def test_extract_with_confidence_output_dictionary_unsupervised(self):
X, _ = load_xy(2)
extractor = MFE(groups="general").fit(X.values)
res = extractor.extract_with_confidence(
3, arguments_extract=dict(out_type=dict))
assert isinstance(res, dict)
assert len(res) == 3
def test_none_cancor(self):
X, y = load_xy(0)
feats = [
"w_lambda",
"p_trace",
"lh_trace",
"roy_root",
]
mfe = MFE(groups=[GNAME], features=feats)
custom_args = {
"can_cors": np.array([]),
"can_cor_eigvals": np.array([]),
}
mfe.fit(X.values, y.values, precomp_groups=None)
extract_args = {cur_feat: custom_args for cur_feat in feats}
vals = mfe.extract(**extract_args, suppress_warnings=True)[1]
assert np.allclose(vals,
np.full(shape=len(vals), fill_value=np.nan),
equal_nan=True)
def test_output_lengths_2(self, dt_id, measure_time):
X, y = load_xy(dt_id)
res = (MFE(measure_time=measure_time).fit(X=X.values,
y=y.values).extract())
vals, names, time = res
assert len(vals) == len(names) == len(time)
def test_verbosity_3(self, verbosity, msg_expected, capsys):
X, y = load_xy(0)
MFE().fit(X=X.values, y=y.values).extract(verbose=verbosity)
captured = capsys.readouterr().out
assert (not msg_expected) or captured
def test_error_transform_num(self):
X, y = load_xy(0)
with pytest.raises(TypeError):
_internal.transform_num(X, num_bins='')
with pytest.raises(ValueError):
_internal.transform_num(X, num_bins=-1)
def test_ft_methods_model_based_02(self, dt_id, ft_name, exp_value,
precompute):
"""Function to test each meta-feature belongs to model-based group."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(
groups=[GNAME],
features=[ft_name],
hypparam_model_dt={
"max_depth": 5,
"min_samples_split": 10,
"criterion": "entropy",
},
random_state=1234,
)
mfe.fit(X.values, y.values, precomp_groups=precomp_group)
if precomp_group is None:
# Note: the precomputation of 'model-based' group is always
# forced due to the need of the 'dt_model' value
mfe._precomp_args_ft = {
"dt_model": mfe._precomp_args_ft.get("dt_model")
}
value = mfe.extract()[1]
if exp_value is np.nan:
assert value[0] is exp_value
else:
assert np.allclose(value, exp_value)
def test_extract_with_time_output_dictionary(self):
X, y = load_xy(2)
extractor = MFE(groups="general",
measure_time="total").fit(X.values, y.values)
res = extractor.extract(out_type=dict)
assert isinstance(res, dict)
assert len(res) == 3
def test_scaling_error_1(self):
with pytest.raises(ValueError):
X, y = load_xy(0)
MFE().fit(X=X.values,
y=y.values,
rescale="invalid",
transform_cat=False)
def test_extract_output_pandas_dataframe(self):
X, y = load_xy(2)
extractor = MFE(groups="general").fit(X.values, y.values)
expected_mtfs = extractor.extract_metafeature_names()
res = extractor.extract(out_type=pd.DataFrame)
assert isinstance(res, pd.DataFrame)
assert res.values.shape == (1, len(expected_mtfs)) and np.array_equal(
res.columns, expected_mtfs)
def test_extract_with_time_output_pandas_dataframe_unsupervised(self):
X, _ = load_xy(2)
extractor = MFE(measure_time="total", groups="general").fit(X.values)
expected_mtfs = extractor.extract_metafeature_names()
res = extractor.extract(out_type=pd.DataFrame)
assert isinstance(res, pd.DataFrame)
assert res.values.shape == (2, len(expected_mtfs)) and np.array_equal(
res.columns, expected_mtfs)
def test_verbosity_2(self, capsys):
X, y = load_xy(0)
MFE().fit(X=X.values, y=y.values).extract(verbose=0)
captured = capsys.readouterr().out
assert not captured
def test_integration_general(self, dt_id, exp_value, precompute):
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], summary="mean").fit(
X.values, y.values, precomp_groups=precomp_group
)
value = mfe.extract()[1]
assert np.allclose(value, exp_value, equal_nan=True)
def test_threshold_attr_conc(self):
X, y = load_xy(1)
mfe = MFE(features="attr_conc", random_state=1234).fit(
X.values, y.values, precomp_groups=False
)
value = mfe.extract(attr_conc={"max_attr_num": 25})[1]
assert np.allclose(value, [0.01682327, 0.04715381], rtol=0.2)
def test_verbosity_with_confidence(self, verbosity, msg_expected, capsys):
X, y = load_xy(2)
MFE().fit(X.values,
y.values).extract_with_confidence(verbose=verbosity)
captured = capsys.readouterr().out
assert ((not msg_expected) and
(not captured)) or (msg_expected and captured)
def test_silhouette_subsampling(self, precompute):
X, y = load_xy(0)
precomp_group = GNAME if precompute else None
mfe = MFE(groups="clustering", features="sil", random_state=1234).fit(
X.values, y.values, precomp_groups=precomp_group
)
value = mfe.extract(sil={"sample_frac": 0.5})[1]
assert np.allclose(value, -0.07137712254830314)
def test_integration_infotheo(self, dt_id, exp_value, precompute):
"""Function to test all info-theory meta-features."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], summary="mean").fit(
X.values, y.values, precomp_groups=precomp_group
)
value = mfe.extract()[1]
np.allclose(value, exp_value, atol=0.001, rtol=0.05, equal_nan=True)
def test_verbosity_from_model(self, verbosity, msg_expected, capsys):
X, y = load_xy(2)
model = sklearn.tree.DecisionTreeClassifier().fit(X.values, y.values)
MFE().extract_from_model(model, verbose=verbosity)
captured = capsys.readouterr().out
assert ((not msg_expected) and
(not captured)) or (msg_expected and captured)
def test_integration_clustering(self, dt_id, exp_value, precompute):
"""Function to test each all clustering meta-features."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], summary="mean").fit(
X.values, y.values, precomp_groups=precomp_group
)
value = mfe.extract()[1]
assert np.allclose(value, exp_value, equal_nan=True)
def test_output_lengths_2(self, dt_id, scaler, exp_mean, exp_var, exp_min,
exp_max):
X, y = load_xy(dt_id)
model = MFE().fit(
X=X.values, y=y.values, rescale=scaler, transform_cat=False)
numeric_data = model._custom_args_ft["N"]
assert (np.allclose(numeric_data.mean(axis=0), exp_mean)
and np.allclose(numeric_data.var(axis=0), exp_var)
and np.allclose(numeric_data.min(axis=0), exp_min)
and np.allclose(numeric_data.max(axis=0), exp_max))
def test_integration_model_based(self, dt_id, exp_value, precompute):
"""Function to test all model-based meta-features."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], summary="mean", random_state=1234)
mfe.fit(X.values, y.values, precomp_groups=precomp_group)
value = mfe.extract()[1]
assert np.allclose(value, exp_value, equal_nan=True)
def test_integration_complexity(self, dt_id, exp_value, precompute):
"""Function to test each meta-feature belongs to complexity group."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], summary="mean", random_state=1234)
mfe.fit(X.values, y.values, precomp_groups=precomp_group)
value = mfe.extract()[1]
assert np.allclose(value, exp_value, equal_nan=True, rtol=0.025)
def test_verbose(self, capsys):
X, y = load_xy(0)
model = MFE(
features=["freq_class", "mean", "class_conc", "one_nn", "nodes"
]).fit(X=X.values, y=y.values)
model.extract(verbose=True)
captured = capsys.readouterr().out
# Expected number of messages in verbose mode of mtf extraction
expected_msg_num = 21
assert captured.count("\n") == expected_msg_num
def test_ft_methods_general(self, dt_id, ft_name, exp_value, precompute):
"""Function to test each meta-feature belongs to general group."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], features=[ft_name]).fit(
X.values, y.values, precomp_groups=precomp_group
)
value = mfe.extract()[1]
if exp_value is np.nan:
assert value[0] is exp_value
else:
assert np.allclose(value, exp_value)
def test_roy_largest_root(self, dt_id, exp_value, precompute, criterion):
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME],
features="roy_root").fit(X.values,
y.values,
precomp_groups=precomp_group)
value = mfe.extract(roy_root={"criterion": criterion})[1]
assert np.allclose(value,
exp_value,
atol=0.001,
rtol=0.05,
equal_nan=True)
def test_ft_methods_itemset(self, dt_id, ft_name, exp_value, precompute):
"""Function to test each meta-feature belongs to itemset group."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME], features=[ft_name], random_state=1234)
mfe.fit(X.values, y.values, precomp_groups=precomp_group)
value = mfe.extract()[1]
if exp_value is np.nan:
assert value[0] is exp_value
else:
assert np.allclose(value, exp_value, equal_nan=True)
def test_integration_statistical(self, dt_id, exp_value, precompute):
"""Function to test all statistical meta-features simultaneously."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME],
summary="mean").fit(X.values,
y.values,
precomp_groups=precomp_group)
value = mfe.extract()[1]
assert np.allclose(value,
exp_value,
atol=0.001,
rtol=0.05,
equal_nan=True)
def test_ft_method_relative(self, dt_id, summary, precompute, sample_size,
exp_value):
"""Test relative and subsampling relative landmarking."""
precomp_group = "relative" if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=["relative"],
summary=summary,
sample_size=sample_size,
random_state=1234)
mfe.fit(X.values, y.values, precomp_groups=precomp_group)
_, vals = mfe.extract()
assert np.allclose(vals, exp_value)
def test_ft_methods_statistical(self, dt_id, ft_name, exp_value,
precompute):
"""Function to test each meta-feature belongs to statistical group."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME],
features=[ft_name]).fit(X.values,
y.values,
precomp_groups=precomp_group)
value = mfe.extract()[1]
assert np.allclose(value,
exp_value,
atol=0.001,
rtol=0.05,
equal_nan=True)
def test_normality_tests(self, dt_id, exp_value, precompute, test,
failure):
"""Test normality tests included in ``nr_norm`` statistical method."""
precomp_group = GNAME if precompute else None
X, y = load_xy(dt_id)
mfe = MFE(groups=[GNAME],
features="nr_norm").fit(X.values,
y.values,
precomp_groups=precomp_group)
value = mfe.extract(nr_norm={"failure": failure, "method": test})[1]
assert np.allclose(value,
exp_value,
atol=0.001,
rtol=0.05,
equal_nan=True)
def test_parse_valid_metafeatures(self, groups):
"""Check the length of valid metafeatures per group."""
X, y = load_xy(0)
mfe = MFE(groups="all",
summary=None,
sample_size=0.5,
random_state=1234)
mfe.fit(X.values, y.values)
res = mfe.extract()
target_mtf = mfe.valid_metafeatures(groups=groups)
names, _ = mfe.parse_by_group(groups, res)
assert not set(names).symmetric_difference(target_mtf)