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Return deserialized models with actual type instead of base type

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This commit is contained in:
Keerthana Elango 2018-07-24 10:46:33 +01:00
parent 06441f583f
commit eca5806518
5 changed files with 54 additions and 40 deletions
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9
GPy/core/gp.py
View file

@ -144,14 +144,14 @@ class GP(Model):
return input_dict
@staticmethod
def _build_from_input_dict(input_dict, data=None):
def _format_input_dict(input_dict, data=None):
import GPy
import numpy as np
if (input_dict['X'] is None) or (input_dict['Y'] is None):
assert(data is not None)
input_dict["X"], input_dict["Y"] = np.array(data[0]), np.array(data[1])
elif data is not None:
print("WARNING: The model has been saved with X,Y! The original values are being overriden!")
warnings.warn("WARNING: The model has been saved with X,Y! The original values are being overridden!")
input_dict["X"], input_dict["Y"] = np.array(data[0]), np.array(data[1])
else:
input_dict["X"], input_dict["Y"] = np.array(input_dict['X']), np.array(input_dict['Y'])
@ -173,6 +173,11 @@ class GP(Model):
input_dict["normalizer"] = GPy.util.normalizer._Norm.from_dict(normalizer)
else:
input_dict["normalizer"] = normalizer
return input_dict
@staticmethod
def _build_from_input_dict(input_dict, data=None):
input_dict = GP._format_input_dict(input_dict, data)
return GP(**input_dict)
def save_model(self, output_filename, compress=True, save_data=True):

38
GPy/core/sparse_gp.py
View file

@ -130,37 +130,13 @@ class SparseGP(GP):
input_dict["Z"] = self.Z.tolist()
return input_dict
@staticmethod
def _format_input_dict(input_dict, data=None):
input_dict = GP._format_input_dict(input_dict, data)
input_dict["Z"] = np.array(input_dict["Z"])
return input_dict
@staticmethod
def _build_from_input_dict(input_dict, data=None):
# Called from the from_dict method.
import GPy
if (input_dict['X'] is None) or (input_dict['Y'] is None):
if data is None:
raise ValueError("The model was serialized whithout the training data. 'data' must be not None!")
input_dict["X"], input_dict["Y"] = np.array(data[0]), np.array(data[1])
elif data is not None:
print("WARNING: The model has been saved with X,Y! The original values are being overriden!")
input_dict["X"], input_dict["Y"] = np.array(data[0]), np.array(data[1])
else:
input_dict["X"], input_dict["Y"] = np.array(input_dict['X']), np.array(input_dict['Y'])
input_dict["Z"] = np.array(input_dict['Z'])
input_dict["kernel"] = GPy.kern.Kern.from_dict(input_dict["kernel"])
input_dict["likelihood"] = GPy.likelihoods.likelihood.Likelihood.from_dict(input_dict["likelihood"])
mean_function = input_dict.get("mean_function")
if mean_function is not None:
input_dict["mean_function"] = GPy.core.mapping.Mapping.from_dict(mean_function)
else:
input_dict["mean_function"] = mean_function
input_dict["inference_method"] = GPy.inference.latent_function_inference.LatentFunctionInference.from_dict(input_dict["inference_method"])
#FIXME: Assumes the Y_metadata is serializable. We should create a Metadata class
Y_metadata = input_dict.get("Y_metadata")
input_dict["Y_metadata"] = Y_metadata
normalizer = input_dict.get("normalizer")
if normalizer is not None:
input_dict["normalizer"] = GPy.util.normalizer._Norm.from_dict(normalizer)
else:
input_dict["normalizer"] = normalizer
input_dict = SparseGP._format_input_dict(input_dict, data)
return SparseGP(**input_dict)

21
GPy/models/gp_classification.py
View file

@ -16,18 +16,27 @@ class GPClassification(GP):
:param X: input observations
:param Y: observed values, can be None if likelihood is not None
:param kernel: a GPy kernel, defaults to rbf
:param likelihood: a GPy likelihood, defaults to Bernoulli
:param inference_method: Latent function inference to use, defaults to EP
:type inference_method: :class:`GPy.inference.latent_function_inference.LatentFunctionInference`
.. Note:: Multiple independent outputs are allowed using columns of Y
"""
def __init__(self, X, Y, kernel=None,Y_metadata=None, mean_function=None):
def __init__(self, X, Y, kernel=None,Y_metadata=None, mean_function=None, inference_method=None,
likelihood=None, normalizer=False):
if kernel is None:
kernel = kern.RBF(X.shape[1])
likelihood = likelihoods.Bernoulli()
if likelihood is None:
likelihood = likelihoods.Bernoulli()
GP.__init__(self, X=X, Y=Y, kernel=kernel, likelihood=likelihood, inference_method=EP(), mean_function=mean_function, name='gp_classification')
if inference_method is None:
inference_method = EP()
GP.__init__(self, X=X, Y=Y, kernel=kernel, likelihood=likelihood, inference_method=inference_method,
mean_function=mean_function, name='gp_classification', normalizer=normalizer)
@staticmethod
def from_gp(gp):
@ -48,3 +57,9 @@ class GPClassification(GP):
def save_model(self, output_filename, compress=True, save_data=True):
self._save_model(output_filename, compress=True, save_data=True)
@staticmethod
def _build_from_input_dict(input_dict, data=None):
input_dict = GPClassification._format_input_dict(input_dict, data)
input_dict.pop('name', None) # Name parameter not required by GPClassification
return GPClassification(**input_dict)

22
GPy/models/sparse_gp_classification.py
View file

@ -17,8 +17,10 @@ class SparseGPClassification(SparseGP):
:param X: input observations
:param Y: observed values
:param likelihood: a GPy likelihood, defaults to Binomial with probit link_function
:param likelihood: a GPy likelihood, defaults to Bernoulli
:param kernel: a GPy kernel, defaults to rbf+white
:param inference_method: Latent function inference to use, defaults to EPDTC
:type inference_method: :class:`GPy.inference.latent_function_inference.LatentFunctionInference`
:param normalize_X: whether to normalize the input data before computing (predictions will be in original scales)
:type normalize_X: False|True
:param normalize_Y: whether to normalize the input data before computing (predictions will be in original scales)
@ -27,11 +29,13 @@ class SparseGPClassification(SparseGP):
"""
def __init__(self, X, Y=None, likelihood=None, kernel=None, Z=None, num_inducing=10, Y_metadata=None):
def __init__(self, X, Y=None, likelihood=None, kernel=None, Z=None, num_inducing=10, Y_metadata=None,
mean_function=None, inference_method=None, normalizer=False):
if kernel is None:
kernel = kern.RBF(X.shape[1])
likelihood = likelihoods.Bernoulli()
if likelihood is None:
likelihood = likelihoods.Bernoulli()
if Z is None:
i = np.random.permutation(X.shape[0])[:num_inducing]
@ -39,7 +43,11 @@ class SparseGPClassification(SparseGP):
else:
assert Z.shape[1] == X.shape[1]
SparseGP.__init__(self, X, Y, Z, kernel, likelihood, inference_method=EPDTC(), name='SparseGPClassification',Y_metadata=Y_metadata)
if inference_method is None:
inference_method = EPDTC()
SparseGP.__init__(self, X, Y, Z, kernel, likelihood, mean_function=mean_function, inference_method=inference_method,
normalizer=normalizer, name='SparseGPClassification', Y_metadata=Y_metadata)
@staticmethod
def from_sparse_gp(sparse_gp):
@ -58,6 +66,12 @@ class SparseGPClassification(SparseGP):
model_dict["class"] = "GPy.models.SparseGPClassification"
return model_dict
@staticmethod
def _build_from_input_dict(input_dict, data=None):
input_dict = SparseGPClassification._format_input_dict(input_dict, data)
input_dict.pop('name', None) # Name parameter not required by SparseGPClassification
return SparseGPClassification(**input_dict)
@staticmethod
def from_dict(input_dict, data=None):
"""

4
GPy/testing/serialization_tests.py
View file

@ -237,7 +237,9 @@ class Test(unittest.TestCase):
m.save_model("temp_test_gp_classifier_with_data.json", compress=True, save_data=True)
m.save_model("temp_test_gp_classifier_without_data.json", compress=True, save_data=False)
m1_r = GPy.models.GPClassification.load_model("temp_test_gp_classifier_with_data.json.zip")
self.assertTrue(type(m) == type(m1_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m1_r)))
m2_r = GPy.models.GPClassification.load_model("temp_test_gp_classifier_without_data.json.zip", (X,Y))
self.assertTrue(type(m) == type(m2_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r)))
os.remove("temp_test_gp_classifier_with_data.json.zip")
os.remove("temp_test_gp_classifier_without_data.json.zip")
@ -259,7 +261,9 @@ class Test(unittest.TestCase):
m.save_model("temp_test_sparse_gp_classifier_with_data.json", compress=True, save_data=True)
m.save_model("temp_test_sparse_gp_classifier_without_data.json", compress=True, save_data=False)
m1_r = GPy.models.SparseGPClassification.load_model("temp_test_sparse_gp_classifier_with_data.json.zip")
self.assertTrue(type(m) == type(m1_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m1_r)))
m2_r = GPy.models.SparseGPClassification.load_model("temp_test_sparse_gp_classifier_without_data.json.zip", (X,Y))
self.assertTrue(type(m) == type(m2_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r)))
os.remove("temp_test_sparse_gp_classifier_with_data.json.zip")
os.remove("temp_test_sparse_gp_classifier_without_data.json.zip")