kde.py

#-------------------------------------------------------------------------------
#
#  Define classes for (uni/multi)-variate kernel density estimation.
#
#  Currently, only Gaussian kernels are implemented.
#
#  Written by: Robert Kern
#
#  Date: 2004-08-09
#
#  Modified: 2005-02-10 by Robert Kern.
#              Contributed to Scipy
#            2005-10-07 by Robert Kern.
#              Some fixes to match the new scipy_core
#
#  Copyright 2004-2005 by Enthought, Inc.
#
#-------------------------------------------------------------------------------

from __future__ import division, print_function, absolute_import

# Standard library imports.
import warnings

# Scipy imports.
from scipy._lib.six import callable, string_types
from scipy import linalg, special
from scipy.special import logsumexp

from numpy import atleast_2d, reshape, zeros, newaxis, dot, exp, pi, sqrt, \
     ravel, power, atleast_1d, squeeze, sum, transpose
import numpy as np
from numpy.random import randint, multivariate_normal

# Local imports.
from . import mvn


__all__ = ['gaussian_kde']


class gaussian_kde(object):
    """Representation of a kernel-density estimate using Gaussian kernels.

    Kernel density estimation is a way to estimate the probability density
    function (PDF) of a random variable in a non-parametric way.
    `gaussian_kde` works for both uni-variate and multi-variate data.   It
    includes automatic bandwidth determination.  The estimation works best for
    a unimodal distribution; bimodal or multi-modal distributions tend to be
    oversmoothed.

    Parameters
    ----------
    dataset : array_like
        Datapoints to estimate from. In case of univariate data this is a 1-D
        array, otherwise a 2-D array with shape (# of dims, # of data).
    bw_method : str, scalar or callable, optional
        The method used to calculate the estimator bandwidth.  This can be
        'scott', 'silverman', a scalar constant or a callable.  If a scalar,
        this will be used directly as `kde.factor`.  If a callable, it should
        take a `gaussian_kde` instance as only parameter and return a scalar.
        If None (default), 'scott' is used.  See Notes for more details.

    Attributes
    ----------
    dataset : ndarray
        The dataset with which `gaussian_kde` was initialized.
    d : int
        Number of dimensions.
    n : int
        Number of datapoints.
    factor : float
        The bandwidth factor, obtained from `kde.covariance_factor`, with which
        the covariance matrix is multiplied.
    covariance : ndarray
        The covariance matrix of `dataset`, scaled by the calculated bandwidth
        (`kde.factor`).
    inv_cov : ndarray
        The inverse of `covariance`.

    Methods
    -------
    evaluate
    __call__
    integrate_gaussian
    integrate_box_1d
    integrate_box
    integrate_kde
    pdf
    logpdf
    resample
    set_bandwidth
    covariance_factor

    Notes
    -----
    Bandwidth selection strongly influences the estimate obtained from the KDE
    (much more so than the actual shape of the kernel).  Bandwidth selection
    can be done by a "rule of thumb", by cross-validation, by "plug-in
    methods" or by other means; see [3]_, [4]_ for reviews.  `gaussian_kde`
    uses a rule of thumb, the default is Scott's Rule.

    Scott's Rule [1]_, implemented as `scotts_factor`, is::

        n**(-1./(d+4)),

    with ``n`` the number of data points and ``d`` the number of dimensions.
    Silverman's Rule [2]_, implemented as `silverman_factor`, is::

        (n * (d + 2) / 4.)**(-1. / (d + 4)).

    Good general descriptions of kernel density estimation can be found in [1]_
    and [2]_, the mathematics for this multi-dimensional implementation can be
    found in [1]_.

    References
    ----------
    .. [1] D.W. Scott, "Multivariate Density Estimation: Theory, Practice, and
           Visualization", John Wiley & Sons, New York, Chicester, 1992.
    .. [2] B.W. Silverman, "Density Estimation for Statistics and Data
           Analysis", Vol. 26, Monographs on Statistics and Applied Probability,
           Chapman and Hall, London, 1986.
    .. [3] B.A. Turlach, "Bandwidth Selection in Kernel Density Estimation: A
           Review", CORE and Institut de Statistique, Vol. 19, pp. 1-33, 1993.
    .. [4] D.M. Bashtannyk and R.J. Hyndman, "Bandwidth selection for kernel
           conditional density estimation", Computational Statistics & Data
           Analysis, Vol. 36, pp. 279-298, 2001.

    Examples
    --------
    Generate some random two-dimensional data:

    >>> from scipy import stats
    >>> def measure(n):
    ...     "Measurement model, return two coupled measurements."
    ...     m1 = np.random.normal(size=n)
    ...     m2 = np.random.normal(scale=0.5, size=n)
    ...     return m1+m2, m1-m2

    >>> m1, m2 = measure(2000)
    >>> xmin = m1.min()
    >>> xmax = m1.max()
    >>> ymin = m2.min()
    >>> ymax = m2.max()

    Perform a kernel density estimate on the data:

    >>> X, Y = np.mgrid[xmin:xmax:100j, ymin:ymax:100j]
    >>> positions = np.vstack([X.ravel(), Y.ravel()])
    >>> values = np.vstack([m1, m2])
    >>> kernel = stats.gaussian_kde(values)
    >>> Z = np.reshape(kernel(positions).T, X.shape)

    Plot the results:

    >>> import matplotlib.pyplot as plt
    >>> fig, ax = plt.subplots()
    >>> ax.imshow(np.rot90(Z), cmap=plt.cm.gist_earth_r,
    ...           extent=[xmin, xmax, ymin, ymax])
    >>> ax.plot(m1, m2, 'k.', markersize=2)
    >>> ax.set_xlim([xmin, xmax])
    >>> ax.set_ylim([ymin, ymax])
    >>> plt.show()

    """
    def __init__(self, dataset, bw_method=None):
        self.dataset = atleast_2d(dataset)
        if not self.dataset.size > 1:
            raise ValueError("`dataset` input should have multiple elements.")

        self.d, self.n = self.dataset.shape
        self.set_bandwidth(bw_method=bw_method)

    def evaluate(self, points):
        """Evaluate the estimated pdf on a set of points.

        Parameters
        ----------
        points : (# of dimensions, # of points)-array
            Alternatively, a (# of dimensions,) vector can be passed in and
            treated as a single point.

        Returns
        -------
        values : (# of points,)-array
            The values at each point.

        Raises
        ------
        ValueError : if the dimensionality of the input points is different than
                     the dimensionality of the KDE.

        """
        points = atleast_2d(points)

        d, m = points.shape
        if d != self.d:
            if d == 1 and m == self.d:
                # points was passed in as a row vector
                points = reshape(points, (self.d, 1))
                m = 1
            else:
                msg = "points have dimension %s, dataset has dimension %s" % (d,
                    self.d)
                raise ValueError(msg)

        result = zeros((m,), dtype=float)

        if m >= self.n:
            # there are more points than data, so loop over data
            for i in range(self.n):
                diff = self.dataset[:, i, newaxis] - points
                tdiff = dot(self.inv_cov, diff)
                energy = sum(diff*tdiff,axis=0) / 2.0
                result = result + exp(-energy)
        else:
            # loop over points
            for i in range(m):
                diff = self.dataset - points[:, i, newaxis]
                tdiff = dot(self.inv_cov, diff)
                energy = sum(diff * tdiff, axis=0) / 2.0
                result[i] = sum(exp(-energy), axis=0)

        result = result / self._norm_factor

        return result

    __call__ = evaluate

    def integrate_gaussian(self, mean, cov):
        """
        Multiply estimated density by a multivariate Gaussian and integrate
        over the whole space.

        Parameters
        ----------
        mean : aray_like
            A 1-D array, specifying the mean of the Gaussian.
        cov : array_like
            A 2-D array, specifying the covariance matrix of the Gaussian.

        Returns
        -------
        result : scalar
            The value of the integral.

        Raises
        ------
        ValueError
            If the mean or covariance of the input Gaussian differs from
            the KDE's dimensionality.

        """
        mean = atleast_1d(squeeze(mean))
        cov = atleast_2d(cov)

        if mean.shape != (self.d,):
            raise ValueError("mean does not have dimension %s" % self.d)
        if cov.shape != (self.d, self.d):
            raise ValueError("covariance does not have dimension %s" % self.d)

        # make mean a column vector
        mean = mean[:, newaxis]

        sum_cov = self.covariance + cov

        # This will raise LinAlgError if the new cov matrix is not s.p.d
        # cho_factor returns (ndarray, bool) where bool is a flag for whether
        # or not ndarray is upper or lower triangular
        sum_cov_chol = linalg.cho_factor(sum_cov)

        diff = self.dataset - mean
        tdiff = linalg.cho_solve(sum_cov_chol, diff)

        sqrt_det = np.prod(np.diagonal(sum_cov_chol[0]))
        norm_const = power(2 * pi, sum_cov.shape[0] / 2.0) * sqrt_det

        energies = sum(diff * tdiff, axis=0) / 2.0
        result = sum(exp(-energies), axis=0) / norm_const / self.n

        return result

    def integrate_box_1d(self, low, high):
        """
        Computes the integral of a 1D pdf between two bounds.

        Parameters
        ----------
        low : scalar
            Lower bound of integration.
        high : scalar
            Upper bound of integration.

        Returns
        -------
        value : scalar
            The result of the integral.

        Raises
        ------
        ValueError
            If the KDE is over more than one dimension.

        """
        if self.d != 1:
            raise ValueError("integrate_box_1d() only handles 1D pdfs")

        stdev = ravel(sqrt(self.covariance))[0]

        normalized_low = ravel((low - self.dataset) / stdev)
        normalized_high = ravel((high - self.dataset) / stdev)

        value = np.mean(special.ndtr(normalized_high) -
                        special.ndtr(normalized_low))
        return value

    def integrate_box(self, low_bounds, high_bounds, maxpts=None):
        """Computes the integral of a pdf over a rectangular interval.

        Parameters
        ----------
        low_bounds : array_like
            A 1-D array containing the lower bounds of integration.
        high_bounds : array_like
            A 1-D array containing the upper bounds of integration.
        maxpts : int, optional
            The maximum number of points to use for integration.

        Returns
        -------
        value : scalar
            The result of the integral.

        """
        if maxpts is not None:
            extra_kwds = {'maxpts': maxpts}
        else:
            extra_kwds = {}

        value, inform = mvn.mvnun(low_bounds, high_bounds, self.dataset,
                                  self.covariance, **extra_kwds)
        if inform:
            msg = ('An integral in mvn.mvnun requires more points than %s' %
                   (self.d * 1000))
            warnings.warn(msg)

        return value

    def integrate_kde(self, other):
        """
        Computes the integral of the product of this  kernel density estimate
        with another.

        Parameters
        ----------
        other : gaussian_kde instance
            The other kde.

        Returns
        -------
        value : scalar
            The result of the integral.

        Raises
        ------
        ValueError
            If the KDEs have different dimensionality.

        """
        if other.d != self.d:
            raise ValueError("KDEs are not the same dimensionality")

        # we want to iterate over the smallest number of points
        if other.n < self.n:
            small = other
            large = self
        else:
            small = self
            large = other

        sum_cov = small.covariance + large.covariance
        sum_cov_chol = linalg.cho_factor(sum_cov)
        result = 0.0
        for i in range(small.n):
            mean = small.dataset[:, i, newaxis]
            diff = large.dataset - mean
            tdiff = linalg.cho_solve(sum_cov_chol, diff)

            energies = sum(diff * tdiff, axis=0) / 2.0
            result += sum(exp(-energies), axis=0)

        sqrt_det = np.prod(np.diagonal(sum_cov_chol[0]))
        norm_const = power(2 * pi, sum_cov.shape[0] / 2.0) * sqrt_det

        result /= norm_const * large.n * small.n

        return result

    def resample(self, size=None):
        """
        Randomly sample a dataset from the estimated pdf.

        Parameters
        ----------
        size : int, optional
            The number of samples to draw.  If not provided, then the size is
            the same as the underlying dataset.

        Returns
        -------
        resample : (self.d, `size`) ndarray
            The sampled dataset.

        """
        if size is None:
            size = self.n

        norm = transpose(multivariate_normal(zeros((self.d,), float),
                         self.covariance, size=size))
        indices = randint(0, self.n, size=size)
        means = self.dataset[:, indices]

        return means + norm

    def scotts_factor(self):
        return power(self.n, -1./(self.d+4))

    def silverman_factor(self):
        return power(self.n*(self.d+2.0)/4.0, -1./(self.d+4))

    #  Default method to calculate bandwidth, can be overwritten by subclass
    covariance_factor = scotts_factor
    covariance_factor.__doc__ = """Computes the coefficient (`kde.factor`) that
        multiplies the data covariance matrix to obtain the kernel covariance
        matrix. The default is `scotts_factor`.  A subclass can overwrite this
        method to provide a different method, or set it through a call to
        `kde.set_bandwidth`."""

    def set_bandwidth(self, bw_method=None):
        """Compute the estimator bandwidth with given method.

        The new bandwidth calculated after a call to `set_bandwidth` is used
        for subsequent evaluations of the estimated density.

        Parameters
        ----------
        bw_method : str, scalar or callable, optional
            The method used to calculate the estimator bandwidth.  This can be
            'scott', 'silverman', a scalar constant or a callable.  If a
            scalar, this will be used directly as `kde.factor`.  If a callable,
            it should take a `gaussian_kde` instance as only parameter and
            return a scalar.  If None (default), nothing happens; the current
            `kde.covariance_factor` method is kept.

        Notes
        -----
        .. versionadded:: 0.11

        Examples
        --------
        >>> import scipy.stats as stats
        >>> x1 = np.array([-7, -5, 1, 4, 5.])
        >>> kde = stats.gaussian_kde(x1)
        >>> xs = np.linspace(-10, 10, num=50)
        >>> y1 = kde(xs)
        >>> kde.set_bandwidth(bw_method='silverman')
        >>> y2 = kde(xs)
        >>> kde.set_bandwidth(bw_method=kde.factor / 3.)
        >>> y3 = kde(xs)

        >>> import matplotlib.pyplot as plt
        >>> fig, ax = plt.subplots()
        >>> ax.plot(x1, np.ones(x1.shape) / (4. * x1.size), 'bo',
        ...         label='Data points (rescaled)')
        >>> ax.plot(xs, y1, label='Scott (default)')
        >>> ax.plot(xs, y2, label='Silverman')
        >>> ax.plot(xs, y3, label='Const (1/3 * Silverman)')
        >>> ax.legend()
        >>> plt.show()

        """
        if bw_method is None:
            pass
        elif bw_method == 'scott':
            self.covariance_factor = self.scotts_factor
        elif bw_method == 'silverman':
            self.covariance_factor = self.silverman_factor
        elif np.isscalar(bw_method) and not isinstance(bw_method, string_types):
            self._bw_method = 'use constant'
            self.covariance_factor = lambda: bw_method
        elif callable(bw_method):
            self._bw_method = bw_method
            self.covariance_factor = lambda: self._bw_method(self)
        else:
            msg = "`bw_method` should be 'scott', 'silverman', a scalar " \
                  "or a callable."
            raise ValueError(msg)

        self._compute_covariance()

    def _compute_covariance(self):
        """Computes the covariance matrix for each Gaussian kernel using
        covariance_factor().
        """
        self.factor = self.covariance_factor()
        # Cache covariance and inverse covariance of the data
        if not hasattr(self, '_data_inv_cov'):
            self._data_covariance = atleast_2d(np.cov(self.dataset, rowvar=1,
                                               bias=False))
            self._data_inv_cov = linalg.inv(self._data_covariance)

        self.covariance = self._data_covariance * self.factor**2
        self.inv_cov = self._data_inv_cov / self.factor**2
        self._norm_factor = sqrt(linalg.det(2*pi*self.covariance)) * self.n

    def pdf(self, x):
        """
        Evaluate the estimated pdf on a provided set of points.

        Notes
        -----
        This is an alias for `gaussian_kde.evaluate`.  See the ``evaluate``
        docstring for more details.

        """
        return self.evaluate(x)

    def logpdf(self, x):
        """
        Evaluate the log of the estimated pdf on a provided set of points.
        """

        points = atleast_2d(x)

        d, m = points.shape
        if d != self.d:
            if d == 1 and m == self.d:
                # points was passed in as a row vector
                points = reshape(points, (self.d, 1))
                m = 1
            else:
                msg = "points have dimension %s, dataset has dimension %s" % (d,
                    self.d)
                raise ValueError(msg)

        result = zeros((m,), dtype=float)

        if m >= self.n:
            # there are more points than data, so loop over data
            energy = zeros((self.n, m), dtype=float)
            for i in range(self.n):
                diff = self.dataset[:, i, newaxis] - points
                tdiff = dot(self.inv_cov, diff)
                energy[i] = sum(diff*tdiff,axis=0) / 2.0
            result = logsumexp(-energy, b=1/self._norm_factor, axis=0)
        else:
            # loop over points
            for i in range(m):
                diff = self.dataset - points[:, i, newaxis]
                tdiff = dot(self.inv_cov, diff)
                energy = sum(diff * tdiff, axis=0) / 2.0
                result[i] = logsumexp(-energy, b=1/self._norm_factor)

        return result