validation.py

"""Utilities for input validation"""

# Authors: Olivier Grisel
#          Gael Varoquaux
#          Andreas Mueller
#          Lars Buitinck
#          Alexandre Gramfort
#          Nicolas Tresegnie
# License: BSD 3 clause

import warnings
import numbers

import numpy as np
import scipy.sparse as sp
from numpy.core.numeric import ComplexWarning

from ..externals import six
from ..utils.fixes import signature
from .. import get_config as _get_config
from ..exceptions import NonBLASDotWarning
from ..exceptions import NotFittedError
from ..exceptions import DataConversionWarning
from ..externals.joblib import Memory


FLOAT_DTYPES = (np.float64, np.float32, np.float16)

# Silenced by default to reduce verbosity. Turn on at runtime for
# performance profiling.
warnings.simplefilter('ignore', NonBLASDotWarning)


def _assert_all_finite(X, allow_nan=False):
    """Like assert_all_finite, but only for ndarray."""
    if _get_config()['assume_finite']:
        return
    X = np.asanyarray(X)
    # First try an O(n) time, O(1) space solution for the common case that
    # everything is finite; fall back to O(n) space np.isfinite to prevent
    # false positives from overflow in sum method.
    is_float = X.dtype.kind in 'fc'
    if is_float and np.isfinite(X.sum()):
        pass
    elif is_float:
        msg_err = "Input contains {} or a value too large for {!r}."
        if (allow_nan and np.isinf(X).any() or
                not allow_nan and not np.isfinite(X).all()):
            type_err = 'infinity' if allow_nan else 'NaN, infinity'
            raise ValueError(msg_err.format(type_err, X.dtype))


def assert_all_finite(X, allow_nan=False):
    """Throw a ValueError if X contains NaN or infinity.

    Parameters
    ----------
    X : array or sparse matrix

    allow_nan : bool
    """
    _assert_all_finite(X.data if sp.issparse(X) else X, allow_nan)


def as_float_array(X, copy=True, force_all_finite=True):
    """Converts an array-like to an array of floats.

    The new dtype will be np.float32 or np.float64, depending on the original
    type. The function can create a copy or modify the argument depending
    on the argument copy.

    Parameters
    ----------
    X : {array-like, sparse matrix}

    copy : bool, optional
        If True, a copy of X will be created. If False, a copy may still be
        returned if X's dtype is not a floating point type.

    force_all_finite : boolean or 'allow-nan', (default=True)
        Whether to raise an error on np.inf and np.nan in X. The possibilities
        are:

        - True: Force all values of X to be finite.
        - False: accept both np.inf and np.nan in X.
        - 'allow-nan':  accept  only  np.nan  values in  X.  Values  cannot  be
          infinite.

        .. versionadded:: 0.20
           ``force_all_finite`` accepts the string ``'allow-nan'``.

    Returns
    -------
    XT : {array, sparse matrix}
        An array of type np.float
    """
    if isinstance(X, np.matrix) or (not isinstance(X, np.ndarray)
                                    and not sp.issparse(X)):
        return check_array(X, ['csr', 'csc', 'coo'], dtype=np.float64,
                           copy=copy, force_all_finite=force_all_finite,
                           ensure_2d=False)
    elif sp.issparse(X) and X.dtype in [np.float32, np.float64]:
        return X.copy() if copy else X
    elif X.dtype in [np.float32, np.float64]:  # is numpy array
        return X.copy('F' if X.flags['F_CONTIGUOUS'] else 'C') if copy else X
    else:
        if X.dtype.kind in 'uib' and X.dtype.itemsize <= 4:
            return_dtype = np.float32
        else:
            return_dtype = np.float64
        return X.astype(return_dtype)


def _is_arraylike(x):
    """Returns whether the input is array-like"""
    return (hasattr(x, '__len__') or
            hasattr(x, 'shape') or
            hasattr(x, '__array__'))


def _num_samples(x):
    """Return number of samples in array-like x."""
    if hasattr(x, 'fit') and callable(x.fit):
        # Don't get num_samples from an ensembles length!
        raise TypeError('Expected sequence or array-like, got '
                        'estimator %s' % x)
    if not hasattr(x, '__len__') and not hasattr(x, 'shape'):
        if hasattr(x, '__array__'):
            x = np.asarray(x)
        else:
            raise TypeError("Expected sequence or array-like, got %s" %
                            type(x))
    if hasattr(x, 'shape'):
        if len(x.shape) == 0:
            raise TypeError("Singleton array %r cannot be considered"
                            " a valid collection." % x)
        return x.shape[0]
    else:
        return len(x)


def _shape_repr(shape):
    """Return a platform independent representation of an array shape

    Under Python 2, the `long` type introduces an 'L' suffix when using the
    default %r format for tuples of integers (typically used to store the shape
    of an array).

    Under Windows 64 bit (and Python 2), the `long` type is used by default
    in numpy shapes even when the integer dimensions are well below 32 bit.
    The platform specific type causes string messages or doctests to change
    from one platform to another which is not desirable.

    Under Python 3, there is no more `long` type so the `L` suffix is never
    introduced in string representation.

    >>> _shape_repr((1, 2))
    '(1, 2)'
    >>> one = 2 ** 64 / 2 ** 64  # force an upcast to `long` under Python 2
    >>> _shape_repr((one, 2 * one))
    '(1, 2)'
    >>> _shape_repr((1,))
    '(1,)'
    >>> _shape_repr(())
    '()'
    """
    if len(shape) == 0:
        return "()"
    joined = ", ".join("%d" % e for e in shape)
    if len(shape) == 1:
        # special notation for singleton tuples
        joined += ','
    return "(%s)" % joined


def check_memory(memory):
    """Check that ``memory`` is joblib.Memory-like.

    joblib.Memory-like means that ``memory`` can be converted into a
    sklearn.externals.joblib.Memory instance (typically a str denoting the
    ``cachedir``) or has the same interface (has a ``cache`` method).

    Parameters
    ----------
    memory : None, str or object with the joblib.Memory interface

    Returns
    -------
    memory : object with the joblib.Memory interface

    Raises
    ------
    ValueError
        If ``memory`` is not joblib.Memory-like.
    """

    if memory is None or isinstance(memory, six.string_types):
        memory = Memory(cachedir=memory, verbose=0)
    elif not hasattr(memory, 'cache'):
        raise ValueError("'memory' should be None, a string or have the same"
                         " interface as sklearn.externals.joblib.Memory."
                         " Got memory='{}' instead.".format(memory))
    return memory


def check_consistent_length(*arrays):
    """Check that all arrays have consistent first dimensions.

    Checks whether all objects in arrays have the same shape or length.

    Parameters
    ----------
    *arrays : list or tuple of input objects.
        Objects that will be checked for consistent length.
    """

    lengths = [_num_samples(X) for X in arrays if X is not None]
    uniques = np.unique(lengths)
    if len(uniques) > 1:
        raise ValueError("Found input variables with inconsistent numbers of"
                         " samples: %r" % [int(l) for l in lengths])


def indexable(*iterables):
    """Make arrays indexable for cross-validation.

    Checks consistent length, passes through None, and ensures that everything
    can be indexed by converting sparse matrices to csr and converting
    non-interable objects to arrays.

    Parameters
    ----------
    *iterables : lists, dataframes, arrays, sparse matrices
        List of objects to ensure sliceability.
    """
    result = []
    for X in iterables:
        if sp.issparse(X):
            result.append(X.tocsr())
        elif hasattr(X, "__getitem__") or hasattr(X, "iloc"):
            result.append(X)
        elif X is None:
            result.append(X)
        else:
            result.append(np.array(X))
    check_consistent_length(*result)
    return result


def _ensure_sparse_format(spmatrix, accept_sparse, dtype, copy,
                          force_all_finite):
    """Convert a sparse matrix to a given format.

    Checks the sparse format of spmatrix and converts if necessary.

    Parameters
    ----------
    spmatrix : scipy sparse matrix
        Input to validate and convert.

    accept_sparse : string, boolean or list/tuple of strings
        String[s] representing allowed sparse matrix formats ('csc',
        'csr', 'coo', 'dok', 'bsr', 'lil', 'dia'). If the input is sparse but
        not in the allowed format, it will be converted to the first listed
        format. True allows the input to be any format. False means
        that a sparse matrix input will raise an error.

    dtype : string, type or None
        Data type of result. If None, the dtype of the input is preserved.

    copy : boolean
        Whether a forced copy will be triggered. If copy=False, a copy might
        be triggered by a conversion.

    force_all_finite : boolean or 'allow-nan', (default=True)
        Whether to raise an error on np.inf and np.nan in X. The possibilities
        are:

        - True: Force all values of X to be finite.
        - False: accept both np.inf and np.nan in X.
        - 'allow-nan':  accept  only  np.nan  values in  X.  Values  cannot  be
          infinite.

        .. versionadded:: 0.20
           ``force_all_finite`` accepts the string ``'allow-nan'``.

    Returns
    -------
    spmatrix_converted : scipy sparse matrix.
        Matrix that is ensured to have an allowed type.
    """
    if dtype is None:
        dtype = spmatrix.dtype

    changed_format = False

    if isinstance(accept_sparse, six.string_types):
        accept_sparse = [accept_sparse]

    if accept_sparse is False:
        raise TypeError('A sparse matrix was passed, but dense '
                        'data is required. Use X.toarray() to '
                        'convert to a dense numpy array.')
    elif isinstance(accept_sparse, (list, tuple)):
        if len(accept_sparse) == 0:
            raise ValueError("When providing 'accept_sparse' "
                             "as a tuple or list, it must contain at "
                             "least one string value.")
        # ensure correct sparse format
        if spmatrix.format not in accept_sparse:
            # create new with correct sparse
            spmatrix = spmatrix.asformat(accept_sparse[0])
            changed_format = True
    elif accept_sparse is not True:
        # any other type
        raise ValueError("Parameter 'accept_sparse' should be a string, "
                         "boolean or list of strings. You provided "
                         "'accept_sparse={}'.".format(accept_sparse))

    if dtype != spmatrix.dtype:
        # convert dtype
        spmatrix = spmatrix.astype(dtype)
    elif copy and not changed_format:
        # force copy
        spmatrix = spmatrix.copy()

    if force_all_finite:
        if not hasattr(spmatrix, "data"):
            warnings.warn("Can't check %s sparse matrix for nan or inf."
                          % spmatrix.format)
        else:
            _assert_all_finite(spmatrix.data,
                               allow_nan=force_all_finite == 'allow-nan')

    return spmatrix


def _ensure_no_complex_data(array):
    if hasattr(array, 'dtype') and array.dtype is not None \
            and hasattr(array.dtype, 'kind') and array.dtype.kind == "c":
        raise ValueError("Complex data not supported\n"
                         "{}\n".format(array))


def check_array(array, accept_sparse=False, dtype="numeric", order=None,
                copy=False, force_all_finite=True, ensure_2d=True,
                allow_nd=False, ensure_min_samples=1, ensure_min_features=1,
                warn_on_dtype=False, estimator=None):
    """Input validation on an array, list, sparse matrix or similar.

    By default, the input is converted to an at least 2D numpy array.
    If the dtype of the array is object, attempt converting to float,
    raising on failure.

    Parameters
    ----------
    array : object
        Input object to check / convert.

    accept_sparse : string, boolean or list/tuple of strings (default=False)
        String[s] representing allowed sparse matrix formats, such as 'csc',
        'csr', etc. If the input is sparse but not in the allowed format,
        it will be converted to the first listed format. True allows the input
        to be any format. False means that a sparse matrix input will
        raise an error.

        .. deprecated:: 0.19
           Passing 'None' to parameter ``accept_sparse`` in methods is
           deprecated in version 0.19 "and will be removed in 0.21. Use
           ``accept_sparse=False`` instead.

    dtype : string, type, list of types or None (default="numeric")
        Data type of result. If None, the dtype of the input is preserved.
        If "numeric", dtype is preserved unless array.dtype is object.
        If dtype is a list of types, conversion on the first type is only
        performed if the dtype of the input is not in the list.

    order : 'F', 'C' or None (default=None)
        Whether an array will be forced to be fortran or c-style.
        When order is None (default), then if copy=False, nothing is ensured
        about the memory layout of the output array; otherwise (copy=True)
        the memory layout of the returned array is kept as close as possible
        to the original array.

    copy : boolean (default=False)
        Whether a forced copy will be triggered. If copy=False, a copy might
        be triggered by a conversion.

    force_all_finite : boolean or 'allow-nan', (default=True)
        Whether to raise an error on np.inf and np.nan in X. The possibilities
        are:

        - True: Force all values of X to be finite.
        - False: accept both np.inf and np.nan in X.
        - 'allow-nan':  accept  only  np.nan  values in  X.  Values  cannot  be
          infinite.

        .. versionadded:: 0.20
           ``force_all_finite`` accepts the string ``'allow-nan'``.

    ensure_2d : boolean (default=True)
        Whether to raise a value error if X is not 2d.

    allow_nd : boolean (default=False)
        Whether to allow X.ndim > 2.

    ensure_min_samples : int (default=1)
        Make sure that the array has a minimum number of samples in its first
        axis (rows for a 2D array). Setting to 0 disables this check.

    ensure_min_features : int (default=1)
        Make sure that the 2D array has some minimum number of features
        (columns). The default value of 1 rejects empty datasets.
        This check is only enforced when the input data has effectively 2
        dimensions or is originally 1D and ``ensure_2d`` is True. Setting to 0
        disables this check.

    warn_on_dtype : boolean (default=False)
        Raise DataConversionWarning if the dtype of the input data structure
        does not match the requested dtype, causing a memory copy.

    estimator : str or estimator instance (default=None)
        If passed, include the name of the estimator in warning messages.

    Returns
    -------
    X_converted : object
        The converted and validated X.

    """
    # accept_sparse 'None' deprecation check
    if accept_sparse is None:
        warnings.warn(
            "Passing 'None' to parameter 'accept_sparse' in methods "
            "check_array and check_X_y is deprecated in version 0.19 "
            "and will be removed in 0.21. Use 'accept_sparse=False' "
            " instead.", DeprecationWarning)
        accept_sparse = False

    # store whether originally we wanted numeric dtype
    dtype_numeric = isinstance(dtype, six.string_types) and dtype == "numeric"

    dtype_orig = getattr(array, "dtype", None)
    if not hasattr(dtype_orig, 'kind'):
        # not a data type (e.g. a column named dtype in a pandas DataFrame)
        dtype_orig = None

    if dtype_numeric:
        if dtype_orig is not None and dtype_orig.kind == "O":
            # if input is object, convert to float.
            dtype = np.float64
        else:
            dtype = None

    if isinstance(dtype, (list, tuple)):
        if dtype_orig is not None and dtype_orig in dtype:
            # no dtype conversion required
            dtype = None
        else:
            # dtype conversion required. Let's select the first element of the
            # list of accepted types.
            dtype = dtype[0]

    if force_all_finite not in (True, False, 'allow-nan'):
        raise ValueError('force_all_finite should be a bool or "allow-nan"'
                         '. Got {!r} instead'.format(force_all_finite))

    if estimator is not None:
        if isinstance(estimator, six.string_types):
            estimator_name = estimator
        else:
            estimator_name = estimator.__class__.__name__
    else:
        estimator_name = "Estimator"
    context = " by %s" % estimator_name if estimator is not None else ""

    if sp.issparse(array):
        _ensure_no_complex_data(array)
        array = _ensure_sparse_format(array, accept_sparse, dtype, copy,
                                      force_all_finite)
    else:
        # If np.array(..) gives ComplexWarning, then we convert the warning
        # to an error. This is needed because specifying a non complex
        # dtype to the function converts complex to real dtype,
        # thereby passing the test made in the lines following the scope
        # of warnings context manager.
        with warnings.catch_warnings():
            try:
                warnings.simplefilter('error', ComplexWarning)
                array = np.array(array, dtype=dtype, order=order, copy=copy)
            except ComplexWarning:
                raise ValueError("Complex data not supported\n"
                                 "{}\n".format(array))

        # It is possible that the np.array(..) gave no warning. This happens
        # when no dtype conversion happend, for example dtype = None. The
        # result is that np.array(..) produces an array of complex dtype
        # and we need to catch and raise exception for such cases.
        _ensure_no_complex_data(array)

        if ensure_2d:
            # If input is scalar raise error
            if array.ndim == 0:
                raise ValueError(
                    "Expected 2D array, got scalar array instead:\narray={}.\n"
                    "Reshape your data either using array.reshape(-1, 1) if "
                    "your data has a single feature or array.reshape(1, -1) "
                    "if it contains a single sample.".format(array))
            # If input is 1D raise error
            if array.ndim == 1:
                raise ValueError(
                    "Expected 2D array, got 1D array instead:\narray={}.\n"
                    "Reshape your data either using array.reshape(-1, 1) if "
                    "your data has a single feature or array.reshape(1, -1) "
                    "if it contains a single sample.".format(array))
            # To ensure that array flags are maintained
            array = np.array(array, dtype=dtype, order=order, copy=copy)

        # in the future np.flexible dtypes will be handled like object dtypes
        if dtype_numeric and np.issubdtype(array.dtype, np.flexible):
            warnings.warn(
                "Beginning in version 0.22, arrays of strings will be "
                "interpreted as decimal numbers if parameter 'dtype' is "
                "'numeric'. It is recommended that you convert the array to "
                "type np.float64 before passing it to check_array.",
                FutureWarning)

        # make sure we actually converted to numeric:
        if dtype_numeric and array.dtype.kind == "O":
            array = array.astype(np.float64)
        if not allow_nd and array.ndim >= 3:
            raise ValueError("Found array with dim %d. %s expected <= 2."
                             % (array.ndim, estimator_name))
        if force_all_finite:
            _assert_all_finite(array,
                               allow_nan=force_all_finite == 'allow-nan')

    shape_repr = _shape_repr(array.shape)
    if ensure_min_samples > 0:
        n_samples = _num_samples(array)
        if n_samples < ensure_min_samples:
            raise ValueError("Found array with %d sample(s) (shape=%s) while a"
                             " minimum of %d is required%s."
                             % (n_samples, shape_repr, ensure_min_samples,
                                context))

    if ensure_min_features > 0 and array.ndim == 2:
        n_features = array.shape[1]
        if n_features < ensure_min_features:
            raise ValueError("Found array with %d feature(s) (shape=%s) while"
                             " a minimum of %d is required%s."
                             % (n_features, shape_repr, ensure_min_features,
                                context))

    if warn_on_dtype and dtype_orig is not None and array.dtype != dtype_orig:
        msg = ("Data with input dtype %s was converted to %s%s."
               % (dtype_orig, array.dtype, context))
        warnings.warn(msg, DataConversionWarning)
    return array


def check_X_y(X, y, accept_sparse=False, dtype="numeric", order=None,
              copy=False, force_all_finite=True, ensure_2d=True,
              allow_nd=False, multi_output=False, ensure_min_samples=1,
              ensure_min_features=1, y_numeric=False,
              warn_on_dtype=False, estimator=None):
    """Input validation for standard estimators.

    Checks X and y for consistent length, enforces X 2d and y 1d.
    Standard input checks are only applied to y, such as checking that y
    does not have np.nan or np.inf targets. For multi-label y, set
    multi_output=True to allow 2d and sparse y.  If the dtype of X is
    object, attempt converting to float, raising on failure.

    Parameters
    ----------
    X : nd-array, list or sparse matrix
        Input data.

    y : nd-array, list or sparse matrix
        Labels.

    accept_sparse : string, boolean or list of string (default=False)
        String[s] representing allowed sparse matrix formats, such as 'csc',
        'csr', etc. If the input is sparse but not in the allowed format,
        it will be converted to the first listed format. True allows the input
        to be any format. False means that a sparse matrix input will
        raise an error.

        .. deprecated:: 0.19
           Passing 'None' to parameter ``accept_sparse`` in methods is
           deprecated in version 0.19 "and will be removed in 0.21. Use
           ``accept_sparse=False`` instead.

    dtype : string, type, list of types or None (default="numeric")
        Data type of result. If None, the dtype of the input is preserved.
        If "numeric", dtype is preserved unless array.dtype is object.
        If dtype is a list of types, conversion on the first type is only
        performed if the dtype of the input is not in the list.

    order : 'F', 'C' or None (default=None)
        Whether an array will be forced to be fortran or c-style.

    copy : boolean (default=False)
        Whether a forced copy will be triggered. If copy=False, a copy might
        be triggered by a conversion.

    force_all_finite : boolean or 'allow-nan', (default=True)
        Whether to raise an error on np.inf and np.nan in X. This parameter
        does not influence whether y can have np.inf or np.nan values.
        The possibilities are:

        - True: Force all values of X to be finite.
        - False: accept both np.inf and np.nan in X.
        - 'allow-nan':  accept  only  np.nan  values in  X.  Values  cannot  be
          infinite.

        .. versionadded:: 0.20
           ``force_all_finite`` accepts the string ``'allow-nan'``.

    ensure_2d : boolean (default=True)
        Whether to make X at least 2d.

    allow_nd : boolean (default=False)
        Whether to allow X.ndim > 2.

    multi_output : boolean (default=False)
        Whether to allow 2-d y (array or sparse matrix). If false, y will be
        validated as a vector. y cannot have np.nan or np.inf values if
        multi_output=True.

    ensure_min_samples : int (default=1)
        Make sure that X has a minimum number of samples in its first
        axis (rows for a 2D array).

    ensure_min_features : int (default=1)
        Make sure that the 2D array has some minimum number of features
        (columns). The default value of 1 rejects empty datasets.
        This check is only enforced when X has effectively 2 dimensions or
        is originally 1D and ``ensure_2d`` is True. Setting to 0 disables
        this check.

    y_numeric : boolean (default=False)
        Whether to ensure that y has a numeric type. If dtype of y is object,
        it is converted to float64. Should only be used for regression
        algorithms.

    warn_on_dtype : boolean (default=False)
        Raise DataConversionWarning if the dtype of the input data structure
        does not match the requested dtype, causing a memory copy.

    estimator : str or estimator instance (default=None)
        If passed, include the name of the estimator in warning messages.

    Returns
    -------
    X_converted : object
        The converted and validated X.

    y_converted : object
        The converted and validated y.
    """
    X = check_array(X, accept_sparse, dtype, order, copy, force_all_finite,
                    ensure_2d, allow_nd, ensure_min_samples,
                    ensure_min_features, warn_on_dtype, estimator)
    if multi_output:
        y = check_array(y, 'csr', force_all_finite=True, ensure_2d=False,
                        dtype=None)
    else:
        y = column_or_1d(y, warn=True)
        _assert_all_finite(y)
    if y_numeric and y.dtype.kind == 'O':
        y = y.astype(np.float64)

    check_consistent_length(X, y)

    return X, y


def column_or_1d(y, warn=False):
    """ Ravel column or 1d numpy array, else raises an error

    Parameters
    ----------
    y : array-like

    warn : boolean, default False
       To control display of warnings.

    Returns
    -------
    y : array

    """
    shape = np.shape(y)
    if len(shape) == 1:
        return np.ravel(y)
    if len(shape) == 2 and shape[1] == 1:
        if warn:
            warnings.warn("A column-vector y was passed when a 1d array was"
                          " expected. Please change the shape of y to "
                          "(n_samples, ), for example using ravel().",
                          DataConversionWarning, stacklevel=2)
        return np.ravel(y)

    raise ValueError("bad input shape {0}".format(shape))


def check_random_state(seed):
    """Turn seed into a np.random.RandomState instance

    Parameters
    ----------
    seed : None | int | instance of RandomState
        If seed is None, return the RandomState singleton used by np.random.
        If seed is an int, return a new RandomState instance seeded with seed.
        If seed is already a RandomState instance, return it.
        Otherwise raise ValueError.
    """
    if seed is None or seed is np.random:
        return np.random.mtrand._rand
    if isinstance(seed, (numbers.Integral, np.integer)):
        return np.random.RandomState(seed)
    if isinstance(seed, np.random.RandomState):
        return seed
    raise ValueError('%r cannot be used to seed a numpy.random.RandomState'
                     ' instance' % seed)


def has_fit_parameter(estimator, parameter):
    """Checks whether the estimator's fit method supports the given parameter.

    Parameters
    ----------
    estimator : object
        An estimator to inspect.

    parameter: str
        The searched parameter.

    Returns
    -------
    is_parameter: bool
        Whether the parameter was found to be a named parameter of the
        estimator's fit method.

    Examples
    --------
    >>> from sklearn.svm import SVC
    >>> has_fit_parameter(SVC(), "sample_weight")
    True

    """
    return parameter in signature(estimator.fit).parameters


def check_symmetric(array, tol=1E-10, raise_warning=True,
                    raise_exception=False):
    """Make sure that array is 2D, square and symmetric.

    If the array is not symmetric, then a symmetrized version is returned.
    Optionally, a warning or exception is raised if the matrix is not
    symmetric.

    Parameters
    ----------
    array : nd-array or sparse matrix
        Input object to check / convert. Must be two-dimensional and square,
        otherwise a ValueError will be raised.
    tol : float
        Absolute tolerance for equivalence of arrays. Default = 1E-10.
    raise_warning : boolean (default=True)
        If True then raise a warning if conversion is required.
    raise_exception : boolean (default=False)
        If True then raise an exception if array is not symmetric.

    Returns
    -------
    array_sym : ndarray or sparse matrix
        Symmetrized version of the input array, i.e. the average of array
        and array.transpose(). If sparse, then duplicate entries are first
        summed and zeros are eliminated.
    """
    if (array.ndim != 2) or (array.shape[0] != array.shape[1]):
        raise ValueError("array must be 2-dimensional and square. "
                         "shape = {0}".format(array.shape))

    if sp.issparse(array):
        diff = array - array.T
        # only csr, csc, and coo have `data` attribute
        if diff.format not in ['csr', 'csc', 'coo']:
            diff = diff.tocsr()
        symmetric = np.all(abs(diff.data) < tol)
    else:
        symmetric = np.allclose(array, array.T, atol=tol)

    if not symmetric:
        if raise_exception:
            raise ValueError("Array must be symmetric")
        if raise_warning:
            warnings.warn("Array is not symmetric, and will be converted "
                          "to symmetric by average with its transpose.")
        if sp.issparse(array):
            conversion = 'to' + array.format
            array = getattr(0.5 * (array + array.T), conversion)()
        else:
            array = 0.5 * (array + array.T)

    return array


def check_is_fitted(estimator, attributes, msg=None, all_or_any=all):
    """Perform is_fitted validation for estimator.

    Checks if the estimator is fitted by verifying the presence of
    "all_or_any" of the passed attributes and raises a NotFittedError with the
    given message.

    Parameters
    ----------
    estimator : estimator instance.
        estimator instance for which the check is performed.

    attributes : attribute name(s) given as string or a list/tuple of strings
        Eg.:
            ``["coef_", "estimator_", ...], "coef_"``

    msg : string
        The default error message is, "This %(name)s instance is not fitted
        yet. Call 'fit' with appropriate arguments before using this method."

        For custom messages if "%(name)s" is present in the message string,
        it is substituted for the estimator name.

        Eg. : "Estimator, %(name)s, must be fitted before sparsifying".

    all_or_any : callable, {all, any}, default all
        Specify whether all or any of the given attributes must exist.

    Returns
    -------
    None

    Raises
    ------
    NotFittedError
        If the attributes are not found.
    """
    if msg is None:
        msg = ("This %(name)s instance is not fitted yet. Call 'fit' with "
               "appropriate arguments before using this method.")

    if not hasattr(estimator, 'fit'):
        raise TypeError("%s is not an estimator instance." % (estimator))

    if not isinstance(attributes, (list, tuple)):
        attributes = [attributes]

    if not all_or_any([hasattr(estimator, attr) for attr in attributes]):
        raise NotFittedError(msg % {'name': type(estimator).__name__})


def check_non_negative(X, whom):
    """
    Check if there is any negative value in an array.

    Parameters
    ----------
    X : array-like or sparse matrix
        Input data.

    whom : string
        Who passed X to this function.
    """
    X = X.data if sp.issparse(X) else X
    if (X < 0).any():
        raise ValueError("Negative values in data passed to %s" % whom)