_discretization.py

# Author: Henry Lin <hlin117@gmail.com>
#         Tom Dupré la Tour

# License: BSD


import numbers
import numpy as np
import warnings

from . import OneHotEncoder

from ..base import BaseEstimator, TransformerMixin
from ..utils.validation import check_array
from ..utils.validation import check_is_fitted
from ..utils.validation import check_random_state
from ..utils.validation import _check_feature_names_in
from ..utils.validation import check_scalar
from ..utils import _safe_indexing


class KBinsDiscretizer(TransformerMixin, BaseEstimator):
    """
    Bin continuous data into intervals.

    Read more in the :ref:`User Guide <preprocessing_discretization>`.

    .. versionadded:: 0.20

    Parameters
    ----------
    n_bins : int or array-like of shape (n_features,), default=5
        The number of bins to produce. Raises ValueError if ``n_bins < 2``.

    encode : {'onehot', 'onehot-dense', 'ordinal'}, default='onehot'
        Method used to encode the transformed result.

        - 'onehot': Encode the transformed result with one-hot encoding
          and return a sparse matrix. Ignored features are always
          stacked to the right.
        - 'onehot-dense': Encode the transformed result with one-hot encoding
          and return a dense array. Ignored features are always
          stacked to the right.
        - 'ordinal': Return the bin identifier encoded as an integer value.

    strategy : {'uniform', 'quantile', 'kmeans'}, default='quantile'
        Strategy used to define the widths of the bins.

        - 'uniform': All bins in each feature have identical widths.
        - 'quantile': All bins in each feature have the same number of points.
        - 'kmeans': Values in each bin have the same nearest center of a 1D
          k-means cluster.

    dtype : {np.float32, np.float64}, default=None
        The desired data-type for the output. If None, output dtype is
        consistent with input dtype. Only np.float32 and np.float64 are
        supported.

        .. versionadded:: 0.24

    subsample : int or None (default='warn')
        Maximum number of samples, used to fit the model, for computational
        efficiency. Used when `strategy="quantile"`.
        `subsample=None` means that all the training samples are used when
        computing the quantiles that determine the binning thresholds.
        Since quantile computation relies on sorting each column of `X` and
        that sorting has an `n log(n)` time complexity,
        it is recommended to use subsampling on datasets with a
        very large number of samples.

        .. deprecated:: 1.1
           In version 1.3 and onwards, `subsample=2e5` will be the default.

    random_state : int, RandomState instance or None, default=None
        Determines random number generation for subsampling.
        Pass an int for reproducible results across multiple function calls.
        See the `subsample` parameter for more details.
        See :term:`Glossary <random_state>`.

        .. versionadded:: 1.1

    Attributes
    ----------
    bin_edges_ : ndarray of ndarray of shape (n_features,)
        The edges of each bin. Contain arrays of varying shapes ``(n_bins_, )``
        Ignored features will have empty arrays.

    n_bins_ : ndarray of shape (n_features,), dtype=np.int_
        Number of bins per feature. Bins whose width are too small
        (i.e., <= 1e-8) are removed with a warning.

    n_features_in_ : int
        Number of features seen during :term:`fit`.

        .. versionadded:: 0.24

    feature_names_in_ : ndarray of shape (`n_features_in_`,)
        Names of features seen during :term:`fit`. Defined only when `X`
        has feature names that are all strings.

        .. versionadded:: 1.0

    See Also
    --------
    Binarizer : Class used to bin values as ``0`` or
        ``1`` based on a parameter ``threshold``.

    Notes
    -----
    In bin edges for feature ``i``, the first and last values are used only for
    ``inverse_transform``. During transform, bin edges are extended to::

      np.concatenate([-np.inf, bin_edges_[i][1:-1], np.inf])

    You can combine ``KBinsDiscretizer`` with
    :class:`~sklearn.compose.ColumnTransformer` if you only want to preprocess
    part of the features.

    ``KBinsDiscretizer`` might produce constant features (e.g., when
    ``encode = 'onehot'`` and certain bins do not contain any data).
    These features can be removed with feature selection algorithms
    (e.g., :class:`~sklearn.feature_selection.VarianceThreshold`).

    Examples
    --------
    >>> from sklearn.preprocessing import KBinsDiscretizer
    >>> X = [[-2, 1, -4,   -1],
    ...      [-1, 2, -3, -0.5],
    ...      [ 0, 3, -2,  0.5],
    ...      [ 1, 4, -1,    2]]
    >>> est = KBinsDiscretizer(n_bins=3, encode='ordinal', strategy='uniform')
    >>> est.fit(X)
    KBinsDiscretizer(...)
    >>> Xt = est.transform(X)
    >>> Xt  # doctest: +SKIP
    array([[ 0., 0., 0., 0.],
           [ 1., 1., 1., 0.],
           [ 2., 2., 2., 1.],
           [ 2., 2., 2., 2.]])

    Sometimes it may be useful to convert the data back into the original
    feature space. The ``inverse_transform`` function converts the binned
    data into the original feature space. Each value will be equal to the mean
    of the two bin edges.

    >>> est.bin_edges_[0]
    array([-2., -1.,  0.,  1.])
    >>> est.inverse_transform(Xt)
    array([[-1.5,  1.5, -3.5, -0.5],
           [-0.5,  2.5, -2.5, -0.5],
           [ 0.5,  3.5, -1.5,  0.5],
           [ 0.5,  3.5, -1.5,  1.5]])
    """

    def __init__(
        self,
        n_bins=5,
        *,
        encode="onehot",
        strategy="quantile",
        dtype=None,
        subsample="warn",
        random_state=None,
    ):
        self.n_bins = n_bins
        self.encode = encode
        self.strategy = strategy
        self.dtype = dtype
        self.subsample = subsample
        self.random_state = random_state

    def fit(self, X, y=None):
        """
        Fit the estimator.

        Parameters
        ----------
        X : array-like of shape (n_samples, n_features)
            Data to be discretized.

        y : None
            Ignored. This parameter exists only for compatibility with
            :class:`~sklearn.pipeline.Pipeline`.

        Returns
        -------
        self : object
            Returns the instance itself.
        """
        X = self._validate_data(X, dtype="numeric")

        supported_dtype = (np.float64, np.float32)
        if self.dtype in supported_dtype:
            output_dtype = self.dtype
        elif self.dtype is None:
            output_dtype = X.dtype
        else:
            raise ValueError(
                "Valid options for 'dtype' are "
                f"{supported_dtype + (None,)}. Got dtype={self.dtype} "
                " instead."
            )

        n_samples, n_features = X.shape

        if self.strategy == "quantile" and self.subsample is not None:
            if self.subsample == "warn":
                if n_samples > 2e5:
                    warnings.warn(
                        "In version 1.3 onwards, subsample=2e5 "
                        "will be used by default. Set subsample explicitly to "
                        "silence this warning in the mean time. Set "
                        "subsample=None to disable subsampling explicitly.",
                        FutureWarning,
                    )
            else:
                self.subsample = check_scalar(
                    self.subsample, "subsample", numbers.Integral, min_val=1
                )
                rng = check_random_state(self.random_state)
                if n_samples > self.subsample:
                    subsample_idx = rng.choice(
                        n_samples, size=self.subsample, replace=False
                    )
                    X = _safe_indexing(X, subsample_idx)
        elif self.strategy != "quantile" and isinstance(
            self.subsample, numbers.Integral
        ):
            raise ValueError(
                f"Invalid parameter for `strategy`: {self.strategy}. "
                '`subsample` must be used with `strategy="quantile"`.'
            )

        valid_encode = ("onehot", "onehot-dense", "ordinal")
        if self.encode not in valid_encode:
            raise ValueError(
                "Valid options for 'encode' are {}. Got encode={!r} instead.".format(
                    valid_encode, self.encode
                )
            )
        valid_strategy = ("uniform", "quantile", "kmeans")
        if self.strategy not in valid_strategy:
            raise ValueError(
                "Valid options for 'strategy' are {}. "
                "Got strategy={!r} instead.".format(valid_strategy, self.strategy)
            )

        n_features = X.shape[1]
        n_bins = self._validate_n_bins(n_features)

        bin_edges = np.zeros(n_features, dtype=object)
        for jj in range(n_features):
            column = X[:, jj]
            col_min, col_max = column.min(), column.max()

            if col_min == col_max:
                warnings.warn(
                    "Feature %d is constant and will be replaced with 0." % jj
                )
                n_bins[jj] = 1
                bin_edges[jj] = np.array([-np.inf, np.inf])
                continue

            if self.strategy == "uniform":
                bin_edges[jj] = np.linspace(col_min, col_max, n_bins[jj] + 1)

            elif self.strategy == "quantile":
                quantiles = np.linspace(0, 100, n_bins[jj] + 1)
                bin_edges[jj] = np.asarray(np.percentile(column, quantiles))

            elif self.strategy == "kmeans":
                from ..cluster import KMeans  # fixes import loops

                # Deterministic initialization with uniform spacing
                uniform_edges = np.linspace(col_min, col_max, n_bins[jj] + 1)
                init = (uniform_edges[1:] + uniform_edges[:-1])[:, None] * 0.5

                # 1D k-means procedure
                km = KMeans(n_clusters=n_bins[jj], init=init, n_init=1)
                centers = km.fit(column[:, None]).cluster_centers_[:, 0]
                # Must sort, centers may be unsorted even with sorted init
                centers.sort()
                bin_edges[jj] = (centers[1:] + centers[:-1]) * 0.5
                bin_edges[jj] = np.r_[col_min, bin_edges[jj], col_max]

            # Remove bins whose width are too small (i.e., <= 1e-8)
            if self.strategy in ("quantile", "kmeans"):
                mask = np.ediff1d(bin_edges[jj], to_begin=np.inf) > 1e-8
                bin_edges[jj] = bin_edges[jj][mask]
                if len(bin_edges[jj]) - 1 != n_bins[jj]:
                    warnings.warn(
                        "Bins whose width are too small (i.e., <= "
                        "1e-8) in feature %d are removed. Consider "
                        "decreasing the number of bins." % jj
                    )
                    n_bins[jj] = len(bin_edges[jj]) - 1

        self.bin_edges_ = bin_edges
        self.n_bins_ = n_bins

        if "onehot" in self.encode:
            self._encoder = OneHotEncoder(
                categories=[np.arange(i) for i in self.n_bins_],
                sparse=self.encode == "onehot",
                dtype=output_dtype,
            )
            # Fit the OneHotEncoder with toy datasets
            # so that it's ready for use after the KBinsDiscretizer is fitted
            self._encoder.fit(np.zeros((1, len(self.n_bins_))))

        return self

    def _validate_n_bins(self, n_features):
        """Returns n_bins_, the number of bins per feature."""
        orig_bins = self.n_bins
        if isinstance(orig_bins, numbers.Number):
            if not isinstance(orig_bins, numbers.Integral):
                raise ValueError(
                    "{} received an invalid n_bins type. "
                    "Received {}, expected int.".format(
                        KBinsDiscretizer.__name__, type(orig_bins).__name__
                    )
                )
            if orig_bins < 2:
                raise ValueError(
                    "{} received an invalid number "
                    "of bins. Received {}, expected at least 2.".format(
                        KBinsDiscretizer.__name__, orig_bins
                    )
                )
            return np.full(n_features, orig_bins, dtype=int)

        n_bins = check_array(orig_bins, dtype=int, copy=True, ensure_2d=False)

        if n_bins.ndim > 1 or n_bins.shape[0] != n_features:
            raise ValueError("n_bins must be a scalar or array of shape (n_features,).")

        bad_nbins_value = (n_bins < 2) | (n_bins != orig_bins)

        violating_indices = np.where(bad_nbins_value)[0]
        if violating_indices.shape[0] > 0:
            indices = ", ".join(str(i) for i in violating_indices)
            raise ValueError(
                "{} received an invalid number "
                "of bins at indices {}. Number of bins "
                "must be at least 2, and must be an int.".format(
                    KBinsDiscretizer.__name__, indices
                )
            )
        return n_bins

    def transform(self, X):
        """
        Discretize the data.

        Parameters
        ----------
        X : array-like of shape (n_samples, n_features)
            Data to be discretized.

        Returns
        -------
        Xt : {ndarray, sparse matrix}, dtype={np.float32, np.float64}
            Data in the binned space. Will be a sparse matrix if
            `self.encode='onehot'` and ndarray otherwise.
        """
        check_is_fitted(self)

        # check input and attribute dtypes
        dtype = (np.float64, np.float32) if self.dtype is None else self.dtype
        Xt = self._validate_data(X, copy=True, dtype=dtype, reset=False)

        bin_edges = self.bin_edges_
        for jj in range(Xt.shape[1]):
            Xt[:, jj] = np.searchsorted(bin_edges[jj][1:-1], Xt[:, jj], side="right")

        if self.encode == "ordinal":
            return Xt

        dtype_init = None
        if "onehot" in self.encode:
            dtype_init = self._encoder.dtype
            self._encoder.dtype = Xt.dtype
        try:
            Xt_enc = self._encoder.transform(Xt)
        finally:
            # revert the initial dtype to avoid modifying self.
            self._encoder.dtype = dtype_init
        return Xt_enc

    def inverse_transform(self, Xt):
        """
        Transform discretized data back to original feature space.

        Note that this function does not regenerate the original data
        due to discretization rounding.

        Parameters
        ----------
        Xt : array-like of shape (n_samples, n_features)
            Transformed data in the binned space.

        Returns
        -------
        Xinv : ndarray, dtype={np.float32, np.float64}
            Data in the original feature space.
        """
        check_is_fitted(self)

        if "onehot" in self.encode:
            Xt = self._encoder.inverse_transform(Xt)

        Xinv = check_array(Xt, copy=True, dtype=(np.float64, np.float32))
        n_features = self.n_bins_.shape[0]
        if Xinv.shape[1] != n_features:
            raise ValueError(
                "Incorrect number of features. Expecting {}, received {}.".format(
                    n_features, Xinv.shape[1]
                )
            )

        for jj in range(n_features):
            bin_edges = self.bin_edges_[jj]
            bin_centers = (bin_edges[1:] + bin_edges[:-1]) * 0.5
            Xinv[:, jj] = bin_centers[np.int_(Xinv[:, jj])]

        return Xinv

    def get_feature_names_out(self, input_features=None):
        """Get output feature names.

        Parameters
        ----------
        input_features : array-like of str or None, default=None
            Input features.

            - If `input_features` is `None`, then `feature_names_in_` is
              used as feature names in. If `feature_names_in_` is not defined,
              then the following input feature names are generated:
              `["x0", "x1", ..., "x(n_features_in_ - 1)"]`.
            - If `input_features` is an array-like, then `input_features` must
              match `feature_names_in_` if `feature_names_in_` is defined.

        Returns
        -------
        feature_names_out : ndarray of str objects
            Transformed feature names.
        """
        input_features = _check_feature_names_in(self, input_features)
        if hasattr(self, "_encoder"):
            return self._encoder.get_feature_names_out(input_features)

        # ordinal encoding
        return input_features