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""" Utility functions for sparse matrix module
"""
from __future__ import division, print_function, absolute_import
import operator
import warnings
import numpy as np
__all__ = ['upcast', 'getdtype', 'isscalarlike', 'isintlike',
'isshape', 'issequence', 'isdense', 'ismatrix', 'get_sum_dtype']
supported_dtypes = ['bool', 'int8', 'uint8', 'short', 'ushort', 'intc',
'uintc', 'longlong', 'ulonglong', 'single', 'double',
'longdouble', 'csingle', 'cdouble', 'clongdouble']
supported_dtypes = [np.typeDict[x] for x in supported_dtypes]
_upcast_memo = {}
def upcast(*args):
"""Returns the nearest supported sparse dtype for the
combination of one or more types.
upcast(t0, t1, ..., tn) -> T where T is a supported dtype
Examples
--------
>>> upcast('int32')
<type 'numpy.int32'>
>>> upcast('bool')
<type 'numpy.bool_'>
>>> upcast('int32','float32')
<type 'numpy.float64'>
>>> upcast('bool',complex,float)
<type 'numpy.complex128'>
"""
t = _upcast_memo.get(hash(args))
if t is not None:
return t
upcast = np.find_common_type(args, [])
for t in supported_dtypes:
if np.can_cast(upcast, t):
_upcast_memo[hash(args)] = t
return t
raise TypeError('no supported conversion for types: %r' % (args,))
def upcast_char(*args):
"""Same as `upcast` but taking dtype.char as input (faster)."""
t = _upcast_memo.get(args)
if t is not None:
return t
t = upcast(*map(np.dtype, args))
_upcast_memo[args] = t
return t
def upcast_scalar(dtype, scalar):
"""Determine data type for binary operation between an array of
type `dtype` and a scalar.
"""
return (np.array([0], dtype=dtype) * scalar).dtype
def downcast_intp_index(arr):
"""
Down-cast index array to np.intp dtype if it is of a larger dtype.
Raise an error if the array contains a value that is too large for
intp.
"""
if arr.dtype.itemsize > np.dtype(np.intp).itemsize:
if arr.size == 0:
return arr.astype(np.intp)
maxval = arr.max()
minval = arr.min()
if maxval > np.iinfo(np.intp).max or minval < np.iinfo(np.intp).min:
raise ValueError("Cannot deal with arrays with indices larger "
"than the machine maximum address size "
"(e.g. 64-bit indices on 32-bit machine).")
return arr.astype(np.intp)
return arr
def to_native(A):
return np.asarray(A, dtype=A.dtype.newbyteorder('native'))
def getdtype(dtype, a=None, default=None):
"""Function used to simplify argument processing. If 'dtype' is not
specified (is None), returns a.dtype; otherwise returns a np.dtype
object created from the specified dtype argument. If 'dtype' and 'a'
are both None, construct a data type out of the 'default' parameter.
Furthermore, 'dtype' must be in 'allowed' set.
"""
# TODO is this really what we want?
if dtype is None:
try:
newdtype = a.dtype
except AttributeError:
if default is not None:
newdtype = np.dtype(default)
else:
raise TypeError("could not interpret data type")
else:
newdtype = np.dtype(dtype)
if newdtype == np.object_:
warnings.warn("object dtype is not supported by sparse matrices")
return newdtype
def get_index_dtype(arrays=(), maxval=None, check_contents=False):
"""
Based on input (integer) arrays `a`, determine a suitable index data
type that can hold the data in the arrays.
Parameters
----------
arrays : tuple of array_like
Input arrays whose types/contents to check
maxval : float, optional
Maximum value needed
check_contents : bool, optional
Whether to check the values in the arrays and not just their types.
Default: False (check only the types)
Returns
-------
dtype : dtype
Suitable index data type (int32 or int64)
"""
int32min = np.iinfo(np.int32).min
int32max = np.iinfo(np.int32).max
dtype = np.intc
if maxval is not None:
if maxval > int32max:
dtype = np.int64
if isinstance(arrays, np.ndarray):
arrays = (arrays,)
for arr in arrays:
arr = np.asarray(arr)
if not np.can_cast(arr.dtype, np.int32):
if check_contents:
if arr.size == 0:
# a bigger type not needed
continue
elif np.issubdtype(arr.dtype, np.integer):
maxval = arr.max()
minval = arr.min()
if minval >= int32min and maxval <= int32max:
# a bigger type not needed
continue
dtype = np.int64
break
return dtype
def get_sum_dtype(dtype):
"""Mimic numpy's casting for np.sum"""
if np.issubdtype(dtype, np.float_):
return np.float_
if dtype.kind == 'u' and np.can_cast(dtype, np.uint):
return np.uint
if np.can_cast(dtype, np.int_):
return np.int_
return dtype
def isscalarlike(x):
"""Is x either a scalar, an array scalar, or a 0-dim array?"""
return np.isscalar(x) or (isdense(x) and x.ndim == 0)
def isintlike(x):
"""Is x appropriate as an index into a sparse matrix? Returns True
if it can be cast safely to a machine int.
"""
# Fast-path check to eliminate non-scalar values. operator.index would
# catch this case too, but the exception catching is slow.
if np.ndim(x) != 0:
return False
try:
operator.index(x)
except (TypeError, ValueError):
try:
loose_int = bool(int(x) == x)
except (TypeError, ValueError):
return False
if loose_int:
warnings.warn("Inexact indices into sparse matrices are deprecated",
DeprecationWarning)
return loose_int
return True
def isshape(x, nonneg=False):
"""Is x a valid 2-tuple of dimensions?
If nonneg, also checks that the dimensions are non-negative.
"""
try:
# Assume it's a tuple of matrix dimensions (M, N)
(M, N) = x
except:
return False
else:
if isintlike(M) and isintlike(N):
if np.ndim(M) == 0 and np.ndim(N) == 0:
if not nonneg or (M >= 0 and N >= 0):
return True
return False
def issequence(t):
return ((isinstance(t, (list, tuple)) and
(len(t) == 0 or np.isscalar(t[0]))) or
(isinstance(t, np.ndarray) and (t.ndim == 1)))
def ismatrix(t):
return ((isinstance(t, (list, tuple)) and
len(t) > 0 and issequence(t[0])) or
(isinstance(t, np.ndarray) and t.ndim == 2))
def isdense(x):
return isinstance(x, np.ndarray)
def validateaxis(axis):
if axis is not None:
axis_type = type(axis)
# In NumPy, you can pass in tuples for 'axis', but they are
# not very useful for sparse matrices given their limited
# dimensions, so let's make it explicit that they are not
# allowed to be passed in
if axis_type == tuple:
raise TypeError(("Tuples are not accepted for the 'axis' "
"parameter. Please pass in one of the "
"following: {-2, -1, 0, 1, None}."))
# If not a tuple, check that the provided axis is actually
# an integer and raise a TypeError similar to NumPy's
if not np.issubdtype(np.dtype(axis_type), np.integer):
raise TypeError("axis must be an integer, not {name}"
.format(name=axis_type.__name__))
if not (-2 <= axis <= 1):
raise ValueError("axis out of range")
def check_shape(args, current_shape=None):
"""Imitate numpy.matrix handling of shape arguments"""
if len(args) == 0:
raise TypeError("function missing 1 required positional argument: "
"'shape'")
elif len(args) == 1:
try:
shape_iter = iter(args[0])
except TypeError:
new_shape = (operator.index(args[0]), )
else:
new_shape = tuple(operator.index(arg) for arg in shape_iter)
else:
new_shape = tuple(operator.index(arg) for arg in args)
if current_shape is None:
if len(new_shape) != 2:
raise ValueError('shape must be a 2-tuple of positive integers')
elif new_shape[0] < 0 or new_shape[1] < 0:
raise ValueError("'shape' elements cannot be negative")
else:
# Check the current size only if needed
current_size = np.prod(current_shape, dtype=int)
# Check for negatives
negative_indexes = [i for i, x in enumerate(new_shape) if x < 0]
if len(negative_indexes) == 0:
new_size = np.prod(new_shape, dtype=int)
if new_size != current_size:
raise ValueError('cannot reshape array of size {} into shape {}'
.format(new_size, new_shape))
elif len(negative_indexes) == 1:
skip = negative_indexes[0]
specified = np.prod(new_shape[0:skip] + new_shape[skip+1:])
unspecified, remainder = divmod(current_size, specified)
if remainder != 0:
err_shape = tuple('newshape' if x < 0 else x for x in new_shape)
raise ValueError('cannot reshape array of size {} into shape {}'
''.format(current_size, err_shape))
new_shape = new_shape[0:skip] + (unspecified,) + new_shape[skip+1:]
else:
raise ValueError('can only specify one unknown dimension')
# Add and remove ones like numpy.matrix.reshape
if len(new_shape) != 2:
new_shape = tuple(arg for arg in new_shape if arg != 1)
if len(new_shape) == 0:
new_shape = (1, 1)
elif len(new_shape) == 1:
new_shape = (1, new_shape[0])
if len(new_shape) > 2:
raise ValueError('shape too large to be a matrix')
return new_shape
def check_reshape_kwargs(kwargs):
"""Unpack keyword arguments for reshape function.
This is useful because keyword arguments after star arguments are not
allowed in Python 2, but star keyword arguments are. This function unpacks
'order' and 'copy' from the star keyword arguments (with defaults) and
throws an error for any remaining.
"""
order = kwargs.pop('order', 'C')
copy = kwargs.pop('copy', False)
if kwargs: # Some unused kwargs remain
raise TypeError('reshape() got unexpected keywords arguments: {}'
.format(', '.join(kwargs.keys())))
return order, copy
###############################################################################
# Wrappers for NumPy types that are deprecated
def matrix(*args, **kwargs):
with warnings.catch_warnings(record=True):
warnings.filterwarnings(
'ignore', '.*the matrix subclass is not the recommended way.*')
return np.matrix(*args, **kwargs)
def asmatrix(*args, **kwargs):
with warnings.catch_warnings(record=True):
warnings.filterwarnings(
'ignore', '.*the matrix subclass is not the recommended way.*')
return np.asmatrix(*args, **kwargs)
def bmat(*args, **kwargs):
with warnings.catch_warnings(record=True):
warnings.filterwarnings(
'ignore', '.*the matrix subclass is not the recommended way.*')
return np.bmat(*args, **kwargs)
class IndexMixin(object):
"""
This class simply exists to hold the methods necessary for fancy indexing.
"""
def _slicetoarange(self, j, shape):
""" Given a slice object, use numpy arange to change it to a 1D
array.
"""
start, stop, step = j.indices(shape)
return np.arange(start, stop, step)
def _unpack_index(self, index):
""" Parse index. Always return a tuple of the form (row, col).
Where row/col is a integer, slice, or array of integers.
"""
# First, check if indexing with single boolean matrix.
from .base import spmatrix # This feels dirty but...
if (isinstance(index, (spmatrix, np.ndarray)) and
(index.ndim == 2) and index.dtype.kind == 'b'):
return index.nonzero()
# Parse any ellipses.
index = self._check_ellipsis(index)
# Next, parse the tuple or object
if isinstance(index, tuple):
if len(index) == 2:
row, col = index
elif len(index) == 1:
row, col = index[0], slice(None)
else:
raise IndexError('invalid number of indices')
else:
row, col = index, slice(None)
# Next, check for validity, or transform the index as needed.
row, col = self._check_boolean(row, col)
return row, col
def _check_ellipsis(self, index):
"""Process indices with Ellipsis. Returns modified index."""
if index is Ellipsis:
return (slice(None), slice(None))
elif isinstance(index, tuple):
# Find first ellipsis
for j, v in enumerate(index):
if v is Ellipsis:
first_ellipsis = j
break
else:
first_ellipsis = None
# Expand the first one
if first_ellipsis is not None:
# Shortcuts
if len(index) == 1:
return (slice(None), slice(None))
elif len(index) == 2:
if first_ellipsis == 0:
if index[1] is Ellipsis:
return (slice(None), slice(None))
else:
return (slice(None), index[1])
else:
return (index[0], slice(None))
# General case
tail = ()
for v in index[first_ellipsis+1:]:
if v is not Ellipsis:
tail = tail + (v,)
nd = first_ellipsis + len(tail)
nslice = max(0, 2 - nd)
return index[:first_ellipsis] + (slice(None),)*nslice + tail
return index
def _check_boolean(self, row, col):
from .base import isspmatrix # ew...
# Supporting sparse boolean indexing with both row and col does
# not work because spmatrix.ndim is always 2.
if isspmatrix(row) or isspmatrix(col):
raise IndexError(
"Indexing with sparse matrices is not supported "
"except boolean indexing where matrix and index "
"are equal shapes.")
if isinstance(row, np.ndarray) and row.dtype.kind == 'b':
row = self._boolean_index_to_array(row)
if isinstance(col, np.ndarray) and col.dtype.kind == 'b':
col = self._boolean_index_to_array(col)
return row, col
def _boolean_index_to_array(self, i):
if i.ndim > 1:
raise IndexError('invalid index shape')
return i.nonzero()[0]
def _index_to_arrays(self, i, j):
i, j = self._check_boolean(i, j)
i_slice = isinstance(i, slice)
if i_slice:
i = self._slicetoarange(i, self.shape[0])[:, None]
else:
i = np.atleast_1d(i)
if isinstance(j, slice):
j = self._slicetoarange(j, self.shape[1])[None, :]
if i.ndim == 1:
i = i[:, None]
elif not i_slice:
raise IndexError('index returns 3-dim structure')
elif isscalarlike(j):
# row vector special case
j = np.atleast_1d(j)
if i.ndim == 1:
i, j = np.broadcast_arrays(i, j)
i = i[:, None]
j = j[:, None]
return i, j
else:
j = np.atleast_1d(j)
if i_slice and j.ndim > 1:
raise IndexError('index returns 3-dim structure')
i, j = np.broadcast_arrays(i, j)
if i.ndim == 1:
# return column vectors for 1-D indexing
i = i[None, :]
j = j[None, :]
elif i.ndim > 2:
raise IndexError("Index dimension must be <= 2")
return i, j
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