def test_check_is_permutation():
p = np.arange(100)
assert_true(_check_is_permutation(p, 100))
assert_false(_check_is_permutation(np.delete(p, 23), 100))
p[0] = 23
assert_false(_check_is_permutation(p, 100))
def test_check_is_permutation():
p = np.arange(100)
assert_true(_check_is_permutation(p, 100))
assert_false(_check_is_permutation(np.delete(p, 23), 100))
p[0] = 23
assert_false(_check_is_permutation(p, 100))
def test_check_is_permutation():
rng = np.random.RandomState(0)
p = np.arange(100)
rng.shuffle(p)
assert_true(_check_is_permutation(p, 100))
assert_false(_check_is_permutation(np.delete(p, 23), 100))
p[0] = 23
assert_false(_check_is_permutation(p, 100))
# Check if the additional duplicate indices are caught
assert_false(_check_is_permutation(np.hstack((p, 0)), 100))
def test_check_is_permutation():
rng = np.random.RandomState(0)
p = np.arange(100)
rng.shuffle(p)
assert_true(_check_is_permutation(p, 100))
assert_false(_check_is_permutation(np.delete(p, 23), 100))
p[0] = 23
assert_false(_check_is_permutation(p, 100))
# Check if the additional duplicate indices are caught
assert_false(_check_is_permutation(np.hstack((p, 0)), 100))
def my_cross_val_predict(estimator,
X,
y=None,
groups=None,
cv=None,
n_jobs=1,
verbose=0,
fit_params=None,
pre_dispatch='2*n_jobs',
method='predict'):
X, y, groups = indexable(X, y, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
# Ensure the estimator has implemented the passed decision function
if not callable(getattr(estimator, method)):
raise AttributeError('{} not implemented in estimator'.format(method))
if method in ['decision_function', 'predict_proba', 'predict_log_proba']:
le = LabelEncoder()
y = le.fit_transform(y)
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs,
verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(
delayed(_my_fit_and_predict)(clone(estimator), X, y, train, test,
verbose, fit_params, method)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _, _ in prediction_blocks]
test_indices = np.concatenate(
[indices_i for _, indices_i, _ in prediction_blocks])
scores = np.concatenate([score_i for _, _, score_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
# Check for sparse predictions
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
else:
predictions = np.concatenate(predictions)
out_predictions = predictions[inv_test_indices]
return out_predictions.reshape(y.shape), scores
def cross_val_predict(estimator, X, y=None, groups=None, cv=None, n_jobs=1,
verbose=0, fit_params=None, pre_dispatch='2*n_jobs',
method='predict', pickle_predictions=False, **pickler_kwargs):
"""Please see sklearn for documenation
This has only been modified so binned regressors can return probabilites
and predictions can be cached during computation
"""
X, y, groups = indexable(X, y, groups)
pickler = CachingPickler(**pickler_kwargs) if pickle_predictions else None
cv = check_cv(cv, y, classifier=is_classifier(estimator))
if method in ['decision_function', 'predict_proba', 'predict_log_proba'] and is_classifier(estimator):
le = LabelEncoder()
y = le.fit_transform(y)
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs, verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(delayed(_fit_and_predict)(
clone(estimator), X, y, train, test, verbose, fit_params, method, pickler)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
if pickle_predictions:
predictions = [pickler.unpickle_data(pred_block_i) for pred_block_i, _ in prediction_blocks]
else:
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
test_indices = np.concatenate([indices_i for _, indices_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
# Check for sparse predictions
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
else:
predictions = np.concatenate(predictions)
return predictions[inv_test_indices]
def my_cross_val_predict(estimator, X, y=None, groups=None, cv=None, n_jobs=1,
verbose=0, fit_params=None, pre_dispatch='2*n_jobs',
method='predict'):
X, y, groups = indexable(X, y, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
# Ensure the estimator has implemented the passed decision function
if not callable(getattr(estimator, method)):
raise AttributeError('{} not implemented in estimator'
.format(method))
if method in ['decision_function', 'predict_proba', 'predict_log_proba']:
le = LabelEncoder()
y = le.fit_transform(y)
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs, verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(delayed(_my_fit_and_predict)(
clone(estimator), X, y, train, test, verbose, fit_params, method)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _, _ in prediction_blocks]
test_indices = np.concatenate([indices_i
for _, indices_i, _ in prediction_blocks])
scores = np.concatenate([score_i for _, _, score_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
# Check for sparse predictions
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
else:
predictions = np.concatenate(predictions)
return predictions[inv_test_indices], scores
def _cross_val_predict(pipeline, X, y=None, cv=None) \
-> Tuple[np.ndarray, np.ndarray, np.ndarray, List[FlexiblePipeline]]:
X, y, groups = indexable(X, y, None)
cv = check_cv(cv, y, classifier=is_classifier(pipeline))
cv.random_state = 42
prediction_blocks = []
probability_blocks = []
fitted_pipelines = []
for train, test in cv.split(X, y, groups):
cloned_pipeline = clone(pipeline)
probability_blocks.append(
(_fit_and_predict(cloned_pipeline, X, y, train, test, 0, {}, 'predict_proba'), test)
)
prediction_blocks.append(cloned_pipeline.predict(X))
fitted_pipelines.append(cloned_pipeline)
# Concatenate the predictions
probabilities = [prob_block_i for prob_block_i, _ in probability_blocks]
predictions = [pred_block_i for pred_block_i in prediction_blocks]
test_indices = np.concatenate([indices_i for _, indices_i in probability_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
probabilities = np.concatenate(probabilities)
predictions = np.concatenate(predictions)
if isinstance(predictions, list):
return y, [p[inv_test_indices] for p in predictions], [p[inv_test_indices] for p in
probabilities], fitted_pipelines
else:
return y, predictions[inv_test_indices], probabilities[inv_test_indices], fitted_pipelines
def _dml_cv_predict_ut_version(estimator, x, y, smpls=None,
n_jobs=None, est_params=None, method='predict'):
# this is an adapted version of the sklearn function cross_val_predict which allows to set fold-specific parameters
# original https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/model_selection/_validation.py
test_indices = np.concatenate([test_index for _, test_index in smpls])
smpls_is_partition = _check_is_permutation(test_indices, _num_samples(x))
if not smpls_is_partition:
assert len(smpls) == 1
train_index, test_index = smpls[0]
# set some defaults aligned with cross_val_predict
fit_params = None
verbose = 0
if method == 'predict_proba':
predictions = np.full((len(y), 2), np.nan)
else:
predictions = np.full(len(y), np.nan)
if est_params is None:
xx = _fit_and_predict(clone(estimator),
x, y, train_index, test_index, verbose, fit_params, method)
else:
assert isinstance(est_params, dict)
xx = _fit_and_predict(clone(estimator).set_params(**est_params),
x, y, train_index, test_index, verbose, fit_params, method)
# implementation is (also at other parts) restricted to a sorted set of test_indices, but this could be fixed
# inv_test_indices = np.argsort(test_indices)
assert np.all(np.diff(test_indices) > 0), 'test_indices not sorted'
if isinstance(xx, np.ndarray):
# this is sklearn >= 0.24
predictions[test_indices] = xx
else:
predictions[test_indices] = xx[0]
return predictions
# set some defaults aligned with cross_val_predict
fit_params = None
verbose = 0
pre_dispatch = '2*n_jobs'
encode = (method == 'predict_proba')
if encode:
y = np.asarray(y)
le = LabelEncoder()
y = le.fit_transform(y)
parallel = Parallel(n_jobs=n_jobs, verbose=verbose,
pre_dispatch=pre_dispatch)
# FixMe: Find a better way to handle the different combinations of paramters and smpls_is_partition
if est_params is None:
prediction_blocks = parallel(delayed(_fit_and_predict)(
estimator,
x, y, train_index, test_index, verbose, fit_params, method)
for idx, (train_index, test_index) in enumerate(smpls))
elif isinstance(est_params, dict):
# if no fold-specific parameters we redirect to the standard method
# warnings.warn("Using the same (hyper-)parameters for all folds")
prediction_blocks = parallel(delayed(_fit_and_predict)(
clone(estimator).set_params(**est_params),
x, y, train_index, test_index, verbose, fit_params, method)
for idx, (train_index, test_index) in enumerate(smpls))
else:
assert len(est_params) == len(smpls), 'provide one parameter setting per fold'
prediction_blocks = parallel(delayed(_fit_and_predict)(
clone(estimator).set_params(**est_params[idx]),
x, y, train_index, test_index, verbose, fit_params, method)
for idx, (train_index, test_index) in enumerate(smpls))
# Concatenate the predictions
if isinstance(prediction_blocks[0], np.ndarray):
# this is sklearn >= 0.24
predictions = [pred_block_i for pred_block_i in prediction_blocks]
else:
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
if not _check_is_permutation(test_indices, _num_samples(x)):
raise ValueError('_dml_cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
elif encode and isinstance(predictions[0], list):
n_labels = y.shape[1]
concat_pred = []
for i_label in range(n_labels):
label_preds = np.concatenate([p[i_label] for p in predictions])
concat_pred.append(label_preds)
predictions = concat_pred
else:
predictions = np.concatenate(predictions)
if isinstance(predictions, list):
return [p[inv_test_indices] for p in predictions]
else:
return predictions[inv_test_indices]
def cross_val_predict(estimator,
X,
y=None,
groups=None,
cv=None,
n_jobs=1,
verbose=0,
fit_params=None,
pre_dispatch='2*n_jobs',
method='predict'):
'''Doc String'''
if isinstance(n_jobs, int):
return model_selection.cross_val_predict(estimator, X, y, groups, cv,
n_jobs, verbose, fit_params,
pre_dispatch, method)
elif not sparkRuns:
raise RuntimeError('n_jobs parameter was not an int, meaning it '
'should have been a SparkContext, but spark '
'was unable to be imported.')
elif not isinstance(n_jobs, pyspark.SparkContext):
raise RuntimeError('n_jobs parameter was not an int, meaning '
'it should have been a SparkContext, but '
'it was not.')
sc = n_jobs
X, y, groups = indexable(X, y, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
cv_iter = list(cv.split(X, y, groups))
# Ensure the estimator has implemented the passed decision function
if not callable(getattr(estimator, method)):
raise AttributeError('{} not implemented in estimator'.format(method))
inds = [tup for tup in cv_iter]
# Because the original python code expects a certain order for the
# elements, we need to respect it.
numInds = list(zip(range(len(inds)), inds))
parNumInds = sc.parallelize(numInds, len(numInds))
X_bc = sc.broadcast(X)
y_bc = sc.broadcast(y)
fap = _fit_and_predict
def fun(tup):
(index, (train, test)) = tup
local_estimator = clone(estimator)
local_X = X_bc.value
local_y = y_bc.value
pred = fap(local_estimator, local_X, local_y, train, test, verbose,
fit_params, method)
return (index, pred)
indexed_out0 = dict(parNumInds.map(fun).collect())
prediction_blocks = [indexed_out0[idx] for idx in range(len(inds))]
X_bc.unpersist()
y_bc.unpersist()
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
test_indices = np.concatenate(
[indices_i for _, indices_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
# Check for sparse predictions
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
else:
predictions = np.concatenate(predictions)
return predictions[inv_test_indices]
def cross_val_predict(estimator, X, y=None, sample_weight=None, sample_weight_steps=None, groups=None, cv=None, n_jobs=1,
verbose=0, fit_params=None, pre_dispatch='2*n_jobs',
method='predict'):
"""Generate cross-validated estimates for each input data point
Read more in the :ref:`User Guide <cross_validation>`.
Parameters
----------
estimator : estimator object implementing 'fit' and 'predict'
The object to use to fit the data.
X : array-like
The data to fit. Can be, for example a list, or an array at least 2d.
y : array-like, optional, default: None
The target variable to try to predict in the case of
supervised learning.
sample_weight: array-like
The sample weights must fit len(y)
sample_weight_steps: list
The pipeline steps the sample_weights are passed as fit_params.
One must provide sample_weight_steps if the underlying estimator is a pipeline
groups : array-like, with shape (n_samples,), optional
Group labels for the samples used while splitting the dataset into
train/test set.
cv : int, cross-validation generator or an iterable, optional
Determines the cross-validation splitting strategy.
Possible inputs for cv are:
- None, to use the default 3-fold cross validation,
- integer, to specify the number of folds in a `(Stratified)KFold`,
- An object to be used as a cross-validation generator.
- An iterable yielding train, test splits.
For integer/None inputs, if the estimator is a classifier and ``y`` is
either binary or multiclass, :class:`StratifiedKFold` is used. In all
other cases, :class:`KFold` is used.
Refer :ref:`User Guide <cross_validation>` for the various
cross-validation strategies that can be used here.
n_jobs : integer, optional
The number of CPUs to use to do the computation. -1 means
'all CPUs'.
verbose : integer, optional
The verbosity level.
fit_params : dict, optional
Parameters to pass to the fit method of the estimator.
pre_dispatch : int, or string, optional
Controls the number of jobs that get dispatched during parallel
execution. Reducing this number can be useful to avoid an
explosion of memory consumption when more jobs get dispatched
than CPUs can process. This parameter can be:
- None, in which case all the jobs are immediately
created and spawned. Use this for lightweight and
fast-running jobs, to avoid delays due to on-demand
spawning of the jobs
- An int, giving the exact number of total jobs that are
spawned
- A string, giving an expression as a function of n_jobs,
as in '2*n_jobs'
method : string, optional, default: 'predict'
Invokes the passed method name of the passed estimator. For
method='predict_proba', the columns correspond to the classes
in sorted order.
Returns
-------
predictions : ndarray
This is the result of calling ``method``
Notes
-----
In the case that one or more classes are absent in a training portion, a
default score needs to be assigned to all instances for that class if
``method`` produces columns per class, as in {'decision_function',
'predict_proba', 'predict_log_proba'}. For ``predict_proba`` this value is
0. In order to ensure finite output, we approximate negative infinity by
the minimum finite float value for the dtype in other cases.
Examples
--------
>>> from sklearn import datasets, linear_model
>>> from sklearn.model_selection import cross_val_predict
>>> diabetes = datasets.load_diabetes()
>>> X = diabetes.data[:150]
>>> y = diabetes.target[:150]
>>> lasso = linear_model.Lasso()
>>> y_pred = cross_val_predict(lasso, X, y)
"""
X, y, sample_weight, groups = indexable(X, y, sample_weight, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
if method in ['decision_function', 'predict_proba', 'predict_log_proba']:
le = LabelEncoder()
y = le.fit_transform(y)
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs, verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(delayed(_fit_and_predict)(
clone(estimator),
X, y,
sample_weight, sample_weight_steps,
train, test, verbose, fit_params, method)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
test_indices = np.concatenate([indices_i
for _, indices_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
# Check for sparse predictions
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
else:
predictions = np.concatenate(predictions)
return predictions[inv_test_indices]
def _cross_val_predict(estimator,
X,
y=None,
*,
groups=None,
cv=None,
n_jobs=None,
verbose=0,
fit_params=None,
pre_dispatch='2*n_jobs',
method='predict',
safe=True):
"""This is a fork from :meth:`~sklearn.model_selection.cross_val_predict` to allow for
non-safe cloning of the models for each fold.
Parameters
----------
estimator : estimator object implementing 'fit' and 'predict'
The object to use to fit the data.
X : array-like of shape (n_samples, n_features)
The data to fit. Can be, for example a list, or an array at least 2d.
y : array-like of shape (n_samples,) or (n_samples, n_outputs), \
default=None
The target variable to try to predict in the case of
supervised learning.
groups : array-like of shape (n_samples,), default=None
Group labels for the samples used while splitting the dataset into
train/test set. Only used in conjunction with a "Group" :term:`cv`
instance (e.g., :class:`GroupKFold`).
cv : int, cross-validation generator or an iterable, default=None
Determines the cross-validation splitting strategy.
Possible inputs for cv are:
- None, to use the default 5-fold cross validation,
- int, to specify the number of folds in a `(Stratified)KFold`,
- CV splitter,
- An iterable yielding (train, test) splits as arrays of indices.
For int/None inputs, if the estimator is a classifier and ``y`` is
either binary or multiclass, :class:`StratifiedKFold` is used. In all
other cases, :class:`KFold` is used.
Refer :ref:`User Guide <cross_validation>` for the various
cross-validation strategies that can be used here.
.. versionchanged:: 0.22
``cv`` default value if None changed from 3-fold to 5-fold.
n_jobs : int, default=None
The number of CPUs to use to do the computation.
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
for more details.
verbose : int, default=0
The verbosity level.
fit_params : dict, defualt=None
Parameters to pass to the fit method of the estimator.
pre_dispatch : int or str, default='2*n_jobs'
Controls the number of jobs that get dispatched during parallel
execution. Reducing this number can be useful to avoid an
explosion of memory consumption when more jobs get dispatched
than CPUs can process. This parameter can be:
- None, in which case all the jobs are immediately
created and spawned. Use this for lightweight and
fast-running jobs, to avoid delays due to on-demand
spawning of the jobs
- An int, giving the exact number of total jobs that are
spawned
- A str, giving an expression as a function of n_jobs,
as in '2*n_jobs'
method : str, default='predict'
Invokes the passed method name of the passed estimator. For
method='predict_proba', the columns correspond to the classes
in sorted order.
safe : bool, default=True
Whether to clone with safe option.
Returns
-------
predictions : ndarray
This is the result of calling ``method``
"""
X, y, groups = indexable(X, y, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
# If classification methods produce multiple columns of output,
# we need to manually encode classes to ensure consistent column ordering.
encode = method in [
'decision_function', 'predict_proba', 'predict_log_proba'
] and y is not None
if encode:
y = np.asarray(y)
if y.ndim == 1:
le = LabelEncoder()
y = le.fit_transform(y)
elif y.ndim == 2:
y_enc = np.zeros_like(y, dtype=np.int)
for i_label in range(y.shape[1]):
y_enc[:, i_label] = LabelEncoder().fit_transform(y[:, i_label])
y = y_enc
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs,
verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(
delayed(_fit_and_predict)(clone(estimator, safe=safe), X, y, train,
test, verbose, fit_params, method)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
test_indices = np.concatenate(
[indices_i for _, indices_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
elif encode and isinstance(predictions[0], list):
# `predictions` is a list of method outputs from each fold.
# If each of those is also a list, then treat this as a
# multioutput-multiclass task. We need to separately concatenate
# the method outputs for each label into an `n_labels` long list.
n_labels = y.shape[1]
concat_pred = []
for i_label in range(n_labels):
label_preds = np.concatenate([p[i_label] for p in predictions])
concat_pred.append(label_preds)
predictions = concat_pred
else:
predictions = np.concatenate(predictions)
if isinstance(predictions, list):
return [p[inv_test_indices] for p in predictions]
else:
return predictions[inv_test_indices]
def cross_val_predict_custom(estimator, X, y=None, groups=None, cv=None,
n_jobs=None, verbose=0, fit_params=None,
pre_dispatch='2*n_jobs', method='predict',
# New stuff
sample_weights=None, objective=None):
""" A copy of the sklearn function but allows for different sample weights to be put in for each run. """
X, y, groups = indexable(X, y, groups)
cv = check_cv(cv, y, classifier=is_classifier(estimator))
# If classification methods produce multiple columns of output,
# we need to manually encode classes to ensure consistent column ordering.
encode = method in ['decision_function', 'predict_proba',
'predict_log_proba']
if encode:
y = np.asarray(y)
if y.ndim == 1:
le = LabelEncoder()
y = le.fit_transform(y)
elif y.ndim == 2:
y_enc = np.zeros_like(y, dtype=np.int)
for i_label in range(y.shape[1]):
y_enc[:, i_label] = LabelEncoder().fit_transform(y[:, i_label])
y = y_enc
# We clone the estimator to make sure that all the folds are
# independent, and that it is pickle-able.
parallel = Parallel(n_jobs=n_jobs, verbose=verbose,
pre_dispatch=pre_dispatch)
prediction_blocks = parallel(delayed(_fit_and_predict)(
clone(estimator), X, y, train, test, verbose, fit_params, method, sample_weights, objective)
for train, test in cv.split(X, y, groups))
# Concatenate the predictions
predictions = [pred_block_i for pred_block_i, _ in prediction_blocks]
test_indices = np.concatenate([indices_i
for _, indices_i in prediction_blocks])
if not _check_is_permutation(test_indices, _num_samples(X)):
raise ValueError('cross_val_predict only works for partitions')
inv_test_indices = np.empty(len(test_indices), dtype=int)
inv_test_indices[test_indices] = np.arange(len(test_indices))
if sp.issparse(predictions[0]):
predictions = sp.vstack(predictions, format=predictions[0].format)
elif encode and isinstance(predictions[0], list):
# `predictions` is a list of method outputs from each fold.
# If each of those is also a list, then treat this as a
# multioutput-multiclass task. We need to separately concatenate
# the method outputs for each label into an `n_labels` long list.
n_labels = y.shape[1]
concat_pred = []
for i_label in range(n_labels):
label_preds = np.concatenate([p[i_label] for p in predictions])
concat_pred.append(label_preds)
predictions = concat_pred
else:
predictions = np.concatenate(predictions)
if isinstance(predictions, list):
return [p[inv_test_indices] for p in predictions]
else:
return predictions[inv_test_indices]