ class Gradcheckable(Parentable):
class Indexable(object):
def _raveled_index(self):
raise NotImplementedError, "Need to be able to get the raveled Index"
def _internal_offset(self):
return 0
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?"
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)
@ -166,7 +166,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
self.priors = ParameterIndexOperations()
if self._default_constraint_ is not None:
self.constrain(self._default_constraint_)
#===========================================================================
# Fixing Parameters:
#===========================================================================
@ -182,21 +182,21 @@ class Constrainable(Nameable, Indexable, Parameterizable):
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__)
self._highest_parent_._set_unfixed(unconstrained)
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)
@ -212,7 +212,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
self._fixes_[fixed_indices] = FIXED
else:
self._fixes_ = None
def _has_fixes(self):
return hasattr(self, "_fixes_") and self._fixes_ is not None
@ -222,17 +222,17 @@ class Constrainable(Nameable, Indexable, Parameterizable):
def set_prior(self, prior, warning=True, update=True):
repriorized = self.unset_priors()
self._add_to_index_operations(self.priors, repriorized, prior, warning, update)
def unset_priors(self, *priors):
return self._remove_from_index_operations(self.priors, priors)
def log_prior(self):
"""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 0.
def _log_prior_gradients(self):
"""evaluate the gradients of the priors"""
import numpy as np
@ -242,7 +242,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
[np.put(ret, ind, p.lnpdf_grad(x[ind])) for p, ind in self.priors.iteritems()]
return ret
return 0.
#===========================================================================
# Constrain operations -> done
#===========================================================================
@ -269,7 +269,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
transformats of this parameter object.
"""
return self._remove_from_index_operations(self.constraints, transforms)
def constrain_positive(self, warning=True, update=True):
"""
:param warning: print a warning if re-constraining parameters.
@ -314,7 +314,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
Remove (lower, upper) bounded constrain from this parameter/
"""
self.unconstrain(Logistic(lower, upper))
def _parent_changed(self, parent):
from index_operations import ParameterIndexOperationsView
self.constraints = ParameterIndexOperationsView(parent.constraints, parent._offset_for(self), self.size)
@ -340,7 +340,7 @@ class Constrainable(Nameable, Indexable, Parameterizable):
removed = np.union1d(removed, unconstrained)
if t is __fixed__:
self._highest_parent_._set_unfixed(unconstrained)
return removed