def test_parameterized(self):
par = Parameterized('parameterized')
p2 = Parameterized('rbf')
p2.p1 = Param('lengthscale', np.random.uniform(0.1,.5,3), Exponent())
p2.link_parameter(p2.p1)
par.p1 = p2
par.p2 = Param('linear', np.random.uniform(0.1, .5, 2), Logexp())
par.link_parameters(par.p1, par.p2)
par.gradient = 10
par.randomize()
pcopy = par.copy()
self.assertIsInstance(pcopy.constraints, ParameterIndexOperations)
self.assertIsInstance(pcopy.rbf.constraints, ParameterIndexOperationsView)
self.assertIs(pcopy.constraints, pcopy.rbf.constraints._param_index_ops)
self.assertIs(pcopy.constraints, pcopy.rbf.lengthscale.constraints._param_index_ops)
self.assertListEqual(par.param_array.tolist(), pcopy.param_array.tolist())
pcopy.gradient = 10 # gradient does not get copied anymore
self.assertListEqual(par.gradient_full.tolist(), pcopy.gradient_full.tolist())
self.assertSequenceEqual(str(par), str(pcopy))
self.assertIsNot(par.param_array, pcopy.param_array)
self.assertIsNot(par.gradient_full, pcopy.gradient_full)
with tempfile.TemporaryFile('w+b') as f:
par.pickle(f)
f.seek(0)
pcopy = paramz.load(f)
self.assertListEqual(par.param_array.tolist(), pcopy.param_array.tolist())
pcopy.gradient = 10
np.testing.assert_allclose(par.linear.gradient_full, pcopy.linear.gradient_full)
np.testing.assert_allclose(pcopy.linear.gradient_full, 10)
self.assertSequenceEqual(str(par), str(pcopy))
def test_parameter_index_operations(self):
pio = ParameterIndexOperations(dict(test1=np.array([4,3,1,6,4]), test2=np.r_[2:130]))
piov = ParameterIndexOperationsView(pio, 20, 250)
#py3 fix
#self.assertListDictEquals(dict(piov.items()), dict(piov.copy().iteritems()))
self.assertListDictEquals(dict(piov.items()), dict(piov.copy().items()))
#py3 fix
#self.assertListDictEquals(dict(pio.iteritems()), dict(pio.copy().items()))
self.assertListDictEquals(dict(pio.items()), dict(pio.copy().items()))
self.assertArrayListEquals(pio.copy().indices(), pio.indices())
self.assertArrayListEquals(piov.copy().indices(), piov.indices())
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(pio, f)
f.seek(0)
pio2 = pickle.load(f)
self.assertListDictEquals(pio._properties, pio2._properties)
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(piov, f)
f.seek(0)
pio2 = paramz.load(f)
#py3 fix
#self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems()))
self.assertListDictEquals(dict(piov.items()), dict(pio2.items()))
def test_parameter_index_operations(self):
pio = ParameterIndexOperations(
dict(test1=np.array([4, 3, 1, 6, 4]), test2=np.r_[2:130]))
piov = ParameterIndexOperationsView(pio, 20, 250)
#py3 fix
#self.assertListDictEquals(dict(piov.items()), dict(piov.copy().iteritems()))
self.assertListDictEquals(dict(piov.items()),
dict(piov.copy().items()))
#py3 fix
#self.assertListDictEquals(dict(pio.iteritems()), dict(pio.copy().items()))
self.assertListDictEquals(dict(pio.items()), dict(pio.copy().items()))
self.assertArrayListEquals(pio.copy().indices(), pio.indices())
self.assertArrayListEquals(piov.copy().indices(), piov.indices())
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(pio, f)
f.seek(0)
pio2 = pickle.load(f)
self.assertListDictEquals(pio._properties, pio2._properties)
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(piov, f)
f.seek(0)
pio2 = paramz.load(f)
#py3 fix
#self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems()))
self.assertListDictEquals(dict(piov.items()), dict(pio2.items()))
def test_observable_array(self):
obs = ObsAr(np.arange(4*2).reshape(4,2))
pcopy = obs.copy()
self.assertListEqual(obs.tolist(), pcopy.tolist())
tmpfile = ''.join(map(str, np.random.randint(10, size=20)))
try:
obs.pickle(tmpfile)
pcopy = paramz.load(tmpfile)
except:
raise
finally:
os.remove(tmpfile)
self.assertListEqual(obs.tolist(), pcopy.tolist())
self.assertSequenceEqual(str(obs), str(pcopy))
def test_param(self):
param = Param('test', np.arange(4*2).reshape(4,2))
param[0].constrain_positive()
param[1].fix()
pcopy = param.copy()
self.assertListEqual(param.tolist(), pcopy.tolist())
self.assertListEqual(str(param).split('\n'), str(pcopy).split('\n'))
self.assertIsNot(param, pcopy)
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(param, f)
f.seek(0)
pcopy = paramz.load(f)
self.assertListEqual(param.tolist(), pcopy.tolist())
self.assertSequenceEqual(str(param), str(pcopy))
def test_observable_array(self):
obs = ObsAr(np.arange(4 * 2).reshape(4, 2))
pcopy = obs.copy()
self.assertListEqual(obs.tolist(), pcopy.tolist())
tmpfile = ''.join(map(str, np.random.randint(10, size=20)))
try:
obs.pickle(tmpfile)
pcopy = paramz.load(tmpfile)
except:
raise
finally:
os.remove(tmpfile)
self.assertListEqual(obs.tolist(), pcopy.tolist())
self.assertSequenceEqual(str(obs), str(pcopy))
def test_param(self):
param = Param('test', np.arange(4 * 2).reshape(4, 2))
param[0].constrain_positive()
param[1].fix()
pcopy = param.copy()
self.assertListEqual(param.tolist(), pcopy.tolist())
self.assertListEqual(str(param).split('\n'), str(pcopy).split('\n'))
self.assertIsNot(param, pcopy)
with tempfile.TemporaryFile('w+b') as f:
pickle.dump(param, f)
f.seek(0)
pcopy = paramz.load(f)
self.assertListEqual(param.tolist(), pcopy.tolist())
self.assertSequenceEqual(str(param), str(pcopy))
def load(file_or_path):
"""
Load a previously pickled model, using `m.pickle('path/to/file.pickle)'
:param file_name: path/to/file.pickle
"""
# This is the pickling pain when changing _src -> src
import sys
import inspect
sys.modules['GPy.kern._src'] = kern.src
for name, module in inspect.getmembers(kern.src):
if not name.startswith('_'):
sys.modules['GPy.kern._src.{}'.format(name)] = module
sys.modules['GPy.inference.optimization'] = inference.optimization
import paramz
return paramz.load(file_or_path)
def test_parameterized(self):
par = Parameterized('parameterized')
p2 = Parameterized('rbf')
p2.p1 = Param('lengthscale', np.random.uniform(0.1, .5, 3), Exponent())
p2.link_parameter(p2.p1)
par.p1 = p2
par.p2 = Param('linear', np.random.uniform(0.1, .5, 2), Logexp())
par.link_parameters(par.p1, par.p2)
par.gradient = 10
par.randomize()
pcopy = par.copy()
self.assertIsInstance(pcopy.constraints, ParameterIndexOperations)
self.assertIsInstance(pcopy.rbf.constraints,
ParameterIndexOperationsView)
self.assertIs(pcopy.constraints,
pcopy.rbf.constraints._param_index_ops)
self.assertIs(pcopy.constraints,
pcopy.rbf.lengthscale.constraints._param_index_ops)
self.assertListEqual(par.param_array.tolist(),
pcopy.param_array.tolist())
pcopy.gradient = 10 # gradient does not get copied anymore
self.assertListEqual(par.gradient_full.tolist(),
pcopy.gradient_full.tolist())
self.assertSequenceEqual(str(par), str(pcopy))
self.assertIsNot(par.param_array, pcopy.param_array)
self.assertIsNot(par.gradient_full, pcopy.gradient_full)
with tempfile.TemporaryFile('w+b') as f:
par.pickle(f)
f.seek(0)
pcopy = paramz.load(f)
self.assertListEqual(par.param_array.tolist(),
pcopy.param_array.tolist())
pcopy.gradient = 10
np.testing.assert_allclose(par.linear.gradient_full,
pcopy.linear.gradient_full)
np.testing.assert_allclose(pcopy.linear.gradient_full, 10)
self.assertSequenceEqual(str(par), str(pcopy))
