https://github.com/GPflow/GPflow
Tip revision: 445112bcb708b6ddce327577cdd9c4a76a185fdf authored by John Bradshaw on 24 October 2017, 10:52:48 UTC
Merge remote-tracking branch 'origin/GPflow-1.0-RC' into john-bradshaw/binary-class-GP
Merge remote-tracking branch 'origin/GPflow-1.0-RC' into john-bradshaw/binary-class-GP
Tip revision: 445112b
test_param.py
# Copyright 2016 the GPflow authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.from __future__ import print_function
from functools import reduce
import unittest
import tensorflow as tf
import numpy as np
import gpflow
from gpflow import settings, test_util
try:
import cPickle as pickle
except ImportError:
import pickle
class NamingTests(test_util.GPflowTestCase):
def test_standard_name(self):
p_index = gpflow.core.parentable.Parentable._read_index() + 1
p = gpflow.Param(1)
self.assertEqual(p.name, 'Parameter')
self.assertEqual(p.hidden_name, '{}/Parameter'.format(p_index))
def test_full_fame(self):
p1_index = gpflow.core.parentable.Parentable._read_index() + 1
p1 = gpflow.Param(1)
p2 = gpflow.Param(1, name='test_name')
self.assertEqual(p1.hidden_full_name, '{index}/Parameter'.format(index=p1_index))
self.assertEqual(p1.full_name, 'Parameter')
self.assertEqual(p2.hidden_full_name, 'test_name')
self.assertEqual(p2.full_name, 'test_name')
model_index = gpflow.core.parentable.Parentable._read_index() + 1
m = gpflow.models.Model()
m.p = p1
self.assertEqual(m.hidden_full_name, '{index}/Model'.format(index=model_index))
self.assertEqual(m.full_name, 'Model')
self.assertEqual(m.p.hidden_full_name, '{index}/Model/p'.format(index=model_index))
self.assertEqual(m.p.full_name, 'Model/p')
self.assertEqual(m.full_name, m.name)
self.assertEqual(m.p.hidden_full_name, '{}/p'.format(m.hidden_name))
self.assertEqual(m.p.full_name, '{}/p'.format(m.name))
class TypesTests(test_util.GPflowTestCase):
def test_default_type(self):
pass
class ParamTests(test_util.GPflowTestCase):
def setUp(self):
self.p = gpflow.Param(1.0)
self.m_index = gpflow.core.parentable.Parentable._read_index() + 1
self.m = gpflow.params.Parameterized()
self.m.p = gpflow.Param(1.0)
self.m.b = gpflow.Param(1.0)
def test_generators(self):
with self.test_context():
self.assertEqual(len(list(self.m.parameters)), 2)
self.assertEqual(len(list(self.m.data_holders)), 0)
self.assertEqual(len(list(self.m.params)), 2)
def test_assign(self):
with self.test_context():
self.p.assign(2.0)
self.assertTrue(self.p.read_value() == 2.0)
self.m.p = 2.0
self.assertTrue(self.m.p.read_value() == 2.0)
def test_create_and_replace(self):
with self.test_context():
tensor = tf.get_variable('a', shape=()) + 1.0
param = gpflow.Param(1e3)
external_param = gpflow.Param(tensor)
new_param = gpflow.Param(1.0, name='new_param')
self.m.b = external_param
self.assertEqual(self.m.b, external_param)
p = self.m.p
self.m.p = param
self.assertEqual(self.m.p, param)
self.assertEqual(p.name, 'Parameter')
self.assertEqual(p.root, p)
self.m.d = new_param
self.assertEqual(self.m.d, new_param)
self.assertEqual(self.m.d.hidden_full_name,
'{index}/{name}/d'
.format(index=self.m_index, name=self.m.name))
self.assertEqual(self.m.d.full_name, '{name}/d'.format(name=self.m.name))
def test_assign_with_compile(self):
with self.test_context():
self.p.compile()
self.m.compile()
self.p.assign(2.0)
self.m.p = 2.0
self.assertEqual(self.p.read_value(), 2.0)
self.assertEqual(self.m.p.read_value(), 2.0)
def test_root(self):
self.assertTrue(self.m.p.root is self.m)
def test_trainable(self):
self.assertTrue(self.p.trainable)
self.p.trainable = False
self.assertFalse(self.p.trainable)
self.assertTrue(self.m.trainable)
self.m.p.trainable = False
self.assertFalse(self.m.p.trainable)
self.assertTrue(self.m.trainable)
def test_trainable_with_compile(self):
with self.test_context():
self.p.compile()
self.m.compile()
self.assertTrue(self.p.trainable)
self.p.trainable = False
self.assertFalse(self.p.trainable)
self.assertTrue(self.m.trainable)
self.m.p.trainable = False
self.assertTrue(self.m.trainable)
self.assertFalse(self.m.p.trainable)
_check_trainable_flag(self.m, self.assertTrue, self.assertFalse)
class ParameterizedNoParametersTests(test_util.GPflowTestCase):
def setUp(self):
self.m = gpflow.params.Parameterized(name='m')
self.m.p = gpflow.params.Parameterized()
self.m.b = gpflow.params.Parameterized()
def test_is_built(self):
with self.test_context():
self.assertEqual(self.m.is_built_coherence(), gpflow.Build.YES)
def test_compile(self):
with self.test_context():
self.m.compile()
self.assertEqual(self.m.is_built_coherence(), gpflow.Build.YES)
def test_generators(self):
with self.test_context():
self.assertEqual(list(self.m.parameters), [])
self.assertEqual(list(self.m.data_holders), [])
self.assertEqual(len(list(self.m.params)), 2)
def test_add_parameter_to_empty_parameterized(self):
with self.test_context():
self.m.compile()
self.m.a = gpflow.Param(10)
self.assertEqual(self.m.is_built_coherence(), gpflow.Build.NO)
self.m.compile()
self.assertEqual(self.m.is_built_coherence(), gpflow.Build.YES)
with self.assertRaises(gpflow.GPflowError):
self.m.b = gpflow.Param(20)
class ParameterizedCompileTests(test_util.GPflowTestCase):
def setUp(self):
with self.test_context() as session:
self.graph = session.graph
tensor = tf.get_variable('a', shape=(), trainable=False)
self.m = gpflow.params.Parameterized(name='m')
self.m.p = gpflow.params.Parameterized()
self.m.a = gpflow.Param(tensor, trainable=False)
self.m.b = gpflow.Param(1.0)
self.m.c = gpflow.Param(np.array([1.0, 2.0]))
self.m.p.d = gpflow.Param(1.0)
def test_compile(self):
with self.test_context(self.graph):
tensor = self.m.a.parameter_tensor
self.m.compile()
self.assertEqual(len(list(self.m.parameters)), 4)
self.assertEqual(len(list(self.m.trainable_tensors)), 3)
self.assertEqual(self.m.a.parameter_tensor, tensor)
for param in self.m.parameters:
self.assertTrue(gpflow.misc.is_tensor(param.parameter_tensor))
self.assertTrue(gpflow.misc.is_tensor(param.constrained_tensor))
self.assertTrue(gpflow.misc.is_tensor(param.prior_tensor))
def test_modify_compiled(self):
with self.test_context(self.graph):
self.m.compile()
self.assertEqual(len(list(self.m.parameters)), 4)
self.assertEqual(len(list(self.m.trainable_tensors)), 3)
for param in self.m.parameters:
self.assertTrue(gpflow.misc.is_tensor(param.parameter_tensor))
self.assertTrue(gpflow.misc.is_tensor(param.constrained_tensor))
self.assertTrue(gpflow.misc.is_tensor(param.prior_tensor))
def test_fails_after_compile(self):
with self.test_context(self.graph):
self.m.compile()
with self.assertRaises(gpflow.GPflowError):
self.m.d = gpflow.Param(1.0)
with self.assertRaises(AttributeError):
_param = self.m.d
def test_fails_at_compile(self):
with self.test_context(self.graph):
with self.assertRaises(gpflow.GPflowError):
self.m.p.d.compile()
with self.assertRaises(gpflow.GPflowError):
self.m.p.compile()
with self.assertRaises(gpflow.GPflowError):
self.m.a.compile()
with self.assertRaises(gpflow.GPflowError):
self.m.b.compile()
with self.assertRaises(gpflow.GPflowError):
self.m.c.compile()
self.m.compile()
class ParameterizedDeepTest(test_util.GPflowTestCase):
def setUp(self):
with self.test_context():
self.m = gpflow.params.Parameterized(name='m')
self.m.a = gpflow.Param(1.0, trainable=False)
self.m.foo = gpflow.params.Parameterized()
self.m.foo.bar = gpflow.params.Parameterized()
self.m.foo.bar.baz = gpflow.Param(1.0)
def test_generators(self):
with self.test_context():
self.assertEqual(len(list(self.m.parameters)), 2)
self.assertEqual(len(list(self.m.data_holders)), 0)
self.assertEqual(len(list(self.m.params)), 2)
def test_root(self):
self.assertTrue(self.m.foo.root is self.m)
self.assertTrue(self.m.foo.bar.root is self.m)
self.assertTrue(self.m.foo.bar.baz.root is self.m)
def test_deep_name(self):
self.assertTrue(self.m.foo.name == 'foo')
self.assertTrue(self.m.foo.bar.name == 'bar')
self.assertTrue(self.m.foo.bar.baz.name == 'baz')
self.assertTrue(self.m.foo.full_name == 'm/foo')
self.assertTrue(self.m.foo.bar.full_name == 'm/foo/bar')
self.assertTrue(self.m.foo.bar.baz.full_name == 'm/foo/bar/baz')
self.assertTrue(self.m.foo.hidden_full_name == 'm/foo')
self.assertTrue(self.m.foo.bar.hidden_full_name == 'm/foo/bar')
self.assertTrue(self.m.foo.bar.baz.hidden_full_name == 'm/foo/bar/baz')
def test_deep_trainable(self):
with self.test_context():
self.m.compile()
self.m.trainable = False
self.assertEqual(len(list(self.m.trainable_tensors)), 0)
_check_trainable_flag(self.m, self.assertTrue, self.assertFalse)
self.m.trainable = True
self.assertEqual(
len(list(self.m.parameters)),
len(list(self.m.trainable_tensors)))
_check_trainable_flag(self.m, self.assertTrue, self.assertFalse)
class ParamLikeInvariantTest(test_util.GPflowTestCase):
def test_self_reference(self):
m = gpflow.params.Parameterized()
with self.assertRaises(ValueError):
m.foo = m
m.foo = gpflow.params.Parameterized()
with self.assertRaises(ValueError):
m.foo.bar = m
def test_reassign(self):
m = gpflow.params.Parameterized()
p = gpflow.params.Parameterized()
m.foo = p # assign
m.foo = p # reassign
def test_compile_from_root(self):
with self.test_context():
m = gpflow.params.Parameterized()
m.a = gpflow.Param(1.0)
m.b = gpflow.Param(1.0)
m.c = gpflow.params.Parameterized()
m.c.a = gpflow.Param(1.0)
with self.assertRaises(gpflow.GPflowError):
m.c.a.compile()
with self.assertRaises(gpflow.GPflowError):
m.c.compile()
with self.assertRaises(gpflow.GPflowError):
m.b.compile()
with self.assertRaises(gpflow.GPflowError):
m.a.compile()
# TODO(@awav):
# m = gpflow.params.Parameterized()
# m.foo = gpflow.params.Parameterized()
# m.foo.bar = gpflow.params.Parameterized()
# with self.assertRaises(ValueError):
# m.baz = m.foo.bar
# TODO(@awav):
#m = gpflow.params.Parameterized()
#m.foo = gpflow.params.Parameterized()
#m.foo.bar = gpflow.params.Parameterized()
#m.boo = gpflow.params.Parameterized()
#with self.assertRaises(ValueError):
# m.boo.far = m.foo.bar
# TODO(@awav):
# def testAddingToAnother(self):
# """
# Adding the same Paramterized object to another tree is fine.
# """
# m1 = gpflow.params.Parameterized()
# m1.foo = gpflow.params.Parameterized()
# m2 = gpflow.params.Parameterized()
# with self.assertRaises(gpflow.GPflowError):
# m2.foo = m1.foo
class TestParamList(test_util.GPflowTestCase):
def test_construction(self):
gpflow.ParamList([])
gpflow.ParamList([gpflow.Param(1)])
gpflow.ParamList([1.0, np.array([1, 2]), gpflow.Param(1.0)])
with self.assertRaises(ValueError):
gpflow.ParamList([gpflow.Param(1), 'stringsnotallowed'])
with self.assertRaises(ValueError):
# tuples not valid in constuctor:
gpflow.ParamList((gpflow.Param(1),))
with self.assertRaises(ValueError):
# param objects not valid in constructor (must be in list)
gpflow.ParamList(gpflow.Param(1))
def test_naming(self):
p1 = gpflow.Param(1.2)
p2 = gpflow.Param(np.array([3.4, 5.6], settings.np_float))
gpflow.ParamList([p1, p2])
self.assertEqual(p1.name, 'item0')
self.assertEqual(p2.name, 'item1')
def test_setitem(self):
with self.test_context():
p1 = gpflow.Param(1.2)
p2 = gpflow.Param(np.array([3.4, 5.6], settings.np_float))
param_list = gpflow.ParamList([p1, p2], name='param_list')
self.assertEqual(p1.read_value(), param_list[0].read_value())
self.assertTrue(np.all(param_list[1].read_value() == p2.read_value()))
param_list[0] = gpflow.Param(2.0)
self.assertEqual(p1.read_value(), 1.2)
self.assertEqual(p1.root, p1)
self.assertEqual(param_list[0].read_value(), 2.0)
arr = np.array([1.1, 2.2], settings.np_float)
param_list[1] = gpflow.Param(arr)
self.assertEqual(p2.root, p2)
self.assertTrue(np.all(param_list[1].read_value() == arr))
param_list.compile()
with self.assertRaises(gpflow.GPflowError):
param_list[0] = gpflow.Param(12)
def test_append(self):
p1 = gpflow.Param(1.2)
p2 = gpflow.Param(np.array([3.4, 5.6], settings.np_float))
param_list = gpflow.ParamList([p1])
param_list.append(p2)
self.assertTrue(p2 in param_list.params)
with self.assertRaises(ValueError):
param_list.append('foo')
def test_len(self):
p1 = gpflow.Param(1.2)
p2 = gpflow.Param(np.array([3.4, 5.6], settings.np_float))
l = gpflow.ParamList([p1])
l.append(p2)
self.assertTrue(len(l) == 2)
def test_with_parameterized(self):
with self.test_context():
pzd = gpflow.params.Parameterized()
p = gpflow.Param(1.2)
pzd.p = p
param_list = gpflow.ParamList([pzd])
param_list[0].p = 5.
self.assertEqual(param_list[0].p.read_value(), 5)
def test_in_model(self):
class Foo(gpflow.models.Model):
def __init__(self):
gpflow.models.Model.__init__(self)
self.param_list = gpflow.ParamList([gpflow.Param(1.), gpflow.Param(12.)])
@gpflow.params_as_tensors
def _build_likelihood(self):
return -tf.add_n([tf.square(x) for x in self.param_list])
with self.test_context():
m = Foo()
m.compile()
optimizer = gpflow.train.ScipyOptimizer(options={'disp': False, 'maxiter': 10})
optimizer.minimize(m)
atol = 1e-6 if settings.np_float is np.float32 else 1e-8
params = [param.read_value() for param in m.parameters]
self.assertTrue(np.allclose(params, 0., atol=atol))
#class TestPickleAndDict(test_util.GPflowTestCase):
# def setUp(self):
# with self.test_context():
# rng = np.random.RandomState(0)
# X = rng.randn(10, 1)
# Y = rng.randn(10, 1)
# self.m = gpflow.models.GPR(X, Y, kern=gpflow.kernels.RBF(1))
#
# def test(self):
# # pickle and reload the model
# s1 = pickle.dumps(self.m)
# m1 = pickle.loads(s1)
# d1 = self.m.get_parameter_dict()
# d2 = m1.get_parameter_dict()
# for key, val in d1.items():
# assert np.all(val == d2[key])
class TestFixWithPrior(test_util.GPflowTestCase):
"""
This tests that models with a fixed parameter which has a prior continue to work
"""
def test_non_trainable_with_prior(self):
with self.test_context():
m = gpflow.models.Model()
m.p = gpflow.Param(1.0, gpflow.transforms.positive)
m.pp = gpflow.Param(1.0, gpflow.transforms.positive)
m.p.prior = gpflow.priors.Gamma(1, 1)
m.pp.prior = gpflow.priors.Gamma(1, 1)
m.p.trainable = False
m._build_likelihood = lambda: tf.zeros([1], tf.float64)
m.compile()
optimizer = gpflow.train.ScipyOptimizer(options={'maxiter': 10})
optimizer.minimize(m)
#class TestRandomizeDefault(test_util.GPflowTestCase):
# """
# This tests that distributions can sample random values without priors
# """
#
# def test(self):
# with self.test_context():
# np.random.seed(1)
# m = gpflow.models.Model()
# m.p = gpflow.Param(1.0)
# m.pp = gpflow.Param(1.0, gpflow.transforms.Log1pe())
# m.pf = gpflow.Param(1.0)
# m.pf.trainable = False
#
# m.pmd = gpflow.Param(np.ones((5, 2)))
# ltr = gpflow.transforms.LowerTriangular(1,2).forward(np.ones(2 * 10))
# m.pmd2 = gpflow.Param(
# ltr, transform=gpflow.transforms.LowerTriangular(1,2))
#
# #should work as (pseudo) random vals a.s. are not 1.0
# m.p.randomize()
# self.assertFalse(m.p.value == 1.0)
# m.pp.randomize()
# self.assertFalse(m.pp.value == 1.0 or m.pp.value <= 0.0)
#
# #check if fixing works
# m.pf.randomize()
# self.assertTrue(m.pf.value == 1.0)
# m.pf.randomize(skipfixed=False)
# self.assertFalse(m.pf.value == 1.0)
#
# #check multidimensional
# pmd_shape = m.pmd.shape
# m.pmd.randomize()
# self.assertFalse(np.any(m.pmd.value == 1.0))
# self.assertEquals(m.pmd.shape, pmd_shape)
#
# #check non size-preserving transform
# pmd2_shape = m.pmd2.shape
# m.pmd2.randomize()
# self.assertFalse(np.any(m.pmd2.value == 1.0))
# self.assertEquals(m.pmd2.shape, pmd2_shape)
#
#class TestRandomizePrior(test_util.GPflowTestCase):
# """
# This tests that distributions can sample random values from priors
# """
#
# def test(self):
# with self.test_context():
# np.random.seed(1)
# from inspect import getargspec
#
# m = gpflow.models.Model()
# m.p = gpflow.Param(1.0)
# m.pmd = gpflow.Param(
# np.eye(5), transform=gpflow.transforms.DiagMatrix())
#
# priors = [obj for obj in gpflow.priors.__dict__.values() if
# isinstance(obj, type) and
# issubclass(obj, gpflow.priors._prior) and
# obj is not gpflow.priors._prior]
#
# with self.assertRaises(NotImplementedError):
# m.p = 1.0
# m.p.prior = gpflow.priors._prior()
# m.p.randomize()
#
# for prior in priors:
# signature = getargspec(prior.__init__)
# params = {}
# if signature.defaults is not None:
# param_names = signature.args[:-len(signature.defaults)]
# else:
# param_names = signature.args
# for param in param_names:
# if param not in params.keys() and param is not 'self':
# params[param] = 1.
#
# m.p = 1.0
# m.p.prior = prior(**params)
# m.pmd.prior = prior(**params)
# m.p.randomize()
# m.pmd.randomize()
# self.assertFalse(m.p.value == 1.0)
# self.assertFalse(np.any(m.pmd.value == np.ones(5)))
# self.assertTrue(m.pmd.value.shape == (5,5))
#
#
#class TestRandomizeFeedPriors(test_util.GPflowTestCase):
# """
# Test if standard randomize behavior can be overriden using
# distributions keyword.
# """
#
# def test(self):
# with self.test_context():
# np.random.seed(1)
# m = gpflow.models.Model()
# m.p = gpflow.Param(1.0)
# with self.assertRaises(NotImplementedError):
# m.p.randomize(distributions={m.p: gpflow.priors._prior()})
# m.p.randomize(distributions={m.p: gpflow.priors.Gaussian(0, 1)})
# self.assertFalse(m.p.value == 1.0)
#
#
#class TestRandomizeHierarchical(test_util.GPflowTestCase):
# """
# This tests that models can randomize all contained parameters
# """
#
# def test(self):
# with self.test_context():
# np.random.seed(1)
# m = gpflow.models.Model()
# m.p = gpflow.Param(1.0)
# m.p2 = gpflow.Param(1.0)
# m.m = gpflow.models.Model()
# m.m.p = gpflow.Param(1.0)
# m.m.p2 = gpflow.Param(1.0)
#
# m.p2.prior = gpflow.priors.Gaussian(0, 1)
# m.m.p2.prior = gpflow.priors.Gaussian(0, 1)
# m.randomize()
#
# self.assertFalse(m.p.value == 1.0)
# self.assertFalse(m.p2.value == 1.0)
# self.assertFalse(m.m.p.value == 1.0)
# self.assertFalse(m.m.p2.value == 1.0)
class TestScopes(test_util.GPflowTestCase):
def setUp(self):
with self.test_context() as session:
self.graph = session.graph
rng = np.random.RandomState(0)
X = rng.randn(10, 1)
Y = rng.randn(10, 1)
k = gpflow.kernels.RBF(1)
self.m = gpflow.models.GPR(X, Y, k)
self.m.compile()
def test_likelihood_name(self):
likelihood = self.m.likelihood_tensor
expected_name = self.m.hidden_name + '/likelihood'
self.assertTrue(likelihood.name.startswith(expected_name))
def test_kern_name(self):
with self.test_context(self.graph):
@gpflow.name_scope('test_kernel')
@gpflow.params_as_tensors
def run_kernel(m):
return m.kern.K(m.X)
K = run_kernel(self.m)
self.assertTrue(K.name.startswith('test_kernel/'))
def _check_trainable_flag(m, assert_true, assert_false):
for param in m.parameters:
assert_bool = assert_false
if param.trainable:
assert_bool = assert_true
assert_bool(gpflow.misc.is_tensor_trainable(param.parameter_tensor))
if __name__ == "__main__":
unittest.main()