def test_safe_indexing_2d_container_axis_1(array_type, indices_type, indices):
# validation of the indices
# we make a copy because indices is mutable and shared between tests
indices_converted = copy(indices)
if indices_type == "slice" and isinstance(indices[1], int):
indices_converted[1] += 1
columns_name = ["col_0", "col_1", "col_2"]
array = _convert_container(
[[1, 2, 3], [4, 5, 6], [7, 8, 9]], array_type, columns_name
)
indices_converted = _convert_container(indices_converted, indices_type)
if isinstance(indices[0], str) and array_type != "dataframe":
err_msg = (
"Specifying the columns using strings is only supported "
"for pandas DataFrames"
)
with pytest.raises(ValueError, match=err_msg):
_safe_indexing(array, indices_converted, axis=1)
else:
subset = _safe_indexing(array, indices_converted, axis=1)
assert_allclose_dense_sparse(
subset, _convert_container([[2, 3], [5, 6], [8, 9]], array_type)
)
def test_safe_indexing_1d_container_mask(array_type, indices_type):
indices = [False] + [True] * 2 + [False] * 6
array = _convert_container([1, 2, 3, 4, 5, 6, 7, 8, 9], array_type)
indices = _convert_container(indices, indices_type)
subset = _safe_indexing(array, indices, axis=0)
assert_allclose_dense_sparse(subset, _convert_container([2, 3],
array_type))
def test_isomap_simple_grid(n_neighbors, radius):
# Isomap should preserve distances when all neighbors are used
n_pts = 25
X = create_sample_data(n_pts=n_pts, add_noise=False)
# distances from each point to all others
if n_neighbors is not None:
G = neighbors.kneighbors_graph(X, n_neighbors, mode="distance")
else:
G = neighbors.radius_neighbors_graph(X, radius, mode="distance")
for eigen_solver in eigen_solvers:
for path_method in path_methods:
clf = manifold.Isomap(
n_neighbors=n_neighbors,
radius=radius,
n_components=2,
eigen_solver=eigen_solver,
path_method=path_method,
)
clf.fit(X)
if n_neighbors is not None:
G_iso = neighbors.kneighbors_graph(clf.embedding_,
n_neighbors,
mode="distance")
else:
G_iso = neighbors.radius_neighbors_graph(clf.embedding_,
radius,
mode="distance")
assert_allclose_dense_sparse(G, G_iso)
def test_check_array_force_all_finite_valid(value, force_all_finite, retype):
X = retype(np.arange(4).reshape(2, 2).astype(np.float))
X[0, 0] = value
X_checked = check_array(X,
force_all_finite=force_all_finite,
accept_sparse=True)
assert_allclose_dense_sparse(X, X_checked)
def test_check_fit_params(indices):
X = np.random.randn(4, 2)
fit_params = {
'list': [1, 2, 3, 4],
'array': np.array([1, 2, 3, 4]),
'sparse-col': sp.csc_matrix([1, 2, 3, 4]).T,
'sparse-row': sp.csc_matrix([1, 2, 3, 4]),
'scalar-int': 1,
'scalar-str': 'xxx',
'None': None,
}
result = _check_fit_params(X, fit_params, indices)
indices_ = indices if indices is not None else list(range(X.shape[0]))
for key in ['sparse-row', 'scalar-int', 'scalar-str', 'None']:
assert result[key] is fit_params[key]
assert result['list'] == _safe_indexing(fit_params['list'], indices_)
assert_array_equal(
result['array'], _safe_indexing(fit_params['array'], indices_)
)
assert_allclose_dense_sparse(
result['sparse-col'],
_safe_indexing(fit_params['sparse-col'], indices_)
)
def check_pipeline_consistency(name, estimator_orig):
if estimator_orig._get_tags()['non_deterministic']:
msg = name + ' is non deterministic'
raise SkipTest(msg)
# check that make_pipeline(est) gives same score as est
X, y = make_blobs(n_samples=30,
centers=[[0, 0, 0], [1, 1, 1]],
random_state=0,
n_features=2,
cluster_std=0.1)
X -= X.min()
X = pairwise_estimator_convert_X(X, estimator_orig, kernel=rbf_kernel)
estimator = clone(estimator_orig)
y = multioutput_estimator_convert_y_2d(estimator, y)
set_random_state(estimator)
pipeline = make_pipeline(estimator)
estimator.fit(X, y)
pipeline.fit(X, y)
funcs = ["score", "fit_transform"]
for func_name in funcs:
func = getattr(estimator, func_name, None)
if func is not None:
func_pipeline = getattr(pipeline, func_name)
result = func(X, y)
result_pipe = func_pipeline(X, y)
assert_allclose_dense_sparse(result, result_pipe)
def test_imputers_add_indicator_sparse(imputer, marker):
X = sparse.csr_matrix(
[
[marker, 1, 5, marker, 1],
[2, marker, 1, marker, 2],
[6, 3, marker, marker, 3],
[1, 2, 9, marker, 4],
]
)
X_true_indicator = sparse.csr_matrix(
[
[1.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 1.0],
[0.0, 0.0, 1.0, 1.0],
[0.0, 0.0, 0.0, 1.0],
]
)
imputer.set_params(missing_values=marker, add_indicator=True)
X_trans = imputer.fit_transform(X)
assert_allclose_dense_sparse(X_trans[:, -4:], X_true_indicator)
assert_array_equal(imputer.indicator_.features_, np.array([0, 1, 2, 3]))
imputer.set_params(add_indicator=False)
X_trans_no_indicator = imputer.fit_transform(X)
assert_allclose_dense_sparse(X_trans[:, :-4], X_trans_no_indicator)
def test_20news_normalization(fetch_20newsgroups_vectorized_fxt):
X = fetch_20newsgroups_vectorized_fxt(normalize=False)
X_ = fetch_20newsgroups_vectorized_fxt(normalize=True)
X_norm = X_['data'][:100]
X = X['data'][:100]
assert_allclose_dense_sparse(X_norm, normalize(X))
assert np.allclose(np.linalg.norm(X_norm.todense(), axis=1), 1)
def test_safe_indexing_1d_container(array_type, indices_type):
indices = [1, 2]
if indices_type == "slice" and isinstance(indices[1], int):
indices[1] += 1
array = _convert_container([1, 2, 3, 4, 5, 6, 7, 8, 9], array_type)
indices = _convert_container(indices, indices_type)
subset = _safe_indexing(array, indices, axis=0)
assert_allclose_dense_sparse(subset, _convert_container([2, 3], array_type))
def test_function_sampler_func(X, y):
def func(X, y):
return X[:10], y[:10]
sampler = FunctionSampler(func=func)
X_res, y_res = sampler.fit_resample(X, y)
assert_allclose_dense_sparse(X_res, X[:10])
assert_array_equal(y_res, y[:10])
def test_safe_indexing_2d_container_axis_0(array_type, indices_type):
indices = [1, 2]
if indices_type == 'slice' and isinstance(indices[1], int):
indices[1] += 1
array = _convert_container([[1, 2, 3], [4, 5, 6], [7, 8, 9]], array_type)
indices = _convert_container(indices, indices_type)
subset = _safe_indexing(array, indices, axis=0)
assert_allclose_dense_sparse(
subset, _convert_container([[4, 5, 6], [7, 8, 9]], array_type))
def test_tfidf_transformer_sparse():
X = sparse.rand(10, 20000, dtype=np.float64, random_state=42)
X_csc = sparse.csc_matrix(X)
X_csr = sparse.csr_matrix(X)
X_trans_csc = TfidfTransformer().fit_transform(X_csc)
X_trans_csr = TfidfTransformer().fit_transform(X_csr)
assert_allclose_dense_sparse(X_trans_csc, X_trans_csr)
assert X_trans_csc.format == X_trans_csr.format
def test_safe_indexing_2d_mask(array_type, indices_type, axis,
expected_subset):
columns_name = ['col_0', 'col_1', 'col_2']
array = _convert_container([[1, 2, 3], [4, 5, 6], [7, 8, 9]], array_type,
columns_name)
indices = [False, True, True]
indices = _convert_container(indices, indices_type)
subset = _safe_indexing(array, indices, axis=axis)
assert_allclose_dense_sparse(
subset, _convert_container(expected_subset, array_type))
def test_check_inverse():
X_dense = np.array([1, 4, 9, 16], dtype=np.float64).reshape((2, 2))
X_list = [X_dense, sparse.csr_matrix(X_dense), sparse.csc_matrix(X_dense)]
for X in X_list:
if sparse.issparse(X):
accept_sparse = True
else:
accept_sparse = False
trans = FunctionTransformer(
func=np.sqrt,
inverse_func=np.around,
accept_sparse=accept_sparse,
check_inverse=True,
validate=True,
)
warning_message = (
"The provided functions are not strictly"
" inverse of each other. If you are sure you"
" want to proceed regardless, set"
" 'check_inverse=False'."
)
with pytest.warns(UserWarning, match=warning_message):
trans.fit(X)
trans = FunctionTransformer(
func=np.expm1,
inverse_func=np.log1p,
accept_sparse=accept_sparse,
check_inverse=True,
validate=True,
)
with warnings.catch_warnings():
warnings.simplefilter("error", UserWarning)
Xt = trans.fit_transform(X)
assert_allclose_dense_sparse(X, trans.inverse_transform(Xt))
# check that we don't check inverse when one of the func or inverse is not
# provided.
trans = FunctionTransformer(
func=np.expm1, inverse_func=None, check_inverse=True, validate=True
)
with warnings.catch_warnings():
warnings.simplefilter("error", UserWarning)
trans.fit(X_dense)
trans = FunctionTransformer(
func=None, inverse_func=np.expm1, check_inverse=True, validate=True
)
with warnings.catch_warnings():
warnings.simplefilter("error", UserWarning)
trans.fit(X_dense)
def test_safe_indexing_2d_read_only_axis_1(
array_read_only, indices_read_only, array_type, indices_type, axis, expected_array
):
array = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
if array_read_only:
array.setflags(write=False)
array = _convert_container(array, array_type)
indices = np.array([1, 2])
if indices_read_only:
indices.setflags(write=False)
indices = _convert_container(indices, indices_type)
subset = _safe_indexing(array, indices, axis=axis)
assert_allclose_dense_sparse(subset, _convert_container(expected_array, array_type))
def test_column_transformer_sparse_array():
X_sparse = sparse.eye(3, 2).tocsr()
# no distinction between 1D and 2D
X_res_first = X_sparse[:, 0]
X_res_both = X_sparse
for col in [0, [0], slice(0, 1)]:
for remainder, res in [('drop', X_res_first),
('passthrough', X_res_both)]:
ct = ColumnTransformer([('trans', Trans(), col)],
remainder=remainder,
sparse_threshold=0.8)
assert sparse.issparse(ct.fit_transform(X_sparse))
assert_allclose_dense_sparse(ct.fit_transform(X_sparse), res)
assert_allclose_dense_sparse(ct.fit(X_sparse).transform(X_sparse),
res)
for col in [[0, 1], slice(0, 2)]:
ct = ColumnTransformer([('trans', Trans(), col)],
sparse_threshold=0.8)
assert sparse.issparse(ct.fit_transform(X_sparse))
assert_allclose_dense_sparse(ct.fit_transform(X_sparse), X_res_both)
assert_allclose_dense_sparse(ct.fit(X_sparse).transform(X_sparse),
X_res_both)
def test_20news_normalization():
try:
X = datasets.fetch_20newsgroups_vectorized(normalize=False,
download_if_missing=False)
X_ = datasets.fetch_20newsgroups_vectorized(normalize=True,
download_if_missing=False)
except IOError:
raise SkipTest("Download 20 newsgroups to run this test")
X_norm = X_['data'][:100]
X = X['data'][:100]
assert_allclose_dense_sparse(X_norm, normalize(X))
assert np.allclose(np.linalg.norm(X_norm.todense(), axis=1), 1)
def test_incremental_pca_batch_rank():
# Test sample size in each batch is always larger or equal to n_components
rng = np.random.RandomState(1999)
n_samples = 100
n_features = 20
X = rng.randn(n_samples, n_features)
all_components = []
batch_sizes = np.arange(20, 90, 3)
for batch_size in batch_sizes:
ipca = IncrementalPCA(n_components=20, batch_size=batch_size).fit(X)
all_components.append(ipca.components_)
for components_i, components_j in zip(all_components[:-1], all_components[1:]):
assert_allclose_dense_sparse(components_i, components_j)
def test_random_projection_numerical_consistency(random_projection_cls):
# Verify numerical consistency among np.float32 and np.float64
atol = 1e-5
rng = np.random.RandomState(42)
X = rng.rand(25, 3000)
rp_32 = random_projection_cls(random_state=0)
rp_64 = random_projection_cls(random_state=0)
projection_32 = rp_32.fit_transform(X.astype(np.float32))
projection_64 = rp_64.fit_transform(X.astype(np.float64))
assert_allclose(projection_64, projection_32, atol=atol)
assert_allclose_dense_sparse(rp_32.components_, rp_64.components_)
def test_function_sampler_func_kwargs(X, y):
def func(X, y, sampling_strategy, random_state):
rus = RandomUnderSampler(
sampling_strategy=sampling_strategy, random_state=random_state
)
return rus.fit_resample(X, y)
sampler = FunctionSampler(
func=func, kw_args={"sampling_strategy": "auto", "random_state": 0}
)
X_res, y_res = sampler.fit_resample(X, y)
X_res_2, y_res_2 = RandomUnderSampler(random_state=0).fit_resample(X, y)
assert_allclose_dense_sparse(X_res, X_res_2)
assert_array_equal(y_res, y_res_2)
def test_safe_sparse_dot_dense_output(dense_output):
rng = np.random.RandomState(0)
A = sparse.random(30, 10, density=0.1, random_state=rng)
B = sparse.random(10, 20, density=0.1, random_state=rng)
expected = A.dot(B)
actual = safe_sparse_dot(A, B, dense_output=dense_output)
assert sparse.issparse(actual) == (not dense_output)
if dense_output:
expected = expected.toarray()
assert_allclose_dense_sparse(actual, expected)
def test_32_equal_64(input_dtype, encode):
# TODO this check is redundant with common checks and can be removed
# once #16290 is merged
X_input = np.array(X, dtype=input_dtype)
# 32 bit output
kbd_32 = KBinsDiscretizer(n_bins=3, encode=encode, dtype=np.float32)
kbd_32.fit(X_input)
Xt_32 = kbd_32.transform(X_input)
# 64 bit output
kbd_64 = KBinsDiscretizer(n_bins=3, encode=encode, dtype=np.float64)
kbd_64.fit(X_input)
Xt_64 = kbd_64.transform(X_input)
assert_allclose_dense_sparse(Xt_32, Xt_64)
def test_stacking_classifier_sparse_passthrough(fmt):
# Check passthrough behavior on a sparse X matrix
X_train, X_test, y_train, _ = train_test_split(
sparse.coo_matrix(scale(X_iris)).asformat(fmt),
y_iris, random_state=42
)
estimators = [('lr', LogisticRegression()), ('svc', LinearSVC())]
rf = RandomForestClassifier(n_estimators=10, random_state=42)
clf = StackingClassifier(
estimators=estimators, final_estimator=rf, cv=5, passthrough=True
)
clf.fit(X_train, y_train)
X_trans = clf.transform(X_test)
assert_allclose_dense_sparse(X_test, X_trans[:, -4:])
assert sparse.issparse(X_trans)
assert X_test.format == X_trans.format
def test_imputation_constant_float(array_constructor):
# Test imputation using the constant strategy on floats
X = np.array([[np.nan, 1.1, 0, np.nan], [1.2, np.nan, 1.3, np.nan],
[0, 0, np.nan, np.nan], [1.4, 1.5, 0, np.nan]])
X_true = np.array([[-1, 1.1, 0, -1], [1.2, -1, 1.3, -1], [0, 0, -1, -1],
[1.4, 1.5, 0, -1]])
X = array_constructor(X)
X_true = array_constructor(X_true)
imputer = SimpleImputer(strategy="constant", fill_value=-1)
X_trans = imputer.fit_transform(X)
assert_allclose_dense_sparse(X_trans, X_true)
def test_check_sparse_pandas_sp_format(sp_format):
# check_array converts pandas dataframe with only sparse arrays into
# sparse matrix
pd = pytest.importorskip("pandas")
sp_mat = _sparse_random_matrix(10, 3)
sdf = pd.DataFrame.sparse.from_spmatrix(sp_mat)
result = check_array(sdf, accept_sparse=sp_format)
if sp_format is True:
# by default pandas converts to coo when accept_sparse is True
sp_format = 'coo'
assert sp.issparse(result)
assert result.format == sp_format
assert_allclose_dense_sparse(sp_mat, result)
def test_stacking_regressor_sparse_passthrough(fmt):
# Check passthrough behavior on a sparse X matrix
X_train, X_test, y_train, _ = train_test_split(sparse.coo_matrix(
scale(X_diabetes)).asformat(fmt),
y_diabetes,
random_state=42)
estimators = [("lr", LinearRegression()), ("svr", LinearSVR())]
rf = RandomForestRegressor(n_estimators=10, random_state=42)
clf = StackingRegressor(estimators=estimators,
final_estimator=rf,
cv=5,
passthrough=True)
clf.fit(X_train, y_train)
X_trans = clf.transform(X_test)
assert_allclose_dense_sparse(X_test, X_trans[:, -10:])
assert sparse.issparse(X_trans)
assert X_test.format == X_trans.format
def test_assert_allclose_dense_sparse():
x = np.arange(9).reshape(3, 3)
msg = "Not equal to tolerance "
y = sparse.csc_matrix(x)
for X in [x, y]:
# basic compare
assert_raise_message(AssertionError, msg, assert_allclose_dense_sparse,
X, X * 2)
assert_allclose_dense_sparse(X, X)
assert_raise_message(ValueError, "Can only compare two sparse",
assert_allclose_dense_sparse, x, y)
A = sparse.diags(np.ones(5), offsets=0).tocsr()
B = sparse.csr_matrix(np.ones((1, 5)))
assert_raise_message(AssertionError, "Arrays are not equal",
assert_allclose_dense_sparse, B, A)
def test_check_dataframe_mixed_float_dtypes():
# pandas dataframe will coerce a boolean into a object, this is a mismatch
# with np.result_type which will return a float
# check_array needs to explicitly check for bool dtype in a dataframe for
# this situation
# https://github.com/scikit-learn/scikit-learn/issues/15787
pd = importorskip("pandas")
df = pd.DataFrame(
{"int": [1, 2, 3], "float": [0, 0.1, 2.1], "bool": [True, False, True]},
columns=["int", "float", "bool"],
)
array = check_array(df, dtype=(np.float64, np.float32, np.float16))
expected_array = np.array(
[[1.0, 0.0, 1.0], [2.0, 0.1, 0.0], [3.0, 2.1, 1.0]], dtype=float
)
assert_allclose_dense_sparse(array, expected_array)
def test_safe_indexing_2d_scalar_axis_1(array_type, expected_output_type,
indices):
columns_name = ['col_0', 'col_1', 'col_2']
array = _convert_container([[1, 2, 3], [4, 5, 6], [7, 8, 9]], array_type,
columns_name)
if isinstance(indices, str) and array_type != 'dataframe':
err_msg = ("Specifying the columns using strings is only supported "
"for pandas DataFrames")
with pytest.raises(ValueError, match=err_msg):
_safe_indexing(array, indices, axis=1)
else:
subset = _safe_indexing(array, indices, axis=1)
expected_output = [3, 6, 9]
if expected_output_type == 'sparse':
# sparse matrix are keeping the 2D shape
expected_output = [[3], [6], [9]]
expected_array = _convert_container(expected_output,
expected_output_type)
assert_allclose_dense_sparse(subset, expected_array)
def test_check_fit_params(indices):
X = np.random.randn(4, 2)
fit_params = {
"list": [1, 2, 3, 4],
"array": np.array([1, 2, 3, 4]),
"sparse-col": sp.csc_matrix([1, 2, 3, 4]).T,
"sparse-row": sp.csc_matrix([1, 2, 3, 4]),
"scalar-int": 1,
"scalar-str": "xxx",
"None": None,
}
result = _check_fit_params(X, fit_params, indices)
indices_ = indices if indices is not None else list(range(X.shape[0]))
for key in ["sparse-row", "scalar-int", "scalar-str", "None"]:
assert result[key] is fit_params[key]
assert result["list"] == _safe_indexing(fit_params["list"], indices_)
assert_array_equal(result["array"], _safe_indexing(fit_params["array"], indices_))
assert_allclose_dense_sparse(
result["sparse-col"], _safe_indexing(fit_params["sparse-col"], indices_)
)