/usr/share/pyshared/sklearn/utils/validation.py is in python-sklearn 0.14.1-2.
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# Authors: Olivier Grisel and Gael Varoquaux and others (please update me)
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import sparse
from ..externals import six
from .fixes import safe_copy
class DataConversionWarning(UserWarning):
"A warning on implicit data conversions happening in the code"
pass
warnings.simplefilter("always", DataConversionWarning)
def _assert_all_finite(X):
"""Like assert_all_finite, but only for ndarray."""
if (X.dtype.char in np.typecodes['AllFloat'] and not np.isfinite(X.sum())
and not np.isfinite(X).all()):
raise ValueError("Array contains NaN or infinity.")
def assert_all_finite(X):
"""Throw a ValueError if X contains NaN or infinity.
Input MUST be an np.ndarray instance or a scipy.sparse matrix."""
# First try an O(n) time, O(1) space solution for the common case that
# there everything is finite; fall back to O(n) space np.isfinite to
# prevent false positives from overflow in sum method.
_assert_all_finite(X.data if sparse.issparse(X) else X)
def safe_asarray(X, dtype=None, order=None, copy=False):
"""Convert X to an array or sparse matrix.
Prevents copying X when possible; sparse matrices are passed through."""
if sparse.issparse(X):
if copy:
X = X.copy()
assert_all_finite(X.data)
else:
X = np.array(X, dtype=dtype, order=order, copy=copy)
assert_all_finite(X)
return X
def as_float_array(X, copy=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.
Returns
-------
XT : {array, sparse matrix}
An array of type np.float
"""
if isinstance(X, np.matrix) or (not isinstance(X, np.ndarray)
and not sparse.issparse(X)):
return safe_asarray(X, dtype=np.float64, copy=copy)
elif sparse.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:
return X.astype(np.float32 if X.dtype == np.int32 else np.float64)
def array2d(X, dtype=None, order=None, copy=False, force_all_finite=True):
"""Returns at least 2-d array with data from X"""
if sparse.issparse(X):
raise TypeError('A sparse matrix was passed, but dense data '
'is required. Use X.toarray() to convert to dense.')
X_2d = np.asarray(np.atleast_2d(X), dtype=dtype, order=order)
if force_all_finite:
_assert_all_finite(X_2d)
if X is X_2d and copy:
X_2d = safe_copy(X_2d)
return X_2d
def _atleast2d_or_sparse(X, dtype, order, copy, sparse_class, convmethod,
force_all_finite):
if sparse.issparse(X):
if dtype is None or X.dtype == dtype:
X = getattr(X, convmethod)()
else:
X = sparse_class(X, dtype=dtype)
if force_all_finite:
_assert_all_finite(X.data)
X.data = np.array(X.data, copy=False, order=order)
else:
X = array2d(X, dtype=dtype, order=order, copy=copy,
force_all_finite=force_all_finite)
if force_all_finite:
_assert_all_finite(X)
return X
def atleast2d_or_csc(X, dtype=None, order=None, copy=False,
force_all_finite=True):
"""Like numpy.atleast_2d, but converts sparse matrices to CSC format.
Also, converts np.matrix to np.ndarray.
"""
return _atleast2d_or_sparse(X, dtype, order, copy, sparse.csc_matrix,
"tocsc", force_all_finite)
def atleast2d_or_csr(X, dtype=None, order=None, copy=False,
force_all_finite=True):
"""Like numpy.atleast_2d, but converts sparse matrices to CSR format
Also, converts np.matrix to np.ndarray.
"""
return _atleast2d_or_sparse(X, dtype, order, copy, sparse.csr_matrix,
"tocsr", force_all_finite)
def _num_samples(x):
"""Return number of samples in array-like x."""
if not hasattr(x, '__len__') and not hasattr(x, 'shape'):
raise TypeError("Expected sequence or array-like, got %r" % x)
return x.shape[0] if hasattr(x, 'shape') else len(x)
def check_arrays(*arrays, **options):
"""Check that all arrays have consistent first dimensions.
Checks whether all objects in arrays have the same shape or length.
By default lists and tuples are converted to numpy arrays.
It is possible to enforce certain properties, such as dtype, continguity
and sparse matrix format (if a sparse matrix is passed).
Converting lists to arrays can be disabled by setting ``allow_lists=True``.
Lists can then contain arbitrary objects and are not checked for dtype,
finiteness or anything else but length. Arrays are still checked
and possibly converted.
Parameters
----------
*arrays : sequence of arrays or scipy.sparse matrices with same shape[0]
Python lists or tuples occurring in arrays are converted to 1D numpy
arrays, unless allow_lists is specified.
sparse_format : 'csr', 'csc' or 'dense', None by default
If not None, any scipy.sparse matrix is converted to
Compressed Sparse Rows or Compressed Sparse Columns representations.
If 'dense', an error is raised when a sparse array is
passed.
copy : boolean, False by default
If copy is True, ensure that returned arrays are copies of the original
(if not already converted to another format earlier in the process).
check_ccontiguous : boolean, False by default
Check that the arrays are C contiguous
dtype : a numpy dtype instance, None by default
Enforce a specific dtype.
allow_lists : bool
Allow lists of arbitrary objects as input, just check their length.
Disables
"""
sparse_format = options.pop('sparse_format', None)
if sparse_format not in (None, 'csr', 'csc', 'dense'):
raise ValueError('Unexpected sparse format: %r' % sparse_format)
copy = options.pop('copy', False)
check_ccontiguous = options.pop('check_ccontiguous', False)
dtype = options.pop('dtype', None)
allow_lists = options.pop('allow_lists', False)
if options:
raise TypeError("Unexpected keyword arguments: %r" % options.keys())
if len(arrays) == 0:
return None
n_samples = _num_samples(arrays[0])
checked_arrays = []
for array in arrays:
array_orig = array
if array is None:
# special case: ignore optional y=None kwarg pattern
checked_arrays.append(array)
continue
size = _num_samples(array)
if size != n_samples:
raise ValueError("Found array with dim %d. Expected %d"
% (size, n_samples))
if not allow_lists or hasattr(array, "shape"):
if sparse.issparse(array):
if sparse_format == 'csr':
array = array.tocsr()
elif sparse_format == 'csc':
array = array.tocsc()
elif sparse_format == 'dense':
raise TypeError('A sparse matrix was passed, but dense '
'data is required. Use X.toarray() to '
'convert to a dense numpy array.')
if check_ccontiguous:
array.data = np.ascontiguousarray(array.data, dtype=dtype)
else:
array.data = np.asarray(array.data, dtype=dtype)
_assert_all_finite(array.data)
else:
if check_ccontiguous:
array = np.ascontiguousarray(array, dtype=dtype)
else:
array = np.asarray(array, dtype=dtype)
_assert_all_finite(array)
if copy and array is array_orig:
array = array.copy()
checked_arrays.append(array)
return checked_arrays
def column_or_1d(y, warn=False):
""" Ravel column or 1d numpy array, else raises an error
Parameters
----------
y : array-like
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 warn_if_not_float(X, estimator='This algorithm'):
"""Warning utility function to check that data type is floating point.
Returns True if a warning was raised (i.e. the input is not float) and
False otherwise, for easier input validation.
"""
if not isinstance(estimator, six.string_types):
estimator = estimator.__class__.__name__
if X.dtype.kind != 'f':
warnings.warn("%s assumes floating point values as input, "
"got %s" % (estimator, X.dtype))
return True
return False
def check_random_state(seed):
"""Turn seed into a np.random.RandomState instance
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)
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