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411 lines
14 KiB
411 lines
14 KiB
# -*- coding: utf-8 -*-
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"""
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This module borrows and adapts `Pipeline` from `sklearn.pipeline` and
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`TransformerMixin` from `sklearn.base` in the scikit-learn framework
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(commit hash d205638475ca542dc46862652e3bb0be663a8eac) to be precise).
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Both are BSD licensed and allow for this sort of thing; attribution
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is given as a comment above each class. License reproduced below:
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BSD 3-Clause License
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Copyright (c) 2007-2022 The scikit-learn developers.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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"""
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from collections import defaultdict
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from itertools import islice
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from typing import Any, Callable, Optional
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from typing_extensions import Protocol
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class TransformerProtocol(Protocol):
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fit: Callable[..., "TransformerProtocol"]
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transform: Callable[[Any], Any]
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# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
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# License: BSD 3 clause
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class TransformerMixin(TransformerProtocol):
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"""Mixin class for all transformers."""
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def fit_transform(self, X: Any, y: Optional[Any] = None, **fit_params: Any) -> Any:
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"""
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Fit to data, then transform it.
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Fits transformer to X and y with optional parameters fit_params
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and returns a transformed version of X.
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Parameters
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----------
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X : ndarray of shape (n_samples, n_features)
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Training set.
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y : ndarray of shape (n_samples,), default=None
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Target values.
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**fit_params : dict
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Additional fit parameters.
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Returns
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-------
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X_new : ndarray array of shape (n_samples, n_features_new)
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Transformed array.
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"""
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# non-optimized default implementation; override when a better
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# method is possible for a given clustering algorithm
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if y is None:
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# fit method of arity 1 (unsupervised transformation)
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return self.fit(X, **fit_params).transform(X)
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else:
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# fit method of arity 2 (supervised transformation)
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return self.fit(X, y, **fit_params).transform(X)
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# Author: Edouard Duchesnay
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# Gael Varoquaux
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# Virgile Fritsch
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# Alexandre Gramfort
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# Lars Buitinck
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# License: BSD
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class Pipeline:
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def __init__(self, steps, verbose=False):
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self.steps = steps
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self.verbose = verbose
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self._validate_steps()
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def _validate_steps(self):
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names, estimators = zip(*self.steps)
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# validate estimators
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transformers = estimators[:-1]
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estimator = estimators[-1]
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for t in transformers:
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if t is None or t == "passthrough":
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continue
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if not (hasattr(t, "fit") or hasattr(t, "fit_transform")) or not hasattr(
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t, "transform"
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):
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raise TypeError(
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"All intermediate steps should be "
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"transformers and implement fit and transform "
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"or be the string 'passthrough' "
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"'%s' (type %s) doesn't" % (t, type(t))
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)
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# We allow last estimator to be None as an identity transformation
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if (
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estimator is not None
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and estimator != "passthrough"
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and not hasattr(estimator, "fit")
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):
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raise TypeError(
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"Last step of Pipeline should implement fit "
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"or be the string 'passthrough'. "
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"'%s' (type %s) doesn't" % (estimator, type(estimator))
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)
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def _iter(self, with_final=True, filter_passthrough=True):
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"""
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Generate (idx, (name, trans)) tuples from self.steps
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When filter_passthrough is True, 'passthrough' and None transformers
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are filtered out.
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"""
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stop = len(self.steps)
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if not with_final:
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stop -= 1
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for idx, (name, trans) in enumerate(islice(self.steps, 0, stop)):
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if not filter_passthrough:
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yield idx, name, trans
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elif trans is not None and trans != "passthrough":
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yield idx, name, trans
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def __len__(self) -> int:
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"""
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Returns the length of the Pipeline
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"""
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return len(self.steps)
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def __getitem__(self, ind):
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"""Returns a sub-pipeline or a single esimtator in the pipeline
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Indexing with an integer will return an estimator; using a slice
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returns another Pipeline instance which copies a slice of this
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Pipeline. This copy is shallow: modifying (or fitting) estimators in
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the sub-pipeline will affect the larger pipeline and vice-versa.
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However, replacing a value in `step` will not affect a copy.
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"""
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if isinstance(ind, slice):
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if ind.step not in (1, None):
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raise ValueError("Pipeline slicing only supports a step of 1")
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return self.__class__(self.steps[ind])
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try:
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name, est = self.steps[ind]
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except TypeError:
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# Not an int, try get step by name
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return self.named_steps[ind]
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return est
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@property
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def _estimator_type(self):
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return self.steps[-1][1]._estimator_type
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@property
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def named_steps(self):
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return dict(self.steps)
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@property
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def _final_estimator(self):
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estimator = self.steps[-1][1]
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return "passthrough" if estimator is None else estimator
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def _log_message(self, step_idx):
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if not self.verbose:
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return None
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name, step = self.steps[step_idx]
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return "(step %d of %d) Processing %s" % (step_idx + 1, len(self.steps), name)
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# Estimator interface
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def _fit(self, X, y=None, **fit_params):
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# shallow copy of steps - this should really be steps_
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self.steps = list(self.steps)
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self._validate_steps()
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fit_params_steps = {name: {} for name, step in self.steps if step is not None}
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for pname, pval in fit_params.items():
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if "__" not in pname:
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raise ValueError(
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"Pipeline.fit does not accept the {} parameter. "
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"You can pass parameters to specific steps of your "
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"pipeline using the stepname__parameter format, e.g. "
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"`Pipeline.fit(X, y, logisticregression__sample_weight"
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"=sample_weight)`.".format(pname)
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)
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step, param = pname.split("__", 1)
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fit_params_steps[step][param] = pval
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for step_idx, name, transformer in self._iter(
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with_final=False, filter_passthrough=False
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):
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if transformer is None or transformer == "passthrough":
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continue
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# Fit or load from cache the current transformer
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X, fitted_transformer = _fit_transform_one(
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transformer, X, y, None, **fit_params_steps[name]
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)
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# Replace the transformer of the step with the fitted
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# transformer. This is necessary when loading the transformer
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# from the cache.
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self.steps[step_idx] = (name, fitted_transformer)
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if self._final_estimator == "passthrough":
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return X, {}
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return X, fit_params_steps[self.steps[-1][0]]
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def fit(self, X, y=None, **fit_params):
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"""Fit the model
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Fit all the transforms one after the other and transform the
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data, then fit the transformed data using the final estimator.
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Parameters
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----------
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X : iterable
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Training data. Must fulfill input requirements of first step of the
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pipeline.
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y : iterable, default=None
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Training targets. Must fulfill label requirements for all steps of
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the pipeline.
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**fit_params : dict of string -> object
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Parameters passed to the ``fit`` method of each step, where
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each parameter name is prefixed such that parameter ``p`` for step
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``s`` has key ``s__p``.
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Returns
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-------
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self : Pipeline
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This estimator
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"""
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Xt, fit_params = self._fit(X, y, **fit_params)
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if self._final_estimator != "passthrough":
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self._final_estimator.fit(Xt, y, **fit_params)
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return self
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def fit_transform(self, X, y=None, **fit_params):
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"""Fit the model and transform with the final estimator
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Fits all the transforms one after the other and transforms the
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data, then uses fit_transform on transformed data with the final
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estimator.
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Parameters
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----------
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X : iterable
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Training data. Must fulfill input requirements of first step of the
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pipeline.
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y : iterable, default=None
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Training targets. Must fulfill label requirements for all steps of
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the pipeline.
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**fit_params : dict of string -> object
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Parameters passed to the ``fit`` method of each step, where
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each parameter name is prefixed such that parameter ``p`` for step
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``s`` has key ``s__p``.
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Returns
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-------
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Xt : array-like of shape (n_samples, n_transformed_features)
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Transformed samples
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"""
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last_step = self._final_estimator
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Xt, fit_params = self._fit(X, y, **fit_params)
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if last_step == "passthrough":
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return Xt
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if hasattr(last_step, "fit_transform"):
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return last_step.fit_transform(Xt, y, **fit_params)
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else:
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return last_step.fit(Xt, y, **fit_params).transform(Xt)
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@property
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def transform(self):
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"""Apply transforms, and transform with the final estimator
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This also works where final estimator is ``None``: all prior
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transformations are applied.
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Parameters
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----------
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X : iterable
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Data to transform. Must fulfill input requirements of first step
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of the pipeline.
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Returns
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-------
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Xt : array-like of shape (n_samples, n_transformed_features)
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"""
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# _final_estimator is None or has transform, otherwise attribute error
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# XXX: Handling the None case means we can't use if_delegate_has_method
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if self._final_estimator != "passthrough":
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self._final_estimator.transform
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return self._transform
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def _transform(self, X):
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Xt = X
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for _, _, transform in self._iter():
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Xt = transform.transform(Xt)
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return Xt
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@property
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def classes_(self):
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return self.steps[-1][-1].classes_
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@property
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def _pairwise(self):
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# check if first estimator expects pairwise input
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return getattr(self.steps[0][1], "_pairwise", False)
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@property
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def n_features_in_(self):
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# delegate to first step (which will call _check_is_fitted)
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return self.steps[0][1].n_features_in_
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def _name_estimators(estimators):
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"""Generate names for estimators."""
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names = [
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estimator if isinstance(estimator, str) else type(estimator).__name__.lower()
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for estimator in estimators
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]
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namecount = defaultdict(int)
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for est, name in zip(estimators, names):
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namecount[name] += 1
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for k, v in list(namecount.items()):
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if v == 1:
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del namecount[k]
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for i in reversed(range(len(estimators))):
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name = names[i]
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if name in namecount:
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names[i] += "-%d" % namecount[name]
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namecount[name] -= 1
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return list(zip(names, estimators))
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def make_pipeline(*steps, **kwargs) -> Pipeline:
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"""Construct a Pipeline from the given estimators.
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This is a shorthand for the Pipeline constructor; it does not require, and
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does not permit, naming the estimators. Instead, their names will be set
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to the lowercase of their types automatically.
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Parameters
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----------
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*steps : list of estimators.
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verbose : bool, default=False
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If True, the time elapsed while fitting each step will be printed as it
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is completed.
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Returns
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-------
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p : Pipeline
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"""
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verbose = kwargs.pop("verbose", False)
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if kwargs:
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raise TypeError(
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'Unknown keyword arguments: "{}"'.format(list(kwargs.keys())[0])
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)
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return Pipeline(_name_estimators(steps), verbose=verbose)
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def _transform_one(transformer, X, y, weight, **fit_params):
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res = transformer.transform(X)
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# if we have a weight for this transformer, multiply output
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if weight is None:
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return res
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return res * weight
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def _fit_transform_one(transformer, X, y, weight, **fit_params):
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"""
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Fits ``transformer`` to ``X`` and ``y``. The transformed result is returned
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with the fitted transformer. If ``weight`` is not ``None``, the result will
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be multiplied by ``weight``.
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"""
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if hasattr(transformer, "fit_transform"):
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res = transformer.fit_transform(X, y, **fit_params)
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else:
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res = transformer.fit(X, y, **fit_params).transform(X)
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if weight is None:
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return res, transformer
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return res * weight, transformer
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