import pytest import numpy as np from functools import partial import itertools from sklearn.base import clone from sklearn.exceptions import ConvergenceWarning from sklearn.utils import check_array from sklearn.utils._testing import assert_array_almost_equal from sklearn.utils._testing import assert_array_equal from sklearn.utils._testing import ignore_warnings from sklearn.utils._testing import TempMemmap from sklearn.decomposition import DictionaryLearning from sklearn.decomposition import MiniBatchDictionaryLearning from sklearn.decomposition import SparseCoder from sklearn.decomposition import dict_learning from sklearn.decomposition import dict_learning_online from sklearn.decomposition import sparse_encode from sklearn.utils.estimator_checks import check_transformer_data_not_an_array from sklearn.utils.estimator_checks import check_transformer_general from sklearn.utils.estimator_checks import check_transformers_unfitted rng_global = np.random.RandomState(0) n_samples, n_features = 10, 8 X = rng_global.randn(n_samples, n_features) def test_sparse_encode_shapes_omp(): rng = np.random.RandomState(0) algorithms = ['omp', 'lasso_lars', 'lasso_cd', 'lars', 'threshold'] for n_components, n_samples in itertools.product([1, 5], [1, 9]): X_ = rng.randn(n_samples, n_features) dictionary = rng.randn(n_components, n_features) for algorithm, n_jobs in itertools.product(algorithms, [1, 3]): code = sparse_encode(X_, dictionary, algorithm=algorithm, n_jobs=n_jobs) assert code.shape == (n_samples, n_components) def test_dict_learning_shapes(): n_components = 5 dico = DictionaryLearning(n_components, random_state=0).fit(X) assert dico.components_.shape == (n_components, n_features) n_components = 1 dico = DictionaryLearning(n_components, random_state=0).fit(X) assert dico.components_.shape == (n_components, n_features) assert dico.transform(X).shape == (X.shape[0], n_components) def test_dict_learning_overcomplete(): n_components = 12 dico = DictionaryLearning(n_components, random_state=0).fit(X) assert dico.components_.shape == (n_components, n_features) def test_max_iter(): def ricker_function(resolution, center, width): """Discrete sub-sampled Ricker (Mexican hat) wavelet""" x = np.linspace(0, resolution - 1, resolution) x = ((2 / (np.sqrt(3 * width) * np.pi ** .25)) * (1 - (x - center) ** 2 / width ** 2) * np.exp(-(x - center) ** 2 / (2 * width ** 2))) return x def ricker_matrix(width, resolution, n_components): """Dictionary of Ricker (Mexican hat) wavelets""" centers = np.linspace(0, resolution - 1, n_components) D = np.empty((n_components, resolution)) for i, center in enumerate(centers): D[i] = ricker_function(resolution, center, width) D /= np.sqrt(np.sum(D ** 2, axis=1))[:, np.newaxis] return D transform_algorithm = 'lasso_cd' resolution = 1024 subsampling = 3 # subsampling factor n_components = resolution // subsampling # Compute a wavelet dictionary D_multi = np.r_[tuple(ricker_matrix(width=w, resolution=resolution, n_components=n_components // 5) for w in (10, 50, 100, 500, 1000))] X = np.linspace(0, resolution - 1, resolution) first_quarter = X < resolution / 4 X[first_quarter] = 3. X[np.logical_not(first_quarter)] = -1. X = X.reshape(1, -1) # check that the underlying model fails to converge with pytest.warns(ConvergenceWarning): model = SparseCoder(D_multi, transform_algorithm=transform_algorithm, transform_max_iter=1) model.fit_transform(X) # check that the underlying model converges w/o warnings with pytest.warns(None) as record: model = SparseCoder(D_multi, transform_algorithm=transform_algorithm, transform_max_iter=2000) model.fit_transform(X) assert not record.list def test_dict_learning_lars_positive_parameter(): n_components = 5 alpha = 1 err_msg = "Positive constraint not supported for 'lars' coding method." with pytest.raises(ValueError, match=err_msg): dict_learning(X, n_components, alpha=alpha, positive_code=True) @pytest.mark.parametrize("transform_algorithm", [ "lasso_lars", "lasso_cd", "threshold", ]) @pytest.mark.parametrize("positive_code", [False, True]) @pytest.mark.parametrize("positive_dict", [False, True]) def test_dict_learning_positivity(transform_algorithm, positive_code, positive_dict): n_components = 5 dico = DictionaryLearning( n_components, transform_algorithm=transform_algorithm, random_state=0, positive_code=positive_code, positive_dict=positive_dict, fit_algorithm="cd").fit(X) code = dico.transform(X) if positive_dict: assert (dico.components_ >= 0).all() else: assert (dico.components_ < 0).any() if positive_code: assert (code >= 0).all() else: assert (code < 0).any() @pytest.mark.parametrize("positive_dict", [False, True]) def test_dict_learning_lars_dict_positivity(positive_dict): n_components = 5 dico = DictionaryLearning( n_components, transform_algorithm="lars", random_state=0, positive_dict=positive_dict, fit_algorithm="cd").fit(X) if positive_dict: assert (dico.components_ >= 0).all() else: assert (dico.components_ < 0).any() def test_dict_learning_lars_code_positivity(): n_components = 5 dico = DictionaryLearning( n_components, transform_algorithm="lars", random_state=0, positive_code=True, fit_algorithm="cd").fit(X) err_msg = "Positive constraint not supported for '{}' coding method." err_msg = err_msg.format("lars") with pytest.raises(ValueError, match=err_msg): dico.transform(X) def test_dict_learning_reconstruction(): n_components = 12 dico = DictionaryLearning(n_components, transform_algorithm='omp', transform_alpha=0.001, random_state=0) code = dico.fit(X).transform(X) assert_array_almost_equal(np.dot(code, dico.components_), X) dico.set_params(transform_algorithm='lasso_lars') code = dico.transform(X) assert_array_almost_equal(np.dot(code, dico.components_), X, decimal=2) # used to test lars here too, but there's no guarantee the number of # nonzero atoms is right. def test_dict_learning_reconstruction_parallel(): # regression test that parallel reconstruction works with n_jobs>1 n_components = 12 dico = DictionaryLearning(n_components, transform_algorithm='omp', transform_alpha=0.001, random_state=0, n_jobs=4) code = dico.fit(X).transform(X) assert_array_almost_equal(np.dot(code, dico.components_), X) dico.set_params(transform_algorithm='lasso_lars') code = dico.transform(X) assert_array_almost_equal(np.dot(code, dico.components_), X, decimal=2) def test_dict_learning_lassocd_readonly_data(): n_components = 12 with TempMemmap(X) as X_read_only: dico = DictionaryLearning(n_components, transform_algorithm='lasso_cd', transform_alpha=0.001, random_state=0, n_jobs=4) with ignore_warnings(category=ConvergenceWarning): code = dico.fit(X_read_only).transform(X_read_only) assert_array_almost_equal(np.dot(code, dico.components_), X_read_only, decimal=2) def test_dict_learning_nonzero_coefs(): n_components = 4 dico = DictionaryLearning(n_components, transform_algorithm='lars', transform_n_nonzero_coefs=3, random_state=0) code = dico.fit(X).transform(X[np.newaxis, 1]) assert len(np.flatnonzero(code)) == 3 dico.set_params(transform_algorithm='omp') code = dico.transform(X[np.newaxis, 1]) assert len(np.flatnonzero(code)) == 3 def test_dict_learning_unknown_fit_algorithm(): n_components = 5 dico = DictionaryLearning(n_components, fit_algorithm='') with pytest.raises(ValueError): dico.fit(X) def test_dict_learning_split(): n_components = 5 dico = DictionaryLearning(n_components, transform_algorithm='threshold', random_state=0) code = dico.fit(X).transform(X) dico.split_sign = True split_code = dico.transform(X) assert_array_almost_equal(split_code[:, :n_components] - split_code[:, n_components:], code) def test_dict_learning_online_shapes(): rng = np.random.RandomState(0) n_components = 8 code, dictionary = dict_learning_online(X, n_components=n_components, alpha=1, random_state=rng) assert code.shape == (n_samples, n_components) assert dictionary.shape == (n_components, n_features) assert np.dot(code, dictionary).shape == X.shape def test_dict_learning_online_lars_positive_parameter(): alpha = 1 err_msg = "Positive constraint not supported for 'lars' coding method." with pytest.raises(ValueError, match=err_msg): dict_learning_online(X, alpha=alpha, positive_code=True) @pytest.mark.parametrize("transform_algorithm", [ "lasso_lars", "lasso_cd", "threshold", ]) @pytest.mark.parametrize("positive_code", [False, True]) @pytest.mark.parametrize("positive_dict", [False, True]) def test_minibatch_dictionary_learning_positivity(transform_algorithm, positive_code, positive_dict): n_components = 8 dico = MiniBatchDictionaryLearning( n_components, transform_algorithm=transform_algorithm, random_state=0, positive_code=positive_code, positive_dict=positive_dict, fit_algorithm='cd').fit(X) code = dico.transform(X) if positive_dict: assert (dico.components_ >= 0).all() else: assert (dico.components_ < 0).any() if positive_code: assert (code >= 0).all() else: assert (code < 0).any() @pytest.mark.parametrize("positive_dict", [False, True]) def test_minibatch_dictionary_learning_lars(positive_dict): n_components = 8 dico = MiniBatchDictionaryLearning( n_components, transform_algorithm="lars", random_state=0, positive_dict=positive_dict, fit_algorithm='cd').fit(X) if positive_dict: assert (dico.components_ >= 0).all() else: assert (dico.components_ < 0).any() @pytest.mark.parametrize("positive_code", [False, True]) @pytest.mark.parametrize("positive_dict", [False, True]) def test_dict_learning_online_positivity(positive_code, positive_dict): rng = np.random.RandomState(0) n_components = 8 code, dictionary = dict_learning_online(X, n_components=n_components, method="cd", alpha=1, random_state=rng, positive_dict=positive_dict, positive_code=positive_code) if positive_dict: assert (dictionary >= 0).all() else: assert (dictionary < 0).any() if positive_code: assert (code >= 0).all() else: assert (code < 0).any() def test_dict_learning_online_verbosity(): n_components = 5 # test verbosity from io import StringIO import sys old_stdout = sys.stdout try: sys.stdout = StringIO() dico = MiniBatchDictionaryLearning(n_components, n_iter=20, verbose=1, random_state=0) dico.fit(X) dico = MiniBatchDictionaryLearning(n_components, n_iter=20, verbose=2, random_state=0) dico.fit(X) dict_learning_online(X, n_components=n_components, alpha=1, verbose=1, random_state=0) dict_learning_online(X, n_components=n_components, alpha=1, verbose=2, random_state=0) finally: sys.stdout = old_stdout assert dico.components_.shape == (n_components, n_features) def test_dict_learning_online_estimator_shapes(): n_components = 5 dico = MiniBatchDictionaryLearning(n_components, n_iter=20, random_state=0) dico.fit(X) assert dico.components_.shape == (n_components, n_features) def test_dict_learning_online_overcomplete(): n_components = 12 dico = MiniBatchDictionaryLearning(n_components, n_iter=20, random_state=0).fit(X) assert dico.components_.shape == (n_components, n_features) def test_dict_learning_online_initialization(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) dico = MiniBatchDictionaryLearning(n_components, n_iter=0, dict_init=V, random_state=0).fit(X) assert_array_equal(dico.components_, V) def test_dict_learning_online_readonly_initialization(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) V.setflags(write=False) MiniBatchDictionaryLearning(n_components, n_iter=1, dict_init=V, random_state=0, shuffle=False).fit(X) def test_dict_learning_online_partial_fit(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] dict1 = MiniBatchDictionaryLearning(n_components, n_iter=10 * len(X), batch_size=1, alpha=1, shuffle=False, dict_init=V, random_state=0).fit(X) dict2 = MiniBatchDictionaryLearning(n_components, alpha=1, n_iter=1, dict_init=V, random_state=0) for i in range(10): for sample in X: dict2.partial_fit(sample[np.newaxis, :]) assert not np.all(sparse_encode(X, dict1.components_, alpha=1) == 0) assert_array_almost_equal(dict1.components_, dict2.components_, decimal=2) def test_dict_learning_iter_offset(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) dict1 = MiniBatchDictionaryLearning(n_components, n_iter=10, dict_init=V, random_state=0, shuffle=False) dict2 = MiniBatchDictionaryLearning(n_components, n_iter=10, dict_init=V, random_state=0, shuffle=False) dict1.fit(X) for sample in X: dict2.partial_fit(sample[np.newaxis, :]) assert dict1.iter_offset_ == dict2.iter_offset_ def test_sparse_encode_shapes(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] for algo in ('lasso_lars', 'lasso_cd', 'lars', 'omp', 'threshold'): code = sparse_encode(X, V, algorithm=algo) assert code.shape == (n_samples, n_components) @pytest.mark.parametrize("algo", [ 'lasso_lars', 'lasso_cd', 'threshold' ]) @pytest.mark.parametrize("positive", [False, True]) def test_sparse_encode_positivity(algo, positive): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] code = sparse_encode(X, V, algorithm=algo, positive=positive) if positive: assert (code >= 0).all() else: assert (code < 0).any() @pytest.mark.parametrize("algo", ['lars', 'omp']) def test_sparse_encode_unavailable_positivity(algo): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] err_msg = "Positive constraint not supported for '{}' coding method." err_msg = err_msg.format(algo) with pytest.raises(ValueError, match=err_msg): sparse_encode(X, V, algorithm=algo, positive=True) def test_sparse_encode_input(): n_components = 100 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] Xf = check_array(X, order='F') for algo in ('lasso_lars', 'lasso_cd', 'lars', 'omp', 'threshold'): a = sparse_encode(X, V, algorithm=algo) b = sparse_encode(Xf, V, algorithm=algo) assert_array_almost_equal(a, b) def test_sparse_encode_error(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] code = sparse_encode(X, V, alpha=0.001) assert not np.all(code == 0) assert np.sqrt(np.sum((np.dot(code, V) - X) ** 2)) < 0.1 def test_sparse_encode_error_default_sparsity(): rng = np.random.RandomState(0) X = rng.randn(100, 64) D = rng.randn(2, 64) code = ignore_warnings(sparse_encode)(X, D, algorithm='omp', n_nonzero_coefs=None) assert code.shape == (100, 2) def test_unknown_method(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init with pytest.raises(ValueError): sparse_encode(X, V, algorithm="") def test_sparse_coder_estimator(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] coder = SparseCoder(dictionary=V, transform_algorithm='lasso_lars', transform_alpha=0.001).transform(X) assert not np.all(coder == 0) assert np.sqrt(np.sum((np.dot(coder, V) - X) ** 2)) < 0.1 def test_sparse_coder_estimator_clone(): n_components = 12 rng = np.random.RandomState(0) V = rng.randn(n_components, n_features) # random init V /= np.sum(V ** 2, axis=1)[:, np.newaxis] coder = SparseCoder(dictionary=V, transform_algorithm='lasso_lars', transform_alpha=0.001) cloned = clone(coder) assert id(cloned) != id(coder) np.testing.assert_allclose(cloned.dictionary, coder.dictionary) assert id(cloned.dictionary) != id(coder.dictionary) assert cloned.n_components_ == coder.n_components_ assert cloned.n_features_in_ == coder.n_features_in_ data = np.random.rand(n_samples, n_features).astype(np.float32) np.testing.assert_allclose(cloned.transform(data), coder.transform(data)) def test_sparse_coder_parallel_mmap(): # Non-regression test for: # https://github.com/scikit-learn/scikit-learn/issues/5956 # Test that SparseCoder does not error by passing reading only # arrays to child processes rng = np.random.RandomState(777) n_components, n_features = 40, 64 init_dict = rng.rand(n_components, n_features) # Ensure that `data` is >2M. Joblib memory maps arrays # if they are larger than 1MB. The 4 accounts for float32 # data type n_samples = int(2e6) // (4 * n_features) data = np.random.rand(n_samples, n_features).astype(np.float32) sc = SparseCoder(init_dict, transform_algorithm='omp', n_jobs=2) sc.fit_transform(data) def test_sparse_coder_common_transformer(): rng = np.random.RandomState(777) n_components, n_features = 40, 3 init_dict = rng.rand(n_components, n_features) sc = SparseCoder(init_dict) check_transformer_data_not_an_array(sc.__class__.__name__, sc) check_transformer_general(sc.__class__.__name__, sc) check_transformer_general_memmap = partial( check_transformer_general, readonly_memmap=True ) check_transformer_general_memmap(sc.__class__.__name__, sc) check_transformers_unfitted(sc.__class__.__name__, sc) # TODO: remove in 1.1 def test_sparse_coder_deprecation(): # check that we raise a deprecation warning when accessing `components_` rng = np.random.RandomState(777) n_components, n_features = 40, 64 init_dict = rng.rand(n_components, n_features) sc = SparseCoder(init_dict) with pytest.warns(FutureWarning, match="'components_' is deprecated"): sc.components_ def test_sparse_coder_n_features_in(): d = np.array([[1, 2, 3], [1, 2, 3]]) sc = SparseCoder(d) assert sc.n_features_in_ == d.shape[1]