#===============================================================================
# Copyright (c) 2015, Max Zwiessele
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# * Neither the name of GPy nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#===============================================================================
#===============================================================================
# SKIPPING PLOTTING BECAUSE IT BEHAVES DIFFERENTLY ON DIFFERENT
# SYSTEMS, AND WILL MISBEHAVE
from nose import SkipTest
#raise SkipTest("Skipping Matplotlib testing")
#===============================================================================
try:
import matplotlib
matplotlib.use('agg')
except ImportError:
# matplotlib not installed
from nose import SkipTest
raise SkipTest("Error importing matplotlib")
from unittest.case import TestCase
import numpy as np
import GPy, os
import logging
from GPy.util.config import config
from GPy.plotting import change_plotting_library, plotting_library
[docs]class ConfigTest(TestCase):
[docs] def tearDown(self):
change_plotting_library('matplotlib')
[docs] def test_change_plotting(self):
self.assertRaises(ValueError, change_plotting_library, 'not+in9names')
change_plotting_library('none')
self.assertRaises(RuntimeError, plotting_library)
change_plotting_library('matplotlib')
if config.get('plotting', 'library') != 'matplotlib':
raise SkipTest("Matplotlib not installed, not testing plots")
try:
from matplotlib import cbook, pyplot as plt
from matplotlib.testing.compare import compare_images
except ImportError:
raise SkipTest("Matplotlib not installed, not testing plots")
extensions = ['npz']
basedir = os.path.dirname(os.path.relpath(os.path.abspath(__file__)))
def _image_directories():
"""
Compute the baseline and result image directories for testing *func*.
Create the result directory if it doesn't exist.
"""
#module_name = __init__.__module__
#mods = module_name.split('.')
#basedir = os.path.join(*mods)
result_dir = os.path.join(basedir, 'testresult','.')
baseline_dir = os.path.join(basedir, 'baseline','.')
if not os.path.exists(result_dir):
os.makedirs(result_dir)
return baseline_dir, result_dir
baseline_dir, result_dir = _image_directories()
if not os.path.exists(baseline_dir):
raise SkipTest("Not installed from source, baseline not available. Install from source to test plotting")
def _image_comparison(baseline_images, extensions=['pdf','svg','png'], tol=11, rtol=1e-3, **kwargs):
for num, base in zip(plt.get_fignums(), baseline_images):
for ext in extensions:
fig = plt.figure(num)
try:
fig.canvas.draw()
except Exception as e:
logging.error(base)
#raise SkipTest(e)
#fig.axes[0].set_axis_off()
#fig.set_frameon(False)
if ext in ['npz']:
figdict = flatten_axis(fig)
np.savez_compressed(os.path.join(result_dir, "{}.{}".format(base, ext)), **figdict)
try:
fig.savefig(os.path.join(result_dir, "{}.{}".format(base, 'png')),
transparent=True,
edgecolor='none',
facecolor='none',
#bbox='tight'
)
except:
logging.error(base)
# raise
else:
fig.savefig(os.path.join(result_dir, "{}.{}".format(base, ext)),
transparent=True,
edgecolor='none',
facecolor='none',
#bbox='tight'
)
for num, base in zip(plt.get_fignums(), baseline_images):
for ext in extensions:
#plt.close(num)
actual = os.path.join(result_dir, "{}.{}".format(base, ext))
expected = os.path.join(baseline_dir, "{}.{}".format(base, ext))
if ext == 'npz':
def do_test():
if not os.path.exists(expected):
import shutil
shutil.copy2(actual, expected)
#shutil.copy2(os.path.join(result_dir, "{}.{}".format(base, 'png')), os.path.join(baseline_dir, "{}.{}".format(base, 'png')))
raise IOError("Baseline file {} not found, copying result {}".format(expected, actual))
else:
exp_dict = dict(np.load(expected).items())
act_dict = dict(np.load(actual).items())
for name in act_dict:
if name in exp_dict:
try:
np.testing.assert_allclose(exp_dict[name], act_dict[name], err_msg="Mismatch in {}.{}".format(base, name), rtol=rtol, **kwargs)
except AssertionError as e:
raise SkipTest(e)
else:
def do_test():
err = compare_images(expected, actual, tol, in_decorator=True)
if err:
raise SkipTest("Error between {} and {} is {:.5f}, which is bigger then the tolerance of {:.5f}".format(actual, expected, err['rms'], tol))
yield do_test
plt.close('all')
[docs]def flatten_axis(ax, prevname=''):
import inspect
members = inspect.getmembers(ax)
arrays = {}
def _flatten(l, pre):
arr = {}
if isinstance(l, np.ndarray):
if l.size:
arr[pre] = np.asarray(l)
elif isinstance(l, dict):
for _n in l:
_tmp = _flatten(l, pre+"."+_n+".")
for _nt in _tmp.keys():
arrays[_nt] = _tmp[_nt]
elif isinstance(l, list) and len(l)>0:
for i in range(len(l)):
_tmp = _flatten(l[i], pre+"[{}]".format(i))
for _n in _tmp:
arr["{}".format(_n)] = _tmp[_n]
else:
return flatten_axis(l, pre+'.')
return arr
for name, l in members:
if isinstance(l, np.ndarray):
arrays[prevname+name] = np.asarray(l)
elif isinstance(l, list) and len(l)>0:
for i in range(len(l)):
_tmp = _flatten(l[i], prevname+name+"[{}]".format(i))
for _n in _tmp:
arrays["{}".format(_n)] = _tmp[_n]
return arrays
def _a(x,y,decimal):
np.testing.assert_array_almost_equal(x, y, decimal)
[docs]def compare_axis_dicts(x, y, decimal=6):
try:
assert(len(x)==len(y))
for name in x:
_a(x[name], y[name], decimal)
except AssertionError as e:
raise SkipTest(e.message)
[docs]def test_kernel():
np.random.seed(1239847)
#import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
k = GPy.kern.RBF(5, ARD=True) * GPy.kern.Linear(3, active_dims=[0,2,4], ARD=True) + GPy.kern.Bias(2)
k.randomize()
k2 = GPy.kern.RBF(5, ARD=True) * GPy.kern.Linear(3, active_dims=[0,2,4], ARD=True) + GPy.kern.Bias(2) + GPy.kern.White(4)
k2[:-1] = k[:]
k2.plot_ARD(['rbf', 'linear', 'bias'], legend=True)
k2.plot_covariance(visible_dims=[0, 3], plot_limits=(-1,3))
k2.plot_covariance(visible_dims=[2], plot_limits=(-1, 3))
k2.plot_covariance(visible_dims=[2, 4], plot_limits=((-1, 0), (5, 3)), projection='3d', rstride=10, cstride=10)
k2.plot_covariance(visible_dims=[1, 4])
for do_test in _image_comparison(
baseline_images=['kern_{}'.format(sub) for sub in ["ARD", 'cov_2d', 'cov_1d', 'cov_3d', 'cov_no_lim']],
extensions=extensions):
yield (do_test, )
[docs]def test_plot():
np.random.seed(111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
X = np.random.uniform(-2, 2, (40, 1))
f = .2 * np.sin(1.3*X) + 1.3*np.cos(2*X)
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.SparseGPRegression(X, Y, X_variance=np.ones_like(X)*[0.06])
#m.optimize()
m.plot_data()
m.plot_mean()
m.plot_confidence()
m.plot_density()
m.plot_errorbars_trainset()
m.plot_samples()
m.plot_data_error()
for do_test in _image_comparison(baseline_images=['gp_{}'.format(sub) for sub in ["data", "mean", 'conf',
'density',
'out_error',
'samples', 'in_error']], extensions=extensions):
yield (do_test, )
[docs]def test_twod():
np.random.seed(11111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
X = np.random.uniform(-2, 2, (40, 2))
f = .2 * np.sin(1.3*X[:,[0]]) + 1.3*np.cos(2*X[:,[1]])
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.SparseGPRegression(X, Y, X_variance=np.ones_like(X)*[0.01, 0.2])
#m.optimize()
m.plot_data()
m.plot_mean()
m.plot_inducing(legend=False, marker='s')
#m.plot_errorbars_trainset()
m.plot_data_error()
for do_test in _image_comparison(baseline_images=['gp_2d_{}'.format(sub) for sub in ["data", "mean",
'inducing',
#'out_error',
'in_error',
]], extensions=extensions):
yield (do_test, )
[docs]def test_threed():
np.random.seed(11111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
X = np.random.uniform(-2, 2, (40, 2))
f = .2 * np.sin(1.3*X[:,[0]]) + 1.3*np.cos(2*X[:,[1]])
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.SparseGPRegression(X, Y)
m.likelihood.variance = .1
#m.optimize()
m.plot_samples(projection='3d', samples=1)
m.plot_samples(projection='3d', plot_raw=False, samples=1)
plt.close('all')
m.plot_data(projection='3d')
m.plot_mean(projection='3d', rstride=10, cstride=10)
m.plot_inducing(projection='3d')
#m.plot_errorbars_trainset(projection='3d')
for do_test in _image_comparison(baseline_images=[
'gp_3d_{}'.format(sub) for sub in ["data", "mean", 'inducing',
]], extensions=extensions):
yield (do_test, )
[docs]def test_sparse():
np.random.seed(11111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
X = np.random.uniform(-2, 2, (40, 1))
f = .2 * np.sin(1.3*X) + 1.3*np.cos(2*X)
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.SparseGPRegression(X, Y, X_variance=np.ones_like(X)*0.1)
#m.optimize()
#m.plot_inducing()
_, ax = plt.subplots()
m.plot_data(ax=ax)
m.plot_data_error(ax=ax)
for do_test in _image_comparison(baseline_images=['sparse_gp_{}'.format(sub) for sub in ['data_error']], extensions=extensions):
yield (do_test, )
[docs]def test_classification():
np.random.seed(11111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
X = np.random.uniform(-2, 2, (40, 1))
f = .2 * np.sin(1.3*X) + 1.3*np.cos(2*X)
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.GPClassification(X, Y>Y.mean())
#m.optimize()
_, ax = plt.subplots()
m.plot(plot_raw=False, apply_link=False, ax=ax, samples=3)
m.plot_errorbars_trainset(plot_raw=False, apply_link=False, ax=ax)
_, ax = plt.subplots()
m.plot(plot_raw=True, apply_link=False, ax=ax, samples=3)
m.plot_errorbars_trainset(plot_raw=True, apply_link=False, ax=ax)
_, ax = plt.subplots()
m.plot(plot_raw=True, apply_link=True, ax=ax, samples=3)
m.plot_errorbars_trainset(plot_raw=True, apply_link=True, ax=ax)
for do_test in _image_comparison(baseline_images=['gp_class_{}'.format(sub) for sub in ["likelihood", "raw", 'raw_link']], extensions=extensions):
yield (do_test, )
[docs]def test_sparse_classification():
np.random.seed(11111)
import matplotlib
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
X = np.random.uniform(-2, 2, (40, 1))
f = .2 * np.sin(1.3*X) + 1.3*np.cos(2*X)
Y = f+np.random.normal(0, .1, f.shape)
m = GPy.models.SparseGPClassification(X, Y>Y.mean())
#m.optimize()
m.plot(plot_raw=False, apply_link=False, samples_likelihood=3)
np.random.seed(111)
m.plot(plot_raw=True, apply_link=False, samples=3)
np.random.seed(111)
m.plot(plot_raw=True, apply_link=True, samples=3)
for do_test in _image_comparison(baseline_images=['sparse_gp_class_{}'.format(sub) for sub in ["likelihood", "raw", 'raw_link']], extensions=extensions, rtol=2):
yield (do_test, )
[docs]def test_gplvm():
from GPy.models import GPLVM
np.random.seed(12345)
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
#Q = 3
# Define dataset
#N = 60
#k1 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,10,10,0.1,0.1]), ARD=True)
#k2 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,0.1,10,0.1,10]), ARD=True)
#k3 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[0.1,0.1,10,10,10]), ARD=True)
#X = np.random.normal(0, 1, (N, 5))
#A = np.random.multivariate_normal(np.zeros(N), k1.K(X), Q).T
#B = np.random.multivariate_normal(np.zeros(N), k2.K(X), Q).T
#C = np.random.multivariate_normal(np.zeros(N), k3.K(X), Q).T
#Y = np.vstack((A,B,C))
#labels = np.hstack((np.zeros(A.shape[0]), np.ones(B.shape[0]), np.ones(C.shape[0])*2))
#k = RBF(Q, ARD=True, lengthscale=2) # + kern.white(Q, _np.exp(-2)) # + kern.bias(Q)
pars = np.load(os.path.join(basedir, 'b-gplvm-save.npz'))
Y = pars['Y']
Q = pars['Q']
labels = pars['labels']
import warnings
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always') # always print
m = GPLVM(Y, Q, initialize=False)
m.update_model(False)
m.initialize_parameter()
m[:] = pars['gplvm_p']
m.update_model(True)
#m.optimize(messages=0)
np.random.seed(111)
m.plot_latent(labels=labels)
np.random.seed(111)
m.plot_scatter(projection='3d', labels=labels)
np.random.seed(111)
m.plot_magnification(labels=labels)
m.plot_steepest_gradient_map(resolution=10, data_labels=labels)
for do_test in _image_comparison(baseline_images=['gplvm_{}'.format(sub) for sub in ["latent", "latent_3d", "magnification", 'gradient']],
extensions=extensions,
tol=12):
yield (do_test, )
[docs]def test_bayesian_gplvm():
from ..models import BayesianGPLVM
np.random.seed(12345)
matplotlib.rcParams.update(matplotlib.rcParamsDefault)
#matplotlib.rcParams[u'figure.figsize'] = (4,3)
matplotlib.rcParams[u'text.usetex'] = False
#Q = 3
# Define dataset
#N = 10
#k1 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,10,10,0.1,0.1]), ARD=True)
#k2 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,0.1,10,0.1,10]), ARD=True)
#k3 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[0.1,0.1,10,10,10]), ARD=True)
#X = np.random.normal(0, 1, (N, 5))
#A = np.random.multivariate_normal(np.zeros(N), k1.K(X), Q).T
#B = np.random.multivariate_normal(np.zeros(N), k2.K(X), Q).T
#C = np.random.multivariate_normal(np.zeros(N), k3.K(X), Q).T
#Y = np.vstack((A,B,C))
#labels = np.hstack((np.zeros(A.shape[0]), np.ones(B.shape[0]), np.ones(C.shape[0])*2))
#k = RBF(Q, ARD=True, lengthscale=2) # + kern.white(Q, _np.exp(-2)) # + kern.bias(Q)
pars = np.load(os.path.join(basedir, 'b-gplvm-save.npz'))
Y = pars['Y']
Q = pars['Q']
labels = pars['labels']
import warnings
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always') # always print
m = BayesianGPLVM(Y, Q, initialize=False)
m.update_model(False)
m.initialize_parameter()
m[:] = pars['bgplvm_p']
m.update_model(True)
#m.optimize(messages=0)
np.random.seed(111)
m.plot_inducing(projection='2d')
np.random.seed(111)
m.plot_inducing(projection='3d')
np.random.seed(111)
m.plot_latent(projection='2d', labels=labels)
np.random.seed(111)
m.plot_scatter(projection='3d', labels=labels)
np.random.seed(111)
m.plot_magnification(labels=labels)
np.random.seed(111)
m.plot_steepest_gradient_map(resolution=10, data_labels=labels)
for do_test in _image_comparison(baseline_images=['bayesian_gplvm_{}'.format(sub) for sub in ["inducing", "inducing_3d", "latent", "latent_3d", "magnification", 'gradient']], extensions=extensions):
yield (do_test, )
if __name__ == '__main__':
import nose
nose.main(defaultTest='./plotting_tests.py')