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Changed get_param and set_param to _get_params and _set_params

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Neil Lawrence 2013-01-18 12:31:37 +00:00
parent 688d6ac7a5
commit 3c700dfa50
33 changed files with 239 additions and 358 deletions
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34
GPy/core/parameterised.py
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@ -87,7 +87,7 @@ class parameterised(object):
Returns
-------
the indices of self.get_param_names which match the regular expression.
the indices of self._get_param_names which match the regular expression.
Notes
-----
@ -96,9 +96,9 @@ class parameterised(object):
if type(expr) is str:
expr = re.compile(expr)
return np.nonzero([expr.search(name) for name in self.get_param_names()])[0]
return np.nonzero([expr.search(name) for name in self._get_param_names()])[0]
elif type(expr) is re._pattern_type:
return np.nonzero([expr.search(name) for name in self.get_param_names()])[0]
return np.nonzero([expr.search(name) for name in self._get_param_names()])[0]
else:
return expr
@ -115,11 +115,11 @@ class parameterised(object):
assert not np.any(matches[:,None]==self.all_constrained_indices()), "Some indices are already constrained"
self.constrained_positive_indices = np.hstack((self.constrained_positive_indices, matches))
#check to ensure constraint is in place
x = self.get_param()
x = self._get_params()
for i,xx in enumerate(x):
if (xx<0) & (i in matches):
x[i] = -xx
self.set_param(x)
self._set_params(x)
def unconstrain(self,which):
@ -163,11 +163,11 @@ class parameterised(object):
assert not np.any(matches[:,None]==self.all_constrained_indices()), "Some indices are already constrained"
self.constrained_negative_indices = np.hstack((self.constrained_negative_indices, matches))
#check to ensure constraint is in place
x = self.get_param()
x = self._get_params()
for i,xx in enumerate(x):
if (xx>0.) and (i in matches):
x[i] = -xx
self.set_param(x)
self._set_params(x)
@ -187,11 +187,11 @@ class parameterised(object):
self.constrained_bounded_uppers.append(upper)
self.constrained_bounded_lowers.append(lower)
#check to ensure constraint is in place
x = self.get_param()
x = self._get_params()
for i,xx in enumerate(x):
if ((xx<=lower)|(xx>=upper)) & (i in matches):
x[i] = sigmoid(xx)*(upper-lower) + lower
self.set_param(x)
self._set_params(x)
def constrain_fixed(self, which, value = None):
@ -213,14 +213,14 @@ class parameterised(object):
if value != None:
self.constrained_fixed_values.append(value)
else:
self.constrained_fixed_values.append(self.get_param()[self.constrained_fixed_indices[-1]])
self.constrained_fixed_values.append(self._get_params()[self.constrained_fixed_indices[-1]])
#self.constrained_fixed_values.append(value)
self.expand_param(self.extract_param())
def extract_param(self):
"""use self.get_param to get the 'true' parameters of the model, which are then tied, constrained and fixed"""
x = self.get_param()
"""use self._get_params to get the 'true' parameters of the model, which are then tied, constrained and fixed"""
x = self._get_params()
x[self.constrained_positive_indices] = np.log(x[self.constrained_positive_indices])
x[self.constrained_negative_indices] = np.log(-x[self.constrained_negative_indices])
[np.put(x,i,np.log(np.clip(x[i]-l,1e-10,np.inf)/np.clip(h-x[i],1e-10,np.inf))) for i,l,h in zip(self.constrained_bounded_indices, self.constrained_bounded_lowers, self.constrained_bounded_uppers)]
@ -233,7 +233,7 @@ class parameterised(object):
def expand_param(self,x):
""" takes the vector x, which is then modified (by untying, reparameterising or inserting fixed values), and then call self.set_param"""
""" takes the vector x, which is then modified (by untying, reparameterising or inserting fixed values), and then call self._set_params"""
#work out how many places are fixed, and where they are. tricky logic!
Nfix_places = 0.
@ -257,14 +257,14 @@ class parameterised(object):
xx[self.constrained_positive_indices] = np.exp(xx[self.constrained_positive_indices])
xx[self.constrained_negative_indices] = -np.exp(xx[self.constrained_negative_indices])
[np.put(xx,i,low+sigmoid(xx[i])*(high-low)) for i,low,high in zip(self.constrained_bounded_indices, self.constrained_bounded_lowers, self.constrained_bounded_uppers)]
self.set_param(xx)
self._set_params(xx)
def extract_param_names(self):
"""
Returns the parameter names as propagated after constraining,
tying or fixing, i.e. a list of the same length as extract_param()
"""
n = self.get_param_names()
n = self._get_param_names()
#remove/concatenate the tied parameter names
if len(self.tied_indices):
@ -294,13 +294,13 @@ class parameterised(object):
"""
Return a string describing the parameter names and their ties and constraints
"""
names = self.get_param_names()
names = self._get_param_names()
N = len(names)
if not N:
return "This object has no free parameters."
header = ['Name','Value','Constraints','Ties']
values = self.get_param() #map(str,self.get_param())
values = self._get_params() #map(str,self._get_params())
#sort out the constraints
constraints = ['']*len(names)
for i in self.constrained_positive_indices: