def test_knn_memory():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
dim = 3
n = 20
np.random.seed(47)
bags = Features(
[np.random.randn(np.random.randint(30, 100), dim) for _ in xrange(n)])
tdir = tempfile.mkdtemp()
div_funcs = ('kl', 'js', 'renyi:.9', 'l2', 'tsallis:.8')
Ks = (3, 4)
est = KNNDivergenceEstimator(div_funcs=div_funcs, Ks=Ks, memory=tdir)
res1 = est.fit_transform(bags)
with LogCapture('skl_groups.divergences.knn', level=logging.INFO) as l:
res2 = est.transform(bags)
assert len(l.records) == 0
assert np.all(res1 == res2)
with LogCapture('skl_groups.divergences.knn', level=logging.INFO) as l:
res3 = est.fit_transform(bags)
for r in l.records:
assert not r.message.startswith("Getting divergences")
assert np.all(res1 == res3)
def test_knn_memory():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
dim = 3
n = 20
np.random.seed(47)
bags = Features([np.random.randn(np.random.randint(30, 100), dim)
for _ in xrange(n)])
tdir = tempfile.mkdtemp()
div_funcs = ('kl', 'js', 'renyi:.9', 'l2', 'tsallis:.8')
Ks = (3, 4)
est = KNNDivergenceEstimator(div_funcs=div_funcs, Ks=Ks, memory=tdir)
res1 = est.fit_transform(bags)
with LogCapture('skl_groups.divergences.knn', level=logging.INFO) as l:
res2 = est.transform(bags)
assert len(l.records) == 0
assert np.all(res1 == res2)
with LogCapture('skl_groups.divergences.knn', level=logging.INFO) as l:
res3 = est.fit_transform(bags)
for r in l.records:
assert not r.message.startswith("Getting divergences")
assert np.all(res1 == res3)
def test_knn_kl():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
# verified by hand
# Dhat(P||Q) = \log m/(n-1) + d / n \sum_{i=1}^n \log \nu_k(i)/rho_k(i)
x = np.reshape([0., 1, 3], (3, 1))
y = np.reshape([.2, 1.2, 3.2, 7.2], (4, 1))
n = x.shape[0]
m = y.shape[0]
x_to_y = np.log(
m /
(n - 1)) + 1 / n * (np.log(1.2 / 3) + np.log(.8 / 2) + np.log(1.8 / 3))
y_to_x = np.log(n / (m - 1)) + 1 / m * (np.log(.8 / 3) + np.log(1.2 / 2) +
np.log(2.2 / 3) + np.log(6.2 / 6))
msg = "got {}, expected {}"
est = KNNDivergenceEstimator(div_funcs=['kl'], Ks=[2], clamp=False)
res = est.fit_transform([x, y]).squeeze()
assert res[0, 0] == 0
assert res[1, 1] == 0
assert np.allclose(res[0, 1], x_to_y), msg.format(res[0, 1], x_to_y)
assert np.allclose(res[1, 0], y_to_x), msg.format(res[1, 0], y_to_x)
def divergence_gen(gen, gt_db, batch=1000, metric='kl', normalize=False,
n_bins=100, whitening=True, classes=None, **kwargs):
"""
Given a generator and the gt function (the one generator
tries to approximate), we measure the discrepancy of the
generated from the gt signals.
"""
# # generate some samples.
batch = gt_db.shape[0]
if classes is None:
gen_samples = gen_images(gen, n=batch, batchsize=batch)
else:
# # conditional case.
gen_csamples, n_ms = [], int(batch // len(classes) + 10)
for cl in classes:
x = gen_images_with_condition(gen, n=n_ms, c=cl, batchsize=n_ms)
gen_csamples.append(x)
gen_csamples = np.concatenate(gen_csamples, 0)
gen_samples = gen_csamples[:gt_db.shape[0]]
if len(gt_db.shape) != 2:
gt_db = gt_db.reshape((batch, -1))
if len(gen_samples.shape) != 2:
gen_samples = gen_samples.reshape((batch, -1))
if gen_samples.dtype == np.uint8:
gen_samples = gen_samples.astype(np.float32)
if normalize:
# # Given that gen_images have a range [0, 255], normalize
# # the images in the [-1, 1] range for the KNN.
gen_samples1 = gen_samples / 127.5 - 1
else:
gen_samples1 = gen_samples
if metric == 'ndb':
global ndb
if ndb is None:
ndb = NDB(training_data=gt_db, number_of_bins=n_bins, whitening=whitening)
metric_val = ndb.evaluate(gen_samples)
chainer.reporter.report({'ndb': metric_val['NDB']})
chainer.reporter.report({'JS': metric_val['JS']})
diver = metric_val['NDB']
else:
# # define an estimator (e.g. KL divergence).
est = KNNDivergenceEstimator(div_funcs=[metric], Ks=[3], clamp=False)
# # fit and return the result.
res_diver = est.fit_transform([gt_db, gen_samples])
try:
diver = res_diver[0, 1]
except:
diver = res_diver[0][0][0, 1]
chainer.reporter.report({'kl': diver})
return diver
def kNNdiv_Kernel(X_white,
kernel,
Knn=3,
div_func='renyi:.5',
Nref=None,
compwise=True,
njobs=1,
W_ica_inv=None):
''' `div_func` kNN divergence estimate between some data X_white and a distribution specified by Kernel.
'''
if isinstance(Knn, int):
Knns = [Knn]
elif isinstance(Knn, list):
Knns = Knn
# if component wise there should be X_white.shape[1]
# kernels for each componenets
if compwise:
if X_white.shape[1] != len(kernel): raise ValueError
# construct reference "bag"
if compwise:
ref_dist = np.zeros((Nref, X_white.shape[1]))
for icomp in range(X_white.shape[1]):
samp = kernel[icomp].sample(Nref)
if isinstance(samp, tuple):
ref_dist[:, icomp] = samp[0].flatten()
else:
ref_dist[:, icomp] = samp.flatten()
else:
samp = kernel.sample(Nref)
if isinstance(samp, tuple):
ref_dist = samp[0]
else:
ref_dist = samp
if W_ica_inv is not None:
ref_dist = np.dot(ref_dist, W_ica_inv.T)
# estimate divergence
kNN = KNNDivergenceEstimator(div_funcs=[div_func],
Ks=Knns,
version='slow',
clamp=False,
n_jobs=njobs)
feat = Features([X_white, ref_dist])
div_knn = kNN.fit_transform(feat)
if len(Knns) == 1:
return div_knn[0][0][0][1]
div_knns = np.zeros(len(Knns))
for i in range(len(Knns)):
div_knns[i] = div_knn[0][i][0][1]
return div_knns
def test_knn_sanity_slow():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
dim = 3
n = 20
np.random.seed(47)
bags = Features(
[np.random.randn(np.random.randint(30, 100), dim) for _ in xrange(n)])
# just make sure it runs
div_funcs = ('kl', 'js', 'renyi:.9', 'l2', 'tsallis:.8')
Ks = (3, 4)
est = KNNDivergenceEstimator(div_funcs=div_funcs, Ks=Ks)
res = est.fit_transform(bags)
assert res.shape == (len(div_funcs), len(Ks), n, n)
assert np.all(np.isfinite(res))
# test that JS blows up when there's a huge difference in bag sizes
# (so that K is too low)
assert_raises(
ValueError,
partial(est.fit_transform, bags + [np.random.randn(1000, dim)]))
# test fit() and then transform() with JS, with different-sized test bags
est = KNNDivergenceEstimator(div_funcs=('js', ), Ks=(5, ))
est.fit(bags, get_rhos=True)
with LogCapture('skl_groups.divergences.knn', level=logging.WARNING) as l:
res = est.transform([np.random.randn(300, dim)])
assert res.shape == (1, 1, 1, len(bags))
assert len(l.records) == 1
assert l.records[0].message.startswith('Y_rhos had a lower max_K')
# test that passing div func more than once raises
def blah(df):
est = KNNDivergenceEstimator(div_funcs=[df, df])
return est.fit(bags)
assert_raises(ValueError, lambda: blah('kl'))
assert_raises(ValueError, lambda: blah('renyi:.8'))
assert_raises(ValueError, lambda: blah('l2'))
def test_knn_sanity_slow():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
dim = 3
n = 20
np.random.seed(47)
bags = Features([np.random.randn(np.random.randint(30, 100), dim)
for _ in xrange(n)])
# just make sure it runs
div_funcs = ('kl', 'js', 'renyi:.9', 'l2', 'tsallis:.8')
Ks = (3, 4)
est = KNNDivergenceEstimator(div_funcs=div_funcs, Ks=Ks)
res = est.fit_transform(bags)
assert res.shape == (len(div_funcs), len(Ks), n, n)
assert np.all(np.isfinite(res))
# test that JS blows up when there's a huge difference in bag sizes
# (so that K is too low)
assert_raises(
ValueError,
partial(est.fit_transform, bags + [np.random.randn(1000, dim)]))
# test fit() and then transform() with JS, with different-sized test bags
est = KNNDivergenceEstimator(div_funcs=('js',), Ks=(5,))
est.fit(bags, get_rhos=True)
with LogCapture('skl_groups.divergences.knn', level=logging.WARNING) as l:
res = est.transform([np.random.randn(300, dim)])
assert res.shape == (1, 1, 1, len(bags))
assert len(l.records) == 1
assert l.records[0].message.startswith('Y_rhos had a lower max_K')
# test that passing div func more than once raises
def blah(df):
est = KNNDivergenceEstimator(div_funcs=[df, df])
return est.fit(bags)
assert_raises(ValueError, lambda: blah('kl'))
assert_raises(ValueError, lambda: blah('renyi:.8'))
assert_raises(ValueError, lambda: blah('l2'))
def kNNdiv_gauss(X_white,
cov_X,
Knn=3,
div_func='renyi:.5',
gauss=None,
Nref=None,
njobs=1):
''' `div_func` kNN divergence estimate between X_white and a
reference Gaussian with covariance matrix cov_X.
'''
if gauss is None:
if Nref is None:
raise ValueError
gauss = np.random.multivariate_normal(
np.zeros(X_white.shape[1]), cov_X,
size=Nref) # Gaussian reference distribution
if gauss.shape[1] != X_white.shape[1]:
raise ValueError(
'dimension between X_white and Gaussian reference distribution do not match'
)
if isinstance(Knn, int):
Knns = [Knn]
elif isinstance(Knn, list):
Knns = Knn
kNN = KNNDivergenceEstimator(div_funcs=[div_func],
Ks=Knns,
version='slow',
clamp=False,
n_jobs=njobs)
feat = Features([X_white, gauss])
div_knn = kNN.fit_transform(feat)
if len(Knns) == 1:
return div_knn[0][0][0][1]
div_knns = np.zeros(len(Knns))
for i in range(len(Knns)):
div_knns[i] = div_knn[0][i][0][1]
return div_knns
def test_knn_kl():
if not have_flann:
raise SkipTest("No flann, so skipping knn tests.")
# verified by hand
# Dhat(P||Q) = \log m/(n-1) + d / n \sum_{i=1}^n \log \nu_k(i)/rho_k(i)
x = np.reshape([0., 1, 3], (3, 1))
y = np.reshape([.2, 1.2, 3.2, 7.2], (4, 1))
n = x.shape[0]
m = y.shape[0]
x_to_y = np.log(m / (n-1)) + 1/n * (
np.log(1.2 / 3) + np.log(.8 / 2) + np.log(1.8 / 3))
y_to_x = np.log(n / (m-1)) + 1/m * (
np.log(.8 / 3) + np.log(1.2 / 2) + np.log(2.2 / 3) + np.log(6.2 / 6))
msg = "got {}, expected {}"
est = KNNDivergenceEstimator(div_funcs=['kl'], Ks=[2], clamp=False)
res = est.fit_transform([x, y]).squeeze()
assert res[0, 0] == 0
assert res[1, 1] == 0
assert np.allclose(res[0, 1], x_to_y), msg.format(res[0, 1], x_to_y)
assert np.allclose(res[1, 0], y_to_x), msg.format(res[1, 0], y_to_x)