def test_RowwiseTransformer_pipeline():
# using pure sklearn
mean_func = lambda X: pd.DataFrame([np.mean(row) for row in X])
first_func = lambda X: pd.DataFrame([row[0] for row in X])
column_transformer = ColumnTransformer(
[('mean', FunctionTransformer(func=mean_func, validate=False), 'ts'),
('first', FunctionTransformer(func=first_func, validate=False), 'ts_copy')])
estimator = RandomForestClassifier(n_estimators=2, random_state=1)
strategy = [
('feature_extract', column_transformer),
('rfestimator', estimator)]
model = Pipeline(steps=strategy)
model.fit(X_train, y_train)
expected = model.predict(X_test)
# using sktime with sklearn pipeline
first_func = lambda X: pd.DataFrame([row[0] for row in X])
column_transformer = ColumnTransformer(
[('mean', RowwiseTransformer(FunctionTransformer(func=np.mean, validate=False)), 'ts'),
('first', FunctionTransformer(func=first_func, validate=False), 'ts_copy')])
estimator = RandomForestClassifier(n_estimators=2, random_state=1)
strategy = [
('feature_extract', column_transformer),
('rfestimator', estimator)]
model = Pipeline(steps=strategy)
model.fit(X_train, y_train)
got = model.predict(X_test)
np.testing.assert_array_equal(expected, got)
def _test_pipeline_predictions(n_intervals=None, random_state=None):
steps = [('segment',
RandomIntervalSegmenter(n_intervals=n_intervals,
check_input=False)),
('transform',
FeatureUnion([('mean',
RowwiseTransformer(
FunctionTransformer(func=np.mean,
validate=False))),
('std',
RowwiseTransformer(
FunctionTransformer(func=np.std,
validate=False)))])),
('clf', DecisionTreeClassifier())]
clf1 = Pipeline(steps, random_state=random_state)
clf1.fit(X_train, y_train)
a = clf1.predict(X_test)
steps = [('transform',
RandomIntervalFeatureExtractor(n_intervals=n_intervals,
features=[np.mean, np.std])),
('clf', DecisionTreeClassifier())]
clf2 = Pipeline(steps, random_state=random_state)
clf2.fit(X_train, y_train)
b = clf2.predict(X_test)
np.array_equal(a, b)
def test_pipeline_predictions(n_intervals, n_estimators):
random_state = 1234
# Due to tie-breaking/floating point rounding in the final decision tree classifier, the results depend on the
# exact column order of the input data
# Compare pipeline predictions outside of ensemble.
steps = [('segment', RandomIntervalSegmenter(n_intervals=n_intervals)),
('transform',
FeatureUnion([('mean',
RowwiseTransformer(
FunctionTransformer(func=np.mean,
validate=False))),
('std',
RowwiseTransformer(
FunctionTransformer(func=np.std,
validate=False))),
('slope',
RowwiseTransformer(
FunctionTransformer(func=time_series_slope,
validate=False)))])),
('clf', DecisionTreeClassifier())]
clf1 = Pipeline(steps, random_state=random_state)
clf1.fit(X_train, y_train)
a = clf1.predict(X_test)
steps = [('transform',
RandomIntervalFeatureExtractor(
n_intervals=n_intervals,
features=[np.mean, np.std, time_series_slope])),
('clf', DecisionTreeClassifier())]
clf2 = Pipeline(steps, random_state=random_state)
clf2.fit(X_train, y_train)
b = clf2.predict(X_test)
np.array_equal(a, b)
def test_RowwiseTransformer_pipeline():
X_train, y_train = load_basic_motions("TRAIN", return_X_y=True)
X_test, y_test = load_basic_motions("TEST", return_X_y=True)
# using pure sklearn
def rowwise_mean(X):
if isinstance(X, pd.Series):
X = pd.DataFrame(X)
Xt = pd.concat([pd.Series(col.apply(np.mean))
for _, col in X.items()], axis=1)
return Xt
def rowwise_first(X):
if isinstance(X, pd.Series):
X = pd.DataFrame(X)
Xt = pd.concat([pd.Series(tabularise(col).iloc[:, 0])
for _, col in X.items()], axis=1)
return Xt
# specify column as a list, otherwise pandas Series are selected and passed on to the transformers
transformer = ColumnTransformer([
('mean', FunctionTransformer(func=rowwise_mean, validate=False), ['dim_0']),
('first', FunctionTransformer(func=rowwise_first, validate=False), ['dim_1'])
])
estimator = RandomForestClassifier(n_estimators=2, random_state=1)
steps = [
('extract', transformer),
('classify', estimator)
]
model = Pipeline(steps=steps)
model.fit(X_train, y_train)
expected = model.predict(X_test)
# using sktime with sklearn pipeline
transformer = ColumnTransformer([
('mean', RowwiseTransformer(FunctionTransformer(func=np.mean, validate=False)), ['dim_0']),
('first', FunctionTransformer(func=rowwise_first, validate=False), ['dim_1'])
])
estimator = RandomForestClassifier(n_estimators=2, random_state=1)
steps = [
('extract', transformer),
('classify', estimator)
]
model = Pipeline(steps=steps)
model.fit(X_train, y_train)
actual = model.predict(X_test)
np.testing.assert_array_equal(expected, actual)
def test_Pipeline_random_state():
steps = [('transform', RandomIntervalFeatureExtractor(features=[np.mean])),
('clf', DecisionTreeClassifier())]
pipe = Pipeline(steps)
# Check that pipe is initiated without random_state
assert pipe.random_state is None
assert pipe.get_params()['random_state'] is None
# Check that all components are initiated without random_state
for step in pipe.steps:
assert step[1].random_state is None
assert step[1].get_params()['random_state'] is None
# Check that if random state is set, it's set to itself and all its random components
rs = 1234
pipe.set_params(**{'random_state': rs})
assert pipe.random_state == rs
assert pipe.get_params()['random_state'] == rs
for step in pipe.steps:
assert step[1].random_state == rs
assert step[1].get_params()['random_state'] == rs
# Check specific results
X_train, y_train = load_gunpoint(return_X_y=True)
X_test, y_test = load_gunpoint("TEST", return_X_y=True)
steps = [
('segment', RandomIntervalSegmenter(n_intervals=3)),
('extract',
RowwiseTransformer(FunctionTransformer(func=np.mean,
validate=False))),
('clf', DecisionTreeClassifier())
]
pipe = Pipeline(steps, random_state=rs)
pipe.fit(X_train, y_train)
y_pred_first = pipe.predict(X_test)
N_ITER = 10
for _ in range(N_ITER):
pipe = Pipeline(steps, random_state=rs)
pipe.fit(X_train, y_train)
y_pred = pipe.predict(X_test)
np.testing.assert_array_equal(y_pred_first, y_pred)
def test_ColumnTransformer_pipeline():
# using Identity function transformers (transform series to series)
id_func = lambda X: X
column_transformer = ColumnTransformer(
[('ts', FunctionTransformer(func=id_func, validate=False), 'ts'),
('ts_copy', FunctionTransformer(func=id_func, validate=False), 'ts_copy')])
steps = [
('feature_extract', column_transformer),
('tabularise', Tabulariser()),
('rfestimator', RandomForestClassifier(n_estimators=2))]
model = Pipeline(steps=steps)
model.fit(X_train, y_train)
y_pred = model.predict(X_test)
assert y_pred.shape[0] == y_test.shape[0]
np.testing.assert_array_equal(np.unique(y_pred), np.unique(y_test))
def test_FeatureUnion_pipeline():
# pipeline with segmentation plus multiple feature extraction
steps = [
('segment', RandomIntervalSegmenter(n_intervals=3, check_input=False)),
('transform', FeatureUnion([
('mean', RowwiseTransformer(FunctionTransformer(func=np.mean, validate=False))),
('std', RowwiseTransformer(FunctionTransformer(func=np.std, validate=False)))
])),
('clf', DecisionTreeClassifier())
]
clf = Pipeline(steps)
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
assert y_pred.shape[0] == y_test.shape[0]
np.testing.assert_array_equal(np.unique(y_pred), np.unique(y_test))
def test_ColumnTransformer_pipeline():
X_train, y_train = load_basic_motions("TRAIN", return_X_y=True)
X_test, y_test = load_basic_motions("TEST", return_X_y=True)
# using Identity function transformers (transform series to series)
id_func = lambda X: X
column_transformer = ColumnTransformer([
('id0', FunctionTransformer(func=id_func, validate=False), ['dim_0']),
('id1', FunctionTransformer(func=id_func, validate=False), ['dim_1'])
])
steps = [('extract', column_transformer), ('tabularise', Tabulariser()),
('classify', RandomForestClassifier(n_estimators=2))]
model = Pipeline(steps=steps)
model.fit(X_train, y_train)
y_pred = model.predict(X_test)
assert y_pred.shape[0] == y_test.shape[0]
np.testing.assert_array_equal(np.unique(y_pred), np.unique(y_test))