From fe763de3f5f3d035a3c3f58a39be0332221b5e5c Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Thu, 24 Mar 2022 19:03:59 +0100
Subject: [PATCH] [gmm] add more dask tests, fixes #38
---
bob/learn/em/gmm.py | 10 +-
bob/learn/em/test/test_gmm.py | 511 +++++++++++++------------------
bob/learn/em/test/test_kmeans.py | 2 +-
3 files changed, 221 insertions(+), 302 deletions(-)
diff --git a/bob/learn/em/gmm.py b/bob/learn/em/gmm.py
index 7629399..38908cc 100644
--- a/bob/learn/em/gmm.py
+++ b/bob/learn/em/gmm.py
@@ -672,12 +672,10 @@ class GMMMachine(BaseEstimator):
def __eq__(self, other):
return (
- np.array_equal(self.means, other.means)
- and np.array_equal(self.variances, other.variances)
- and np.array_equal(
- self.variance_thresholds, other.variance_thresholds
- )
- and np.array_equal(self.weights, other.weights)
+ np.allclose(self.means, other.means)
+ and np.allclose(self.variances, other.variances)
+ and np.allclose(self.variance_thresholds, other.variance_thresholds)
+ and np.allclose(self.weights, other.weights)
)
def is_similar_to(self, other, rtol=1e-5, atol=1e-8):
diff --git a/bob/learn/em/test/test_gmm.py b/bob/learn/em/test/test_gmm.py
index 6e4b5d0..a896263 100644
--- a/bob/learn/em/test/test_gmm.py
+++ b/bob/learn/em/test/test_gmm.py
@@ -14,7 +14,6 @@ import tempfile
from copy import deepcopy
-import dask.array as da
import numpy as np
from dask.distributed import Client
@@ -44,6 +43,33 @@ def multiprocess_dask_client():
client.close()
+def loadGMM():
+ gmm = GMMMachine(n_gaussians=2)
+
+ gmm.weights = load_array(
+ resource_filename("bob.learn.em", "data/gmm.init_weights.hdf5")
+ )
+ gmm.means = load_array(
+ resource_filename("bob.learn.em", "data/gmm.init_means.hdf5")
+ )
+ gmm.variances = load_array(
+ resource_filename("bob.learn.em", "data/gmm.init_variances.hdf5")
+ )
+
+ return gmm
+
+
+def assert_gmm_equal(gmm1, gmm2):
+ """Asserts that two GMMs are equal"""
+ np.testing.assert_almost_equal(gmm1.weights, gmm2.weights)
+ np.testing.assert_almost_equal(gmm1.means, gmm2.means)
+ np.testing.assert_almost_equal(gmm1.variances, gmm2.variances)
+ np.testing.assert_almost_equal(
+ gmm1.variance_thresholds, gmm2.variance_thresholds
+ )
+ assert gmm1 == gmm2
+
+
def test_GMMStats():
# Test a GMMStats
# Initializes a GMMStats
@@ -197,20 +223,16 @@ def test_GMMMachine():
gmm6.variances = variances
gmm6.variance_thresholds = varianceThresholds2
- assert gmm == gmm2
+ assert_gmm_equal(gmm, gmm2)
assert (gmm != gmm2) is False
assert gmm.is_similar_to(gmm2)
assert gmm != gmm3
- assert (gmm == gmm3) is False
assert gmm.is_similar_to(gmm3) is False
assert gmm != gmm4
- assert (gmm == gmm4) is False
assert gmm.is_similar_to(gmm4) is False
assert gmm != gmm5
- assert (gmm == gmm5) is False
assert gmm.is_similar_to(gmm5) is False
assert gmm != gmm6
- assert (gmm == gmm6) is False
assert gmm.is_similar_to(gmm6) is False
# Saving and loading
@@ -225,7 +247,7 @@ def test_GMMMachine():
assert type(gmm1.update_weights) is np.bool_
assert type(gmm1.trainer) is str
assert gmm1.ubm is None
- assert gmm == gmm1
+ assert_gmm_equal(gmm, gmm1)
# Using load
gmm1 = GMMMachine(n_gaussians=gmm.n_gaussians)
gmm1.load(HDF5File(filename, "r"))
@@ -235,13 +257,13 @@ def test_GMMMachine():
assert type(gmm1.update_weights) is np.bool_
assert type(gmm1.trainer) is str
assert gmm1.ubm is None
- assert gmm == gmm1
+ assert_gmm_equal(gmm, gmm1)
with tempfile.NamedTemporaryFile(suffix=".hdf5") as f:
filename = f.name
gmm.save(filename)
gmm1 = GMMMachine.from_hdf5(filename)
- assert gmm == gmm1
+ assert_gmm_equal(gmm, gmm1)
# Weights
n_gaussians = 5
@@ -465,13 +487,15 @@ def test_gmm_kmeans_plusplus_init():
data = np.array(
[[1.5, 1], [1, 1.5], [-1, 0.5], [-1.5, 0], [2, 2], [2.5, 2.5]]
)
- machine = machine.fit(data)
- expected_means = np.array([[2.25, 2.25], [-1.25, 0.25], [1.25, 1.25]])
- expected_variances = np.array(
- [[1 / 16, 1 / 16], [1 / 16, 1 / 16], [1 / 16, 1 / 16]]
- )
- np.testing.assert_almost_equal(machine.means, expected_means, decimal=3)
- np.testing.assert_almost_equal(machine.variances, expected_variances)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ machine = machine.fit(data)
+ expected_means = np.array([[2.25, 2.25], [-1.25, 0.25], [1.25, 1.25]])
+ expected_variances = np.array(
+ [[1 / 16, 1 / 16], [1 / 16, 1 / 16], [1 / 16, 1 / 16]]
+ )
+ np.testing.assert_almost_equal(machine.means, expected_means, decimal=3)
+ np.testing.assert_almost_equal(machine.variances, expected_variances)
def test_gmm_kmeans_parallel_init():
@@ -509,16 +533,18 @@ def test_likelihood():
machine = GMMMachine(n_gaussians)
machine.means = np.repeat([[0], [1], [-1]], 3, 1)
machine.variances = np.ones_like(machine.means)
- log_likelihood = machine.log_likelihood(data)
- expected_ll = np.array(
- [
- -3.6519900964986527,
- -3.83151883210222,
- -3.83151883210222,
- -5.344374066745753,
- ]
- )
- np.testing.assert_almost_equal(log_likelihood, expected_ll)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ log_likelihood = machine.log_likelihood(data)
+ expected_ll = np.array(
+ [
+ -3.6519900964986527,
+ -3.83151883210222,
+ -3.83151883210222,
+ -5.344374066745753,
+ ]
+ )
+ np.testing.assert_almost_equal(log_likelihood, expected_ll)
def test_likelihood_variance():
@@ -533,16 +559,18 @@ def test_likelihood_variance():
[1, 1, 1],
]
)
- log_likelihood = machine.log_likelihood(data)
- expected_ll = np.array(
- [
- -2.202846959440514,
- -3.8699524542323793,
- -4.229029034375473,
- -6.940892214952679,
- ]
- )
- np.testing.assert_almost_equal(log_likelihood, expected_ll)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ log_likelihood = machine.log_likelihood(data)
+ expected_ll = np.array(
+ [
+ -2.202846959440514,
+ -3.8699524542323793,
+ -4.229029034375473,
+ -6.940892214952679,
+ ]
+ )
+ np.testing.assert_almost_equal(log_likelihood, expected_ll)
def test_likelihood_weight():
@@ -552,16 +580,18 @@ def test_likelihood_weight():
machine.means = np.repeat([[0], [1], [-1]], 3, 1)
machine.variances = np.ones_like(machine.means)
machine.weights = [0.6, 0.1, 0.3]
- log_likelihood = machine.log_likelihood(data)
- expected_ll = np.array(
- [
- -4.206596356117164,
- -3.492325679996329,
- -3.634745457950943,
- -6.49485678536014,
- ]
- )
- np.testing.assert_almost_equal(log_likelihood, expected_ll)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ log_likelihood = machine.log_likelihood(data)
+ expected_ll = np.array(
+ [
+ -4.206596356117164,
+ -3.492325679996329,
+ -3.634745457950943,
+ -6.49485678536014,
+ ]
+ )
+ np.testing.assert_almost_equal(log_likelihood, expected_ll)
def test_GMMMachine_object():
@@ -688,27 +718,31 @@ def test_ml_transformer():
machine.means = np.array([[2, 2, 2], [8, 8, 8]])
machine.variances = np.ones_like(machine.means)
- machine = machine.fit(data)
-
- expected_means = np.array([[1.5, 1.5, 2.0], [7.0, 8.0, 8.0]])
- np.testing.assert_almost_equal(machine.means, expected_means)
- expected_weights = np.array([2 / 5, 3 / 5])
- np.testing.assert_almost_equal(machine.weights, expected_weights)
- eps = np.finfo(float).eps
- expected_variances = np.array([[1 / 4, 1 / 4, eps], [eps, 2 / 3, 2 / 3]])
- np.testing.assert_almost_equal(machine.variances, expected_variances)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ machine = machine.fit(data)
+
+ expected_means = np.array([[1.5, 1.5, 2.0], [7.0, 8.0, 8.0]])
+ np.testing.assert_almost_equal(machine.means, expected_means)
+ expected_weights = np.array([2 / 5, 3 / 5])
+ np.testing.assert_almost_equal(machine.weights, expected_weights)
+ eps = np.finfo(float).eps
+ expected_variances = np.array(
+ [[1 / 4, 1 / 4, eps], [eps, 2 / 3, 2 / 3]]
+ )
+ np.testing.assert_almost_equal(machine.variances, expected_variances)
- stats = machine.transform(test_data)
+ stats = machine.transform(test_data)
- expected_stats = GMMStats(n_gaussians, n_features)
- expected_stats.init_fields(
- log_likelihood=-6755399441055685.0,
- t=test_data.shape[0],
- n=np.array([2, 2], dtype=float),
- sum_px=np.array([[2, 2, 3], [16, 17, 17]], dtype=float),
- sum_pxx=np.array([[2, 2, 5], [128, 145, 145]], dtype=float),
- )
- assert stats.is_similar_to(expected_stats)
+ expected_stats = GMMStats(n_gaussians, n_features)
+ expected_stats.init_fields(
+ log_likelihood=-6755399441055685.0,
+ t=test_data.shape[0],
+ n=np.array([2, 2], dtype=float),
+ sum_px=np.array([[2, 2, 3], [16, 17, 17]], dtype=float),
+ sum_pxx=np.array([[2, 2, 5], [128, 145, 145]], dtype=float),
+ )
+ assert stats.is_similar_to(expected_stats)
def test_map_transformer():
@@ -732,79 +766,69 @@ def test_map_transformer():
update_weights=True,
)
- machine = machine.fit(post_data)
+ for transform in (to_numpy, to_dask_array):
+ post_data = transform(post_data)
+ machine = machine.fit(post_data)
- expected_means = np.array(
- [[1.83333333, 1.83333333, 2.0], [7.57142857, 8, 8]]
- )
- np.testing.assert_almost_equal(machine.means, expected_means)
- eps = np.finfo(float).eps
- expected_vars = np.array([[eps, eps, eps], [eps, eps, eps]])
- np.testing.assert_almost_equal(machine.variances, expected_vars)
- expected_weights = np.array([0.46226415, 0.53773585])
- np.testing.assert_almost_equal(machine.weights, expected_weights)
-
- stats = machine.transform(test_data)
-
- expected_stats = GMMStats(n_gaussians, n_features)
- expected_stats.init_fields(
- log_likelihood=-1.3837590691807108e16,
- t=test_data.shape[0],
- n=np.array([2, 2], dtype=float),
- sum_px=np.array([[2, 2, 3], [16, 17, 17]], dtype=float),
- sum_pxx=np.array([[2, 2, 5], [128, 145, 145]], dtype=float),
- )
- assert stats.is_similar_to(expected_stats)
+ expected_means = np.array(
+ [[1.83333333, 1.83333333, 2.0], [7.57142857, 8, 8]]
+ )
+ np.testing.assert_almost_equal(machine.means, expected_means)
+ eps = np.finfo(float).eps
+ expected_vars = np.array([[eps, eps, eps], [eps, eps, eps]])
+ np.testing.assert_almost_equal(machine.variances, expected_vars)
+ expected_weights = np.array([0.46226415, 0.53773585])
+ np.testing.assert_almost_equal(machine.weights, expected_weights)
+
+ stats = machine.transform(test_data)
+
+ expected_stats = GMMStats(n_gaussians, n_features)
+ expected_stats.init_fields(
+ log_likelihood=-1.3837590691807108e16,
+ t=test_data.shape[0],
+ n=np.array([2, 2], dtype=float),
+ sum_px=np.array([[2, 2, 3], [16, 17, 17]], dtype=float),
+ sum_pxx=np.array([[2, 2, 5], [128, 145, 145]], dtype=float),
+ )
+ assert stats.is_similar_to(expected_stats)
# Tests from `test_em.py`
-def loadGMM():
- gmm = GMMMachine(n_gaussians=2)
-
- gmm.weights = load_array(
- resource_filename("bob.learn.em", "data/gmm.init_weights.hdf5")
- )
- gmm.means = load_array(
- resource_filename("bob.learn.em", "data/gmm.init_means.hdf5")
- )
- gmm.variances = load_array(
- resource_filename("bob.learn.em", "data/gmm.init_variances.hdf5")
- )
-
- return gmm
-
-
def test_gmm_ML_1():
"""Trains a GMMMachine with ML_GMMTrainer"""
ar = load_array(
resource_filename("bob.learn.em", "data/faithful.torch3_f64.hdf5")
)
- gmm = loadGMM()
+ gmm_ref = GMMMachine.from_hdf5(
+ HDF5File(resource_filename("bob.learn.em", "data/gmm_ML.hdf5"), "r")
+ )
- # test rng handling
- gmm.convergence_threshold = 0.001
- gmm.update_means = True
- gmm.update_variances = True
- gmm.update_weights = True
- gmm.random_state = np.random.RandomState(seed=12345)
- gmm = gmm.fit(ar)
+ for transform in (to_numpy, to_dask_array):
+ ar = transform(ar)
- gmm = loadGMM()
- gmm.convergence_threshold = 0.001
- gmm.update_means = True
- gmm.update_variances = True
- gmm.update_weights = True
- gmm = gmm.fit(ar)
+ gmm = loadGMM()
- # Generate reference
- # gmm.save(HDF5File(resource_filename("bob.learn.em", "data/gmm_ML.hdf5"), "w"))
+ # test rng handling
+ gmm.convergence_threshold = 0.001
+ gmm.update_means = True
+ gmm.update_variances = True
+ gmm.update_weights = True
+ gmm.random_state = np.random.RandomState(seed=12345)
+ gmm = gmm.fit(ar)
- gmm_ref = GMMMachine.from_hdf5(
- HDF5File(resource_filename("bob.learn.em", "data/gmm_ML.hdf5"), "r")
- )
- assert gmm == gmm_ref
+ gmm = loadGMM()
+ gmm.convergence_threshold = 0.001
+ gmm.update_means = True
+ gmm.update_variances = True
+ gmm.update_weights = True
+ # Generate reference
+ # gmm.save(HDF5File(resource_filename("bob.learn.em", "data/gmm_ML.hdf5"), "w"))
+
+ gmm = gmm.fit(ar)
+
+ assert_gmm_equal(gmm, gmm_ref)
def test_gmm_ML_2():
@@ -813,33 +837,6 @@ def test_gmm_ML_2():
resource_filename("bob.learn.em", "data/dataNormalized.hdf5")
)
- # Initialize GMMMachine
- gmm = GMMMachine(n_gaussians=5)
- gmm.means = load_array(
- resource_filename("bob.learn.em", "data/meansAfterKMeans.hdf5")
- ).astype("float64")
- gmm.variances = load_array(
- resource_filename("bob.learn.em", "data/variancesAfterKMeans.hdf5")
- ).astype("float64")
- gmm.weights = np.exp(
- load_array(
- resource_filename("bob.learn.em", "data/weightsAfterKMeans.hdf5")
- ).astype("float64")
- )
-
- threshold = 0.001
- gmm.variance_thresholds = threshold
-
- # Initialize ML Trainer
- gmm.mean_var_update_threshold = 0.001
- gmm.max_fitting_steps = 25
- gmm.convergence_threshold = 0.000001
- gmm.update_means = True
- gmm.update_variances = True
- gmm.update_weights = True
-
- # Run ML
- gmm = gmm.fit(ar)
# Test results
# Load torch3vision reference
meansML_ref = load_array(
@@ -852,10 +849,42 @@ def test_gmm_ML_2():
resource_filename("bob.learn.em", "data/weightsAfterML.hdf5")
)
- # Compare to current results
- np.testing.assert_allclose(gmm.means, meansML_ref, atol=3e-3)
- np.testing.assert_allclose(gmm.variances, variancesML_ref, atol=3e-3)
- np.testing.assert_allclose(gmm.weights, weightsML_ref, atol=1e-4)
+ for transform in (to_numpy, to_dask_array):
+ ar = transform(ar)
+ # Initialize GMMMachine
+ gmm = GMMMachine(n_gaussians=5)
+ gmm.means = load_array(
+ resource_filename("bob.learn.em", "data/meansAfterKMeans.hdf5")
+ ).astype("float64")
+ gmm.variances = load_array(
+ resource_filename("bob.learn.em", "data/variancesAfterKMeans.hdf5")
+ ).astype("float64")
+ gmm.weights = np.exp(
+ load_array(
+ resource_filename(
+ "bob.learn.em", "data/weightsAfterKMeans.hdf5"
+ )
+ ).astype("float64")
+ )
+
+ threshold = 0.001
+ gmm.variance_thresholds = threshold
+
+ # Initialize ML Trainer
+ gmm.mean_var_update_threshold = 0.001
+ gmm.max_fitting_steps = 25
+ gmm.convergence_threshold = 0.000001
+ gmm.update_means = True
+ gmm.update_variances = True
+ gmm.update_weights = True
+
+ # Run ML
+ gmm = gmm.fit(ar)
+
+ # Compare to current results
+ np.testing.assert_allclose(gmm.means, meansML_ref, atol=3e-3)
+ np.testing.assert_allclose(gmm.variances, variancesML_ref, atol=3e-3)
+ np.testing.assert_allclose(gmm.weights, weightsML_ref, atol=1e-4)
def test_gmm_MAP_1():
@@ -890,8 +919,6 @@ def test_gmm_MAP_1():
gmm.update_variances = False
gmm.update_weights = False
- gmm = gmm.fit(ar)
-
# Generate reference
# gmm.save(HDF5File(resource_filename("bob.learn.em", "data/gmm_MAP.hdf5"), "w"))
@@ -899,9 +926,15 @@ def test_gmm_MAP_1():
HDF5File(resource_filename("bob.learn.em", "data/gmm_MAP.hdf5"), "r")
)
- np.testing.assert_almost_equal(gmm.means, gmm_ref.means, decimal=3)
- np.testing.assert_almost_equal(gmm.variances, gmm_ref.variances, decimal=3)
- np.testing.assert_almost_equal(gmm.weights, gmm_ref.weights, decimal=3)
+ for transform in (to_numpy, to_dask_array):
+ ar = transform(ar)
+ gmm = gmm.fit(ar)
+
+ np.testing.assert_almost_equal(gmm.means, gmm_ref.means, decimal=3)
+ np.testing.assert_almost_equal(
+ gmm.variances, gmm_ref.variances, decimal=3
+ )
+ np.testing.assert_almost_equal(gmm.weights, gmm_ref.weights, decimal=3)
def test_gmm_MAP_2():
@@ -934,14 +967,16 @@ def test_gmm_MAP_2():
gmm_adapted.variances = variances
gmm_adapted.weights = weights
- gmm_adapted = gmm_adapted.fit(data)
-
new_means = load_array(
resource_filename("bob.learn.em", "data/new_adapted_mean.hdf5")
)
- # Compare to matlab reference
- np.testing.assert_allclose(new_means.T, gmm_adapted.means, rtol=1e-4)
+ for transform in (to_numpy, to_dask_array):
+ data = transform(data)
+ gmm_adapted = gmm_adapted.fit(data)
+
+ # Compare to matlab reference
+ np.testing.assert_allclose(new_means.T, gmm_adapted.means, rtol=1e-4)
def test_gmm_MAP_3():
@@ -981,9 +1016,6 @@ def test_gmm_MAP_3():
)
gmm.variance_thresholds = threshold
- # Train
- gmm = gmm.fit(ar)
-
# Test results
# Load torch3vision reference
meansMAP_ref = load_array(
@@ -996,13 +1028,18 @@ def test_gmm_MAP_3():
resource_filename("bob.learn.em", "data/weightsAfterMAP.hdf5")
)
- # Compare to current results
- # Gaps are quite large. This might be explained by the fact that there is no
- # adaptation of a given Gaussian in torch3 when the corresponding responsibilities
- # are below the responsibilities threshold
- np.testing.assert_allclose(gmm.means, meansMAP_ref, atol=2e-1)
- np.testing.assert_allclose(gmm.variances, variancesMAP_ref, atol=1e-4)
- np.testing.assert_allclose(gmm.weights, weightsMAP_ref, atol=1e-4)
+ for transform in (to_numpy, to_dask_array):
+ ar = transform(ar)
+ # Train
+ gmm = gmm.fit(ar)
+
+ # Compare to current results
+ # Gaps are quite large. This might be explained by the fact that there is no
+ # adaptation of a given Gaussian in torch3 when the corresponding responsibilities
+ # are below the responsibilities threshold
+ np.testing.assert_allclose(gmm.means, meansMAP_ref, atol=2e-1)
+ np.testing.assert_allclose(gmm.variances, variancesMAP_ref, atol=1e-4)
+ np.testing.assert_allclose(gmm.weights, weightsMAP_ref, atol=1e-4)
def test_gmm_test():
@@ -1028,126 +1065,10 @@ def test_gmm_test():
# Test against the model
score_mean_ref = -1.50379e06
- score = gmm.log_likelihood(ar).sum()
- score /= len(ar)
-
- # Compare current results to torch3vision
- assert abs(score - score_mean_ref) / score_mean_ref < 1e-4
-
-
-def test_gmm_ML_dask():
- # Trains a GMMMachine with dask array data; compares to a reference
-
- ar = da.array(
- load_array(
- resource_filename("bob.learn.em", "data/dataNormalized.hdf5")
- )
- )
-
- # Initialize GMMMachine
- gmm = GMMMachine(n_gaussians=5)
- gmm.means = load_array(
- resource_filename("bob.learn.em", "data/meansAfterKMeans.hdf5")
- ).astype("float64")
- gmm.variances = load_array(
- resource_filename("bob.learn.em", "data/variancesAfterKMeans.hdf5")
- ).astype("float64")
- gmm.weights = np.exp(
- load_array(
- resource_filename("bob.learn.em", "data/weightsAfterKMeans.hdf5")
- ).astype("float64")
- )
-
- threshold = 0.001
- gmm.variance_thresholds = threshold
-
- # Initialize ML Trainer
- gmm.mean_var_update_threshold = 0.001
- gmm.max_fitting_steps = 25
- gmm.convergence_threshold = 0.00001
- gmm.update_means = True
- gmm.update_variances = True
- gmm.update_weights = True
-
- # Run ML
- gmm.fit(ar)
-
- # Test results
- # Load torch3vision reference
- meansML_ref = load_array(
- resource_filename("bob.learn.em", "data/meansAfterML.hdf5")
- )
- variancesML_ref = load_array(
- resource_filename("bob.learn.em", "data/variancesAfterML.hdf5")
- )
- weightsML_ref = load_array(
- resource_filename("bob.learn.em", "data/weightsAfterML.hdf5")
- )
-
- # Compare to current results
- np.testing.assert_allclose(gmm.means, meansML_ref, atol=3e-3)
- np.testing.assert_allclose(gmm.variances, variancesML_ref, atol=3e-3)
- np.testing.assert_allclose(gmm.weights, weightsML_ref, atol=1e-4)
-
-
-def test_gmm_MAP_dask():
- # Test a GMMMachine for MAP with a dask array as data.
- ar = da.array(
- load_array(resource_filename("bob.learn.em", "data/dataforMAP.hdf5"))
- )
-
- # Initialize GMMMachine
- n_gaussians = 5
- prior_gmm = GMMMachine(n_gaussians)
- prior_gmm.means = load_array(
- resource_filename("bob.learn.em", "data/meansAfterML.hdf5")
- )
- prior_gmm.variances = load_array(
- resource_filename("bob.learn.em", "data/variancesAfterML.hdf5")
- )
- prior_gmm.weights = load_array(
- resource_filename("bob.learn.em", "data/weightsAfterML.hdf5")
- )
-
- threshold = 0.001
- prior_gmm.variance_thresholds = threshold
-
- # Initialize MAP Trainer
- prior = 0.001
- accuracy = 0.00001
- gmm = GMMMachine(
- n_gaussians,
- trainer="map",
- ubm=prior_gmm,
- convergence_threshold=prior,
- max_fitting_steps=1,
- update_means=True,
- update_variances=False,
- update_weights=False,
- mean_var_update_threshold=accuracy,
- map_relevance_factor=None,
- )
- gmm.variance_thresholds = threshold
-
- # Train
- gmm = gmm.fit(ar)
-
- # Test results
- # Load torch3vision reference
- meansMAP_ref = load_array(
- resource_filename("bob.learn.em", "data/meansAfterMAP.hdf5")
- )
- variancesMAP_ref = load_array(
- resource_filename("bob.learn.em", "data/variancesAfterMAP.hdf5")
- )
- weightsMAP_ref = load_array(
- resource_filename("bob.learn.em", "data/weightsAfterMAP.hdf5")
- )
+ for transform in (to_numpy, to_dask_array):
+ ar = transform(ar)
+ score = gmm.log_likelihood(ar).sum()
+ score /= len(ar)
- # Compare to current results
- # Gaps are quite large. This might be explained by the fact that there is no
- # adaptation of a given Gaussian in torch3 when the corresponding responsibilities
- # are below the responsibilities threshold
- np.testing.assert_allclose(gmm.means, meansMAP_ref, atol=2e-1)
- np.testing.assert_allclose(gmm.variances, variancesMAP_ref, atol=1e-4)
- np.testing.assert_allclose(gmm.weights, weightsMAP_ref, atol=1e-4)
+ # Compare current results to torch3vision
+ assert abs(score - score_mean_ref) / score_mean_ref < 1e-4
diff --git a/bob/learn/em/test/test_kmeans.py b/bob/learn/em/test/test_kmeans.py
index 8edc205..613a562 100644
--- a/bob/learn/em/test/test_kmeans.py
+++ b/bob/learn/em/test/test_kmeans.py
@@ -33,7 +33,7 @@ def to_dask_array(*args):
for x in args:
x = np.asarray(x)
chunks = list(x.shape)
- chunks[0] //= 2
+ chunks[0] = int(np.ceil(chunks[0] / 2))
result.append(da.from_array(x, chunks=chunks))
if len(result) == 1:
return result[0]
--
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