peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/scipy
/sparse
/_base.py
"""Base class for sparse matrices""" | |
from warnings import warn | |
import numpy as np | |
from scipy._lib._util import VisibleDeprecationWarning | |
from ._sputils import (asmatrix, check_reshape_kwargs, check_shape, | |
get_sum_dtype, isdense, isscalarlike, | |
matrix, validateaxis,) | |
from ._matrix import spmatrix | |
__all__ = ['isspmatrix', 'issparse', 'sparray', | |
'SparseWarning', 'SparseEfficiencyWarning'] | |
class SparseWarning(Warning): | |
pass | |
class SparseFormatWarning(SparseWarning): | |
pass | |
class SparseEfficiencyWarning(SparseWarning): | |
pass | |
# The formats that we might potentially understand. | |
_formats = {'csc': [0, "Compressed Sparse Column"], | |
'csr': [1, "Compressed Sparse Row"], | |
'dok': [2, "Dictionary Of Keys"], | |
'lil': [3, "List of Lists"], | |
'dod': [4, "Dictionary of Dictionaries"], | |
'sss': [5, "Symmetric Sparse Skyline"], | |
'coo': [6, "COOrdinate"], | |
'lba': [7, "Linpack BAnded"], | |
'egd': [8, "Ellpack-itpack Generalized Diagonal"], | |
'dia': [9, "DIAgonal"], | |
'bsr': [10, "Block Sparse Row"], | |
'msr': [11, "Modified compressed Sparse Row"], | |
'bsc': [12, "Block Sparse Column"], | |
'msc': [13, "Modified compressed Sparse Column"], | |
'ssk': [14, "Symmetric SKyline"], | |
'nsk': [15, "Nonsymmetric SKyline"], | |
'jad': [16, "JAgged Diagonal"], | |
'uss': [17, "Unsymmetric Sparse Skyline"], | |
'vbr': [18, "Variable Block Row"], | |
'und': [19, "Undefined"] | |
} | |
# These univariate ufuncs preserve zeros. | |
_ufuncs_with_fixed_point_at_zero = frozenset([ | |
np.sin, np.tan, np.arcsin, np.arctan, np.sinh, np.tanh, np.arcsinh, | |
np.arctanh, np.rint, np.sign, np.expm1, np.log1p, np.deg2rad, | |
np.rad2deg, np.floor, np.ceil, np.trunc, np.sqrt]) | |
MAXPRINT = 50 | |
class _spbase: | |
""" This class provides a base class for all sparse arrays. It | |
cannot be instantiated. Most of the work is provided by subclasses. | |
""" | |
__array_priority__ = 10.1 | |
_format = 'und' # undefined | |
def ndim(self) -> int: | |
return len(self._shape) | |
def _shape_as_2d(self): | |
s = self._shape | |
return (1, s[-1]) if len(s) == 1 else s | |
def _bsr_container(self): | |
from ._bsr import bsr_array | |
return bsr_array | |
def _coo_container(self): | |
from ._coo import coo_array | |
return coo_array | |
def _csc_container(self): | |
from ._csc import csc_array | |
return csc_array | |
def _csr_container(self): | |
from ._csr import csr_array | |
return csr_array | |
def _dia_container(self): | |
from ._dia import dia_array | |
return dia_array | |
def _dok_container(self): | |
from ._dok import dok_array | |
return dok_array | |
def _lil_container(self): | |
from ._lil import lil_array | |
return lil_array | |
def __init__(self, maxprint=MAXPRINT): | |
self._shape = None | |
if self.__class__.__name__ == '_spbase': | |
raise ValueError("This class is not intended" | |
" to be instantiated directly.") | |
self.maxprint = maxprint | |
# Use this in 1.14.0 and later: | |
# | |
# @property | |
# def shape(self): | |
# return self._shape | |
def reshape(self, *args, **kwargs): | |
"""reshape(self, shape, order='C', copy=False) | |
Gives a new shape to a sparse array/matrix without changing its data. | |
Parameters | |
---------- | |
shape : length-2 tuple of ints | |
The new shape should be compatible with the original shape. | |
order : {'C', 'F'}, optional | |
Read the elements using this index order. 'C' means to read and | |
write the elements using C-like index order; e.g., read entire first | |
row, then second row, etc. 'F' means to read and write the elements | |
using Fortran-like index order; e.g., read entire first column, then | |
second column, etc. | |
copy : bool, optional | |
Indicates whether or not attributes of self should be copied | |
whenever possible. The degree to which attributes are copied varies | |
depending on the type of sparse array being used. | |
Returns | |
------- | |
reshaped : sparse array/matrix | |
A sparse array/matrix with the given `shape`, not necessarily of the same | |
format as the current object. | |
See Also | |
-------- | |
numpy.reshape : NumPy's implementation of 'reshape' for ndarrays | |
""" | |
# If the shape already matches, don't bother doing an actual reshape | |
# Otherwise, the default is to convert to COO and use its reshape | |
is_array = isinstance(self, sparray) | |
shape = check_shape(args, self.shape, allow_1d=is_array) | |
order, copy = check_reshape_kwargs(kwargs) | |
if shape == self.shape: | |
if copy: | |
return self.copy() | |
else: | |
return self | |
return self.tocoo(copy=copy).reshape(shape, order=order, copy=False) | |
def resize(self, shape): | |
"""Resize the array/matrix in-place to dimensions given by ``shape`` | |
Any elements that lie within the new shape will remain at the same | |
indices, while non-zero elements lying outside the new shape are | |
removed. | |
Parameters | |
---------- | |
shape : (int, int) | |
number of rows and columns in the new array/matrix | |
Notes | |
----- | |
The semantics are not identical to `numpy.ndarray.resize` or | |
`numpy.resize`. Here, the same data will be maintained at each index | |
before and after reshape, if that index is within the new bounds. In | |
numpy, resizing maintains contiguity of the array, moving elements | |
around in the logical array but not within a flattened representation. | |
We give no guarantees about whether the underlying data attributes | |
(arrays, etc.) will be modified in place or replaced with new objects. | |
""" | |
# As an inplace operation, this requires implementation in each format. | |
raise NotImplementedError( | |
f'{type(self).__name__}.resize is not implemented') | |
def astype(self, dtype, casting='unsafe', copy=True): | |
"""Cast the array/matrix elements to a specified type. | |
Parameters | |
---------- | |
dtype : string or numpy dtype | |
Typecode or data-type to which to cast the data. | |
casting : {'no', 'equiv', 'safe', 'same_kind', 'unsafe'}, optional | |
Controls what kind of data casting may occur. | |
Defaults to 'unsafe' for backwards compatibility. | |
'no' means the data types should not be cast at all. | |
'equiv' means only byte-order changes are allowed. | |
'safe' means only casts which can preserve values are allowed. | |
'same_kind' means only safe casts or casts within a kind, | |
like float64 to float32, are allowed. | |
'unsafe' means any data conversions may be done. | |
copy : bool, optional | |
If `copy` is `False`, the result might share some memory with this | |
array/matrix. If `copy` is `True`, it is guaranteed that the result and | |
this array/matrix do not share any memory. | |
""" | |
dtype = np.dtype(dtype) | |
if self.dtype != dtype: | |
return self.tocsr().astype( | |
dtype, casting=casting, copy=copy).asformat(self.format) | |
elif copy: | |
return self.copy() | |
else: | |
return self | |
def _ascontainer(cls, X, **kwargs): | |
if issubclass(cls, sparray): | |
return np.asarray(X, **kwargs) | |
else: | |
return asmatrix(X, **kwargs) | |
def _container(cls, X, **kwargs): | |
if issubclass(cls, sparray): | |
return np.array(X, **kwargs) | |
else: | |
return matrix(X, **kwargs) | |
def _asfptype(self): | |
"""Upcast array to a floating point format (if necessary)""" | |
fp_types = ['f', 'd', 'F', 'D'] | |
if self.dtype.char in fp_types: | |
return self | |
else: | |
for fp_type in fp_types: | |
if self.dtype <= np.dtype(fp_type): | |
return self.astype(fp_type) | |
raise TypeError('cannot upcast [%s] to a floating ' | |
'point format' % self.dtype.name) | |
def __iter__(self): | |
for r in range(self.shape[0]): | |
yield self[r] | |
def _getmaxprint(self): | |
"""Maximum number of elements to display when printed.""" | |
return self.maxprint | |
def count_nonzero(self): | |
"""Number of non-zero entries, equivalent to | |
np.count_nonzero(a.toarray()) | |
Unlike the nnz property, which return the number of stored | |
entries (the length of the data attribute), this method counts the | |
actual number of non-zero entries in data. | |
""" | |
raise NotImplementedError("count_nonzero not implemented for %s." % | |
self.__class__.__name__) | |
def _getnnz(self, axis=None): | |
"""Number of stored values, including explicit zeros. | |
Parameters | |
---------- | |
axis : None, 0, or 1 | |
Select between the number of values across the whole array, in | |
each column, or in each row. | |
See also | |
-------- | |
count_nonzero : Number of non-zero entries | |
""" | |
raise NotImplementedError("getnnz not implemented for %s." % | |
self.__class__.__name__) | |
def nnz(self) -> int: | |
"""Number of stored values, including explicit zeros. | |
See also | |
-------- | |
count_nonzero : Number of non-zero entries | |
""" | |
return self._getnnz() | |
def size(self) -> int: | |
"""Number of stored values. | |
See also | |
-------- | |
count_nonzero : Number of non-zero values. | |
""" | |
return self._getnnz() | |
def format(self) -> str: | |
"""Format string for matrix.""" | |
return self._format | |
def A(self) -> np.ndarray: | |
"""DEPRECATED: Return a dense array. | |
.. deprecated:: 1.11.0 | |
`.A` is deprecated and will be removed in v1.14.0. | |
Use `.toarray()` instead. | |
""" | |
if isinstance(self, sparray): | |
message = ("`.A` is deprecated and will be removed in v1.14.0. " | |
"Use `.toarray()` instead.") | |
warn(VisibleDeprecationWarning(message), stacklevel=2) | |
return self.toarray() | |
def T(self): | |
"""Transpose.""" | |
return self.transpose() | |
def H(self): | |
"""DEPRECATED: Returns the (complex) conjugate transpose. | |
.. deprecated:: 1.11.0 | |
`.H` is deprecated and will be removed in v1.14.0. | |
Please use `.T.conjugate()` instead. | |
""" | |
if isinstance(self, sparray): | |
message = ("`.H` is deprecated and will be removed in v1.14.0. " | |
"Please use `.T.conjugate()` instead.") | |
warn(VisibleDeprecationWarning(message), stacklevel=2) | |
return self.T.conjugate() | |
def real(self): | |
return self._real() | |
def imag(self): | |
return self._imag() | |
def __repr__(self): | |
_, format_name = _formats[self.format] | |
sparse_cls = 'array' if isinstance(self, sparray) else 'matrix' | |
shape_str = 'x'.join(str(x) for x in self.shape) | |
return ( | |
f"<{shape_str} sparse {sparse_cls} of type '{self.dtype.type}'\n" | |
f"\twith {self.nnz} stored elements in {format_name} format>" | |
) | |
def __str__(self): | |
maxprint = self._getmaxprint() | |
A = self.tocoo() | |
# helper function, outputs "(i,j) v" | |
def tostr(row, col, data): | |
triples = zip(list(zip(row, col)), data) | |
return '\n'.join([(' {}\t{}'.format(*t)) for t in triples]) | |
if self.nnz > maxprint: | |
half = maxprint // 2 | |
out = tostr(A.row[:half], A.col[:half], A.data[:half]) | |
out += "\n :\t:\n" | |
half = maxprint - maxprint//2 | |
out += tostr(A.row[-half:], A.col[-half:], A.data[-half:]) | |
else: | |
out = tostr(A.row, A.col, A.data) | |
return out | |
def __bool__(self): # Simple -- other ideas? | |
if self.shape == (1, 1): | |
return self.nnz != 0 | |
else: | |
raise ValueError("The truth value of an array with more than one " | |
"element is ambiguous. Use a.any() or a.all().") | |
__nonzero__ = __bool__ | |
# What should len(sparse) return? For consistency with dense matrices, | |
# perhaps it should be the number of rows? But for some uses the number of | |
# non-zeros is more important. For now, raise an exception! | |
def __len__(self): | |
raise TypeError("sparse array length is ambiguous; use getnnz()" | |
" or shape[0]") | |
def asformat(self, format, copy=False): | |
"""Return this array/matrix in the passed format. | |
Parameters | |
---------- | |
format : {str, None} | |
The desired sparse format ("csr", "csc", "lil", "dok", "array", ...) | |
or None for no conversion. | |
copy : bool, optional | |
If True, the result is guaranteed to not share data with self. | |
Returns | |
------- | |
A : This array/matrix in the passed format. | |
""" | |
if format is None or format == self.format: | |
if copy: | |
return self.copy() | |
else: | |
return self | |
else: | |
try: | |
convert_method = getattr(self, 'to' + format) | |
except AttributeError as e: | |
raise ValueError(f'Format {format} is unknown.') from e | |
# Forward the copy kwarg, if it's accepted. | |
try: | |
return convert_method(copy=copy) | |
except TypeError: | |
return convert_method() | |
################################################################### | |
# NOTE: All arithmetic operations use csr_matrix by default. | |
# Therefore a new sparse array format just needs to define a | |
# .tocsr() method to provide arithmetic support. Any of these | |
# methods can be overridden for efficiency. | |
#################################################################### | |
def multiply(self, other): | |
"""Point-wise multiplication by another array/matrix.""" | |
return self.tocsr().multiply(other) | |
def maximum(self, other): | |
"""Element-wise maximum between this and another array/matrix.""" | |
return self.tocsr().maximum(other) | |
def minimum(self, other): | |
"""Element-wise minimum between this and another array/matrix.""" | |
return self.tocsr().minimum(other) | |
def dot(self, other): | |
"""Ordinary dot product | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import csr_array | |
>>> A = csr_array([[1, 2, 0], [0, 0, 3], [4, 0, 5]]) | |
>>> v = np.array([1, 0, -1]) | |
>>> A.dot(v) | |
array([ 1, -3, -1], dtype=int64) | |
""" | |
if np.isscalar(other): | |
return self * other | |
else: | |
return self @ other | |
def power(self, n, dtype=None): | |
"""Element-wise power.""" | |
return self.tocsr().power(n, dtype=dtype) | |
def __eq__(self, other): | |
return self.tocsr().__eq__(other) | |
def __ne__(self, other): | |
return self.tocsr().__ne__(other) | |
def __lt__(self, other): | |
return self.tocsr().__lt__(other) | |
def __gt__(self, other): | |
return self.tocsr().__gt__(other) | |
def __le__(self, other): | |
return self.tocsr().__le__(other) | |
def __ge__(self, other): | |
return self.tocsr().__ge__(other) | |
def __abs__(self): | |
return abs(self.tocsr()) | |
def __round__(self, ndigits=0): | |
return round(self.tocsr(), ndigits=ndigits) | |
def _add_sparse(self, other): | |
return self.tocsr()._add_sparse(other) | |
def _add_dense(self, other): | |
return self.tocoo()._add_dense(other) | |
def _sub_sparse(self, other): | |
return self.tocsr()._sub_sparse(other) | |
def _sub_dense(self, other): | |
return self.todense() - other | |
def _rsub_dense(self, other): | |
# note: this can't be replaced by other + (-self) for unsigned types | |
return other - self.todense() | |
def __add__(self, other): # self + other | |
if isscalarlike(other): | |
if other == 0: | |
return self.copy() | |
# Now we would add this scalar to every element. | |
raise NotImplementedError('adding a nonzero scalar to a ' | |
'sparse array is not supported') | |
elif issparse(other): | |
if other.shape != self.shape: | |
raise ValueError("inconsistent shapes") | |
return self._add_sparse(other) | |
elif isdense(other): | |
other = np.broadcast_to(other, self.shape) | |
return self._add_dense(other) | |
else: | |
return NotImplemented | |
def __radd__(self,other): # other + self | |
return self.__add__(other) | |
def __sub__(self, other): # self - other | |
if isscalarlike(other): | |
if other == 0: | |
return self.copy() | |
raise NotImplementedError('subtracting a nonzero scalar from a ' | |
'sparse array is not supported') | |
elif issparse(other): | |
if other.shape != self.shape: | |
raise ValueError("inconsistent shapes") | |
return self._sub_sparse(other) | |
elif isdense(other): | |
other = np.broadcast_to(other, self.shape) | |
return self._sub_dense(other) | |
else: | |
return NotImplemented | |
def __rsub__(self,other): # other - self | |
if isscalarlike(other): | |
if other == 0: | |
return -self.copy() | |
raise NotImplementedError('subtracting a sparse array from a ' | |
'nonzero scalar is not supported') | |
elif isdense(other): | |
other = np.broadcast_to(other, self.shape) | |
return self._rsub_dense(other) | |
else: | |
return NotImplemented | |
def _matmul_dispatch(self, other): | |
"""np.array-like matmul & `np.matrix`-like mul, i.e. `dot` or `NotImplemented` | |
interpret other and call one of the following | |
self._mul_scalar() | |
self._matmul_vector() | |
self._matmul_multivector() | |
self._matmul_sparse() | |
""" | |
# This method has to be different from `__matmul__` because it is also | |
# called by sparse matrix classes. | |
# Currently matrix multiplication is only supported | |
# for 2D arrays. Hence we unpacked and use only the | |
# two last axes' lengths. | |
M, N = self._shape_as_2d | |
if other.__class__ is np.ndarray: | |
# Fast path for the most common case | |
if other.shape == (N,): | |
return self._matmul_vector(other) | |
elif other.shape == (N, 1): | |
result = self._matmul_vector(other.ravel()) | |
if self.ndim == 1: | |
return result | |
return result.reshape(M, 1) | |
elif other.ndim == 2 and other.shape[0] == N: | |
return self._matmul_multivector(other) | |
if isscalarlike(other): | |
# scalar value | |
return self._mul_scalar(other) | |
if issparse(other): | |
if self.shape[-1] != other.shape[0]: | |
raise ValueError('dimension mismatch') | |
if other.ndim == 1: | |
raise ValueError('Cannot yet multiply a 1d sparse array') | |
return self._matmul_sparse(other) | |
# If it's a list or whatever, treat it like an array | |
other_a = np.asanyarray(other) | |
if other_a.ndim == 0 and other_a.dtype == np.object_: | |
# Not interpretable as an array; return NotImplemented so that | |
# other's __rmatmul__ can kick in if that's implemented. | |
return NotImplemented | |
try: | |
other.shape | |
except AttributeError: | |
other = other_a | |
if other.ndim == 1 or other.ndim == 2 and other.shape[1] == 1: | |
# dense row or column vector | |
if other.shape != (N,) and other.shape != (N, 1): | |
raise ValueError('dimension mismatch') | |
result = self._matmul_vector(np.ravel(other)) | |
if isinstance(other, np.matrix): | |
result = self._ascontainer(result) | |
if other.ndim == 2 and other.shape[1] == 1: | |
# If 'other' was an (nx1) column vector, reshape the result | |
result = result.reshape(-1, 1) | |
return result | |
elif other.ndim == 2: | |
## | |
# dense 2D array or matrix ("multivector") | |
if other.shape[0] != N: | |
raise ValueError('dimension mismatch') | |
result = self._matmul_multivector(np.asarray(other)) | |
if isinstance(other, np.matrix): | |
result = self._ascontainer(result) | |
return result | |
else: | |
raise ValueError('could not interpret dimensions') | |
def __mul__(self, *args, **kwargs): | |
return self.multiply(*args, **kwargs) | |
def __rmul__(self, *args, **kwargs): # other * self | |
return self.multiply(*args, **kwargs) | |
# by default, use CSR for __mul__ handlers | |
def _mul_scalar(self, other): | |
return self.tocsr()._mul_scalar(other) | |
def _matmul_vector(self, other): | |
return self.tocsr()._matmul_vector(other) | |
def _matmul_multivector(self, other): | |
return self.tocsr()._matmul_multivector(other) | |
def _matmul_sparse(self, other): | |
return self.tocsr()._matmul_sparse(other) | |
def _rmatmul_dispatch(self, other): | |
if isscalarlike(other): | |
return self._mul_scalar(other) | |
else: | |
# Don't use asarray unless we have to | |
try: | |
tr = other.transpose() | |
except AttributeError: | |
tr = np.asarray(other).transpose() | |
ret = self.transpose()._matmul_dispatch(tr) | |
if ret is NotImplemented: | |
return NotImplemented | |
return ret.transpose() | |
####################### | |
# matmul (@) operator # | |
####################### | |
def __matmul__(self, other): | |
if isscalarlike(other): | |
raise ValueError("Scalar operands are not allowed, " | |
"use '*' instead") | |
return self._matmul_dispatch(other) | |
def __rmatmul__(self, other): | |
if isscalarlike(other): | |
raise ValueError("Scalar operands are not allowed, " | |
"use '*' instead") | |
return self._rmatmul_dispatch(other) | |
#################### | |
# Other Arithmetic # | |
#################### | |
def _divide(self, other, true_divide=False, rdivide=False): | |
if isscalarlike(other): | |
if rdivide: | |
if true_divide: | |
return np.true_divide(other, self.todense()) | |
else: | |
return np.divide(other, self.todense()) | |
if true_divide and np.can_cast(self.dtype, np.float64): | |
return self.astype(np.float64)._mul_scalar(1./other) | |
else: | |
r = self._mul_scalar(1./other) | |
scalar_dtype = np.asarray(other).dtype | |
if (np.issubdtype(self.dtype, np.integer) and | |
np.issubdtype(scalar_dtype, np.integer)): | |
return r.astype(self.dtype) | |
else: | |
return r | |
elif isdense(other): | |
if not rdivide: | |
if true_divide: | |
recip = np.true_divide(1., other) | |
else: | |
recip = np.divide(1., other) | |
return self.multiply(recip) | |
else: | |
if true_divide: | |
return np.true_divide(other, self.todense()) | |
else: | |
return np.divide(other, self.todense()) | |
elif issparse(other): | |
if rdivide: | |
return other._divide(self, true_divide, rdivide=False) | |
self_csr = self.tocsr() | |
if true_divide and np.can_cast(self.dtype, np.float64): | |
return self_csr.astype(np.float64)._divide_sparse(other) | |
else: | |
return self_csr._divide_sparse(other) | |
else: | |
return NotImplemented | |
def __truediv__(self, other): | |
return self._divide(other, true_divide=True) | |
def __div__(self, other): | |
# Always do true division | |
return self._divide(other, true_divide=True) | |
def __rtruediv__(self, other): | |
# Implementing this as the inverse would be too magical -- bail out | |
return NotImplemented | |
def __rdiv__(self, other): | |
# Implementing this as the inverse would be too magical -- bail out | |
return NotImplemented | |
def __neg__(self): | |
return -self.tocsr() | |
def __iadd__(self, other): | |
return NotImplemented | |
def __isub__(self, other): | |
return NotImplemented | |
def __imul__(self, other): | |
return NotImplemented | |
def __idiv__(self, other): | |
return self.__itruediv__(other) | |
def __itruediv__(self, other): | |
return NotImplemented | |
def __pow__(self, *args, **kwargs): | |
return self.power(*args, **kwargs) | |
def transpose(self, axes=None, copy=False): | |
""" | |
Reverses the dimensions of the sparse array/matrix. | |
Parameters | |
---------- | |
axes : None, optional | |
This argument is in the signature *solely* for NumPy | |
compatibility reasons. Do not pass in anything except | |
for the default value. | |
copy : bool, optional | |
Indicates whether or not attributes of `self` should be | |
copied whenever possible. The degree to which attributes | |
are copied varies depending on the type of sparse array/matrix | |
being used. | |
Returns | |
------- | |
p : `self` with the dimensions reversed. | |
Notes | |
----- | |
If `self` is a `csr_array` or a `csc_array`, then this will return a | |
`csc_array` or a `csr_array`, respectively. | |
See Also | |
-------- | |
numpy.transpose : NumPy's implementation of 'transpose' for ndarrays | |
""" | |
return self.tocsr(copy=copy).transpose(axes=axes, copy=False) | |
def conjugate(self, copy=True): | |
"""Element-wise complex conjugation. | |
If the array/matrix is of non-complex data type and `copy` is False, | |
this method does nothing and the data is not copied. | |
Parameters | |
---------- | |
copy : bool, optional | |
If True, the result is guaranteed to not share data with self. | |
Returns | |
------- | |
A : The element-wise complex conjugate. | |
""" | |
if np.issubdtype(self.dtype, np.complexfloating): | |
return self.tocsr(copy=copy).conjugate(copy=False) | |
elif copy: | |
return self.copy() | |
else: | |
return self | |
def conj(self, copy=True): | |
return self.conjugate(copy=copy) | |
conj.__doc__ = conjugate.__doc__ | |
def _real(self): | |
return self.tocsr()._real() | |
def _imag(self): | |
return self.tocsr()._imag() | |
def nonzero(self): | |
"""Nonzero indices of the array/matrix. | |
Returns a tuple of arrays (row,col) containing the indices | |
of the non-zero elements of the array. | |
Examples | |
-------- | |
>>> from scipy.sparse import csr_array | |
>>> A = csr_array([[1,2,0],[0,0,3],[4,0,5]]) | |
>>> A.nonzero() | |
(array([0, 0, 1, 2, 2]), array([0, 1, 2, 0, 2])) | |
""" | |
# convert to COOrdinate format | |
A = self.tocoo() | |
nz_mask = A.data != 0 | |
return (A.row[nz_mask], A.col[nz_mask]) | |
def _getcol(self, j): | |
"""Returns a copy of column j of the array, as an (m x 1) sparse | |
array (column vector). | |
""" | |
if self.ndim == 1: | |
raise ValueError("getcol not provided for 1d arrays. Use indexing A[j]") | |
# Subclasses should override this method for efficiency. | |
# Post-multiply by a (n x 1) column vector 'a' containing all zeros | |
# except for a_j = 1 | |
N = self.shape[-1] | |
if j < 0: | |
j += N | |
if j < 0 or j >= N: | |
raise IndexError("index out of bounds") | |
col_selector = self._csc_container(([1], [[j], [0]]), | |
shape=(N, 1), dtype=self.dtype) | |
result = self @ col_selector | |
return result | |
def _getrow(self, i): | |
"""Returns a copy of row i of the array, as a (1 x n) sparse | |
array (row vector). | |
""" | |
if self.ndim == 1: | |
raise ValueError("getrow not meaningful for a 1d array") | |
# Subclasses should override this method for efficiency. | |
# Pre-multiply by a (1 x m) row vector 'a' containing all zeros | |
# except for a_i = 1 | |
M = self.shape[0] | |
if i < 0: | |
i += M | |
if i < 0 or i >= M: | |
raise IndexError("index out of bounds") | |
row_selector = self._csr_container(([1], [[0], [i]]), | |
shape=(1, M), dtype=self.dtype) | |
return row_selector @ self | |
# The following dunder methods cannot be implemented. | |
# | |
# def __array__(self): | |
# # Sparse matrices rely on NumPy wrapping them in object arrays under | |
# # the hood to make unary ufuncs work on them. So we cannot raise | |
# # TypeError here - which would be handy to not give users object | |
# # arrays they probably don't want (they're looking for `.toarray()`). | |
# # | |
# # Conversion with `toarray()` would also break things because of the | |
# # behavior discussed above, plus we want to avoid densification by | |
# # accident because that can too easily blow up memory. | |
# | |
# def __array_ufunc__(self): | |
# # We cannot implement __array_ufunc__ due to mismatching semantics. | |
# # See gh-7707 and gh-7349 for details. | |
# | |
# def __array_function__(self): | |
# # We cannot implement __array_function__ due to mismatching semantics. | |
# # See gh-10362 for details. | |
def todense(self, order=None, out=None): | |
""" | |
Return a dense representation of this sparse array/matrix. | |
Parameters | |
---------- | |
order : {'C', 'F'}, optional | |
Whether to store multi-dimensional data in C (row-major) | |
or Fortran (column-major) order in memory. The default | |
is 'None', which provides no ordering guarantees. | |
Cannot be specified in conjunction with the `out` | |
argument. | |
out : ndarray, 2-D, optional | |
If specified, uses this array (or `numpy.matrix`) as the | |
output buffer instead of allocating a new array to | |
return. The provided array must have the same shape and | |
dtype as the sparse array/matrix on which you are calling the | |
method. | |
Returns | |
------- | |
arr : numpy.matrix, 2-D | |
A NumPy matrix object with the same shape and containing | |
the same data represented by the sparse array/matrix, with the | |
requested memory order. If `out` was passed and was an | |
array (rather than a `numpy.matrix`), it will be filled | |
with the appropriate values and returned wrapped in a | |
`numpy.matrix` object that shares the same memory. | |
""" | |
return self._ascontainer(self.toarray(order=order, out=out)) | |
def toarray(self, order=None, out=None): | |
""" | |
Return a dense ndarray representation of this sparse array/matrix. | |
Parameters | |
---------- | |
order : {'C', 'F'}, optional | |
Whether to store multidimensional data in C (row-major) | |
or Fortran (column-major) order in memory. The default | |
is 'None', which provides no ordering guarantees. | |
Cannot be specified in conjunction with the `out` | |
argument. | |
out : ndarray, 2-D, optional | |
If specified, uses this array as the output buffer | |
instead of allocating a new array to return. The provided | |
array must have the same shape and dtype as the sparse | |
array/matrix on which you are calling the method. For most | |
sparse types, `out` is required to be memory contiguous | |
(either C or Fortran ordered). | |
Returns | |
------- | |
arr : ndarray, 2-D | |
An array with the same shape and containing the same | |
data represented by the sparse array/matrix, with the requested | |
memory order. If `out` was passed, the same object is | |
returned after being modified in-place to contain the | |
appropriate values. | |
""" | |
return self.tocoo(copy=False).toarray(order=order, out=out) | |
# Any sparse array format deriving from _spbase must define one of | |
# tocsr or tocoo. The other conversion methods may be implemented for | |
# efficiency, but are not required. | |
def tocsr(self, copy=False): | |
"""Convert this array/matrix to Compressed Sparse Row format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant csr_array/matrix. | |
""" | |
return self.tocoo(copy=copy).tocsr(copy=False) | |
def todok(self, copy=False): | |
"""Convert this array/matrix to Dictionary Of Keys format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant dok_array/matrix. | |
""" | |
return self.tocoo(copy=copy).todok(copy=False) | |
def tocoo(self, copy=False): | |
"""Convert this array/matrix to COOrdinate format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant coo_array/matrix. | |
""" | |
return self.tocsr(copy=False).tocoo(copy=copy) | |
def tolil(self, copy=False): | |
"""Convert this array/matrix to List of Lists format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant lil_array/matrix. | |
""" | |
return self.tocsr(copy=False).tolil(copy=copy) | |
def todia(self, copy=False): | |
"""Convert this array/matrix to sparse DIAgonal format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant dia_array/matrix. | |
""" | |
return self.tocoo(copy=copy).todia(copy=False) | |
def tobsr(self, blocksize=None, copy=False): | |
"""Convert this array/matrix to Block Sparse Row format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant bsr_array/matrix. | |
When blocksize=(R, C) is provided, it will be used for construction of | |
the bsr_array/matrix. | |
""" | |
return self.tocsr(copy=False).tobsr(blocksize=blocksize, copy=copy) | |
def tocsc(self, copy=False): | |
"""Convert this array/matrix to Compressed Sparse Column format. | |
With copy=False, the data/indices may be shared between this array/matrix and | |
the resultant csc_array/matrix. | |
""" | |
return self.tocsr(copy=copy).tocsc(copy=False) | |
def copy(self): | |
"""Returns a copy of this array/matrix. | |
No data/indices will be shared between the returned value and current | |
array/matrix. | |
""" | |
return self.__class__(self, copy=True) | |
def sum(self, axis=None, dtype=None, out=None): | |
""" | |
Sum the array/matrix elements over a given axis. | |
Parameters | |
---------- | |
axis : {-2, -1, 0, 1, None} optional | |
Axis along which the sum is computed. The default is to | |
compute the sum of all the array/matrix elements, returning a scalar | |
(i.e., `axis` = `None`). | |
dtype : dtype, optional | |
The type of the returned array/matrix and of the accumulator in which | |
the elements are summed. The dtype of `a` is used by default | |
unless `a` has an integer dtype of less precision than the default | |
platform integer. In that case, if `a` is signed then the platform | |
integer is used while if `a` is unsigned then an unsigned integer | |
of the same precision as the platform integer is used. | |
.. versionadded:: 0.18.0 | |
out : np.matrix, optional | |
Alternative output matrix in which to place the result. It must | |
have the same shape as the expected output, but the type of the | |
output values will be cast if necessary. | |
.. versionadded:: 0.18.0 | |
Returns | |
------- | |
sum_along_axis : np.matrix | |
A matrix with the same shape as `self`, with the specified | |
axis removed. | |
See Also | |
-------- | |
numpy.matrix.sum : NumPy's implementation of 'sum' for matrices | |
""" | |
validateaxis(axis) | |
# Mimic numpy's casting. | |
res_dtype = get_sum_dtype(self.dtype) | |
if self.ndim == 1: | |
if axis not in (None, -1, 0): | |
raise ValueError("axis must be None, -1 or 0") | |
ret = (self @ np.ones(self.shape, dtype=res_dtype)).astype(dtype) | |
if out is not None: | |
if any(dim != 1 for dim in out.shape): | |
raise ValueError("dimensions do not match") | |
out[...] = ret | |
return ret | |
# We use multiplication by a matrix of ones to achieve this. | |
# For some sparse array formats more efficient methods are | |
# possible -- these should override this function. | |
M, N = self.shape | |
if axis is None: | |
# sum over rows and columns | |
return ( | |
self @ self._ascontainer(np.ones((N, 1), dtype=res_dtype)) | |
).sum(dtype=dtype, out=out) | |
if axis < 0: | |
axis += 2 | |
# axis = 0 or 1 now | |
if axis == 0: | |
# sum over columns | |
ret = self._ascontainer( | |
np.ones((1, M), dtype=res_dtype) | |
) @ self | |
else: | |
# sum over rows | |
ret = self @ self._ascontainer( | |
np.ones((N, 1), dtype=res_dtype) | |
) | |
if out is not None and out.shape != ret.shape: | |
raise ValueError("dimensions do not match") | |
return ret.sum(axis=axis, dtype=dtype, out=out) | |
def mean(self, axis=None, dtype=None, out=None): | |
""" | |
Compute the arithmetic mean along the specified axis. | |
Returns the average of the array/matrix elements. The average is taken | |
over all elements in the array/matrix by default, otherwise over the | |
specified axis. `float64` intermediate and return values are used | |
for integer inputs. | |
Parameters | |
---------- | |
axis : {-2, -1, 0, 1, None} optional | |
Axis along which the mean is computed. The default is to compute | |
the mean of all elements in the array/matrix (i.e., `axis` = `None`). | |
dtype : data-type, optional | |
Type to use in computing the mean. For integer inputs, the default | |
is `float64`; for floating point inputs, it is the same as the | |
input dtype. | |
.. versionadded:: 0.18.0 | |
out : np.matrix, optional | |
Alternative output matrix in which to place the result. It must | |
have the same shape as the expected output, but the type of the | |
output values will be cast if necessary. | |
.. versionadded:: 0.18.0 | |
Returns | |
------- | |
m : np.matrix | |
See Also | |
-------- | |
numpy.matrix.mean : NumPy's implementation of 'mean' for matrices | |
""" | |
validateaxis(axis) | |
res_dtype = self.dtype.type | |
integral = (np.issubdtype(self.dtype, np.integer) or | |
np.issubdtype(self.dtype, np.bool_)) | |
# output dtype | |
if dtype is None: | |
if integral: | |
res_dtype = np.float64 | |
else: | |
res_dtype = np.dtype(dtype).type | |
# intermediate dtype for summation | |
inter_dtype = np.float64 if integral else res_dtype | |
inter_self = self.astype(inter_dtype) | |
if self.ndim == 1: | |
if axis not in (None, -1, 0): | |
raise ValueError("axis must be None, -1 or 0") | |
res = inter_self / self.shape[-1] | |
return res.sum(dtype=res_dtype, out=out) | |
if axis is None: | |
return (inter_self / (self.shape[0] * self.shape[1]))\ | |
.sum(dtype=res_dtype, out=out) | |
if axis < 0: | |
axis += 2 | |
# axis = 0 or 1 now | |
if axis == 0: | |
return (inter_self * (1.0 / self.shape[0])).sum( | |
axis=0, dtype=res_dtype, out=out) | |
else: | |
return (inter_self * (1.0 / self.shape[1])).sum( | |
axis=1, dtype=res_dtype, out=out) | |
def diagonal(self, k=0): | |
"""Returns the kth diagonal of the array/matrix. | |
Parameters | |
---------- | |
k : int, optional | |
Which diagonal to get, corresponding to elements a[i, i+k]. | |
Default: 0 (the main diagonal). | |
.. versionadded:: 1.0 | |
See also | |
-------- | |
numpy.diagonal : Equivalent numpy function. | |
Examples | |
-------- | |
>>> from scipy.sparse import csr_array | |
>>> A = csr_array([[1, 2, 0], [0, 0, 3], [4, 0, 5]]) | |
>>> A.diagonal() | |
array([1, 0, 5]) | |
>>> A.diagonal(k=1) | |
array([2, 3]) | |
""" | |
return self.tocsr().diagonal(k=k) | |
def trace(self, offset=0): | |
"""Returns the sum along diagonals of the sparse array/matrix. | |
Parameters | |
---------- | |
offset : int, optional | |
Which diagonal to get, corresponding to elements a[i, i+offset]. | |
Default: 0 (the main diagonal). | |
""" | |
return self.diagonal(k=offset).sum() | |
def setdiag(self, values, k=0): | |
""" | |
Set diagonal or off-diagonal elements of the array/matrix. | |
Parameters | |
---------- | |
values : array_like | |
New values of the diagonal elements. | |
Values may have any length. If the diagonal is longer than values, | |
then the remaining diagonal entries will not be set. If values are | |
longer than the diagonal, then the remaining values are ignored. | |
If a scalar value is given, all of the diagonal is set to it. | |
k : int, optional | |
Which off-diagonal to set, corresponding to elements a[i,i+k]. | |
Default: 0 (the main diagonal). | |
""" | |
M, N = self.shape | |
if (k > 0 and k >= N) or (k < 0 and -k >= M): | |
raise ValueError("k exceeds array dimensions") | |
self._setdiag(np.asarray(values), k) | |
def _setdiag(self, values, k): | |
"""This part of the implementation gets overridden by the | |
different formats. | |
""" | |
M, N = self.shape | |
if k < 0: | |
if values.ndim == 0: | |
# broadcast | |
max_index = min(M+k, N) | |
for i in range(max_index): | |
self[i - k, i] = values | |
else: | |
max_index = min(M+k, N, len(values)) | |
if max_index <= 0: | |
return | |
for i, v in enumerate(values[:max_index]): | |
self[i - k, i] = v | |
else: | |
if values.ndim == 0: | |
# broadcast | |
max_index = min(M, N-k) | |
for i in range(max_index): | |
self[i, i + k] = values | |
else: | |
max_index = min(M, N-k, len(values)) | |
if max_index <= 0: | |
return | |
for i, v in enumerate(values[:max_index]): | |
self[i, i + k] = v | |
def _process_toarray_args(self, order, out): | |
if out is not None: | |
if order is not None: | |
raise ValueError('order cannot be specified if out ' | |
'is not None') | |
if out.shape != self.shape or out.dtype != self.dtype: | |
raise ValueError('out array must be same dtype and shape as ' | |
'sparse array') | |
out[...] = 0. | |
return out | |
else: | |
return np.zeros(self.shape, dtype=self.dtype, order=order) | |
def _get_index_dtype(self, arrays=(), maxval=None, check_contents=False): | |
""" | |
Determine index dtype for array. | |
This wraps _sputils.get_index_dtype, providing compatibility for both | |
array and matrix API sparse matrices. Matrix API sparse matrices would | |
attempt to downcast the indices - which can be computationally | |
expensive and undesirable for users. The array API changes this | |
behaviour. | |
See discussion: https://github.com/scipy/scipy/issues/16774 | |
The get_index_dtype import is due to implementation details of the test | |
suite. It allows the decorator ``with_64bit_maxval_limit`` to mock a | |
lower int32 max value for checks on the matrix API's downcasting | |
behaviour. | |
""" | |
from ._sputils import get_index_dtype | |
# Don't check contents for array API | |
return get_index_dtype(arrays, | |
maxval, | |
(check_contents and not isinstance(self, sparray))) | |
## All methods below are deprecated and should be removed in | |
## scipy 1.14.0 | |
## | |
## Also uncomment the definition of shape above. | |
def get_shape(self): | |
"""Get shape of a sparse array/matrix. | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use `X.shape` instead. | |
""" | |
msg = ( | |
"`get_shape` is deprecated and will be removed in v1.14.0; " | |
"use `X.shape` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self._shape | |
def set_shape(self, shape): | |
"""See `reshape`. | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use `X.reshape` instead. | |
""" | |
msg = ( | |
"Shape assignment is deprecated and will be removed in v1.14.0; " | |
"use `reshape` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
# Make sure copy is False since this is in place | |
# Make sure format is unchanged because we are doing a __dict__ swap | |
new_self = self.reshape(shape, copy=False).asformat(self.format) | |
self.__dict__ = new_self.__dict__ | |
shape = property( | |
fget=lambda self: self._shape, | |
fset=set_shape, | |
doc="""The shape of the array. | |
Note that, starting in SciPy 1.14.0, this property will no longer be | |
settable. To change the array shape, use `X.reshape` instead. | |
""" | |
) | |
def asfptype(self): | |
"""Upcast array/matrix to a floating point format (if necessary) | |
.. deprecated:: 1.11.0 | |
This method is for internal use only, and will be removed from the | |
public API in SciPy 1.14.0. | |
""" | |
msg = ( | |
"`asfptype` is an internal function, and is deprecated " | |
"as part of the public API. It will be removed in v1.14.0." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self._asfptype() | |
def getmaxprint(self): | |
"""Maximum number of elements to display when printed. | |
.. deprecated:: 1.11.0 | |
This method is for internal use only, and will be removed from the | |
public API in SciPy 1.14.0. | |
""" | |
msg = ( | |
"`getmaxprint` is an internal function, and is deprecated " | |
"as part of the public API. It will be removed in v1.14.0." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self._getmaxprint() | |
def getformat(self): | |
"""Sparse array/matrix storage format. | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use `X.format` instead. | |
""" | |
msg = ( | |
"`getformat` is deprecated and will be removed in v1.14.0; " | |
"use `X.format` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self.format | |
def getnnz(self, axis=None): | |
"""Number of stored values, including explicit zeros. | |
Parameters | |
---------- | |
axis : None, 0, or 1 | |
Select between the number of values across the whole array/matrix, in | |
each column, or in each row. | |
See also | |
-------- | |
count_nonzero : Number of non-zero entries | |
""" | |
return self._getnnz(axis=axis) | |
def getH(self): | |
"""Return the Hermitian transpose of this array/matrix. | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use `X.conj().T` instead. | |
""" | |
msg = ( | |
"`getH` is deprecated and will be removed in v1.14.0; " | |
"use `X.conj().T` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self.conjugate().transpose() | |
def getcol(self, j): | |
"""Returns a copy of column j of the array/matrix, as an (m x 1) sparse | |
array/matrix (column vector). | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use array/matrix indexing instead. | |
""" | |
msg = ( | |
"`getcol` is deprecated and will be removed in v1.14.0; " | |
f"use `X[:, [{j}]]` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self._getcol(j) | |
def getrow(self, i): | |
"""Returns a copy of row i of the array/matrix, as a (1 x n) sparse | |
array/matrix (row vector). | |
.. deprecated:: 1.11.0 | |
This method will be removed in SciPy 1.14.0. | |
Use array/matrix indexing instead. | |
""" | |
msg = ( | |
"`getrow` is deprecated and will be removed in v1.14.0; " | |
f"use `X[[{i}]]` instead." | |
) | |
warn(msg, DeprecationWarning, stacklevel=2) | |
return self._getrow(i) | |
## End 1.14.0 deprecated methods | |
class sparray: | |
"""A namespace class to separate sparray from spmatrix""" | |
pass | |
sparray.__doc__ = _spbase.__doc__ | |
def issparse(x): | |
"""Is `x` of a sparse array or sparse matrix type? | |
Parameters | |
---------- | |
x | |
object to check for being a sparse array or sparse matrix | |
Returns | |
------- | |
bool | |
True if `x` is a sparse array or a sparse matrix, False otherwise | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import csr_array, csr_matrix, issparse | |
>>> issparse(csr_matrix([[5]])) | |
True | |
>>> issparse(csr_array([[5]])) | |
True | |
>>> issparse(np.array([[5]])) | |
False | |
>>> issparse(5) | |
False | |
""" | |
return isinstance(x, _spbase) | |
def isspmatrix(x): | |
"""Is `x` of a sparse matrix type? | |
Parameters | |
---------- | |
x | |
object to check for being a sparse matrix | |
Returns | |
------- | |
bool | |
True if `x` is a sparse matrix, False otherwise | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import csr_array, csr_matrix, isspmatrix | |
>>> isspmatrix(csr_matrix([[5]])) | |
True | |
>>> isspmatrix(csr_array([[5]])) | |
False | |
>>> isspmatrix(np.array([[5]])) | |
False | |
>>> isspmatrix(5) | |
False | |
""" | |
return isinstance(x, spmatrix) | |