peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/scipy
/sparse
/_construct.py
"""Functions to construct sparse matrices and arrays | |
""" | |
__docformat__ = "restructuredtext en" | |
__all__ = ['spdiags', 'eye', 'identity', 'kron', 'kronsum', | |
'hstack', 'vstack', 'bmat', 'rand', 'random', 'diags', 'block_diag', | |
'diags_array', 'block_array', 'eye_array', 'random_array'] | |
import numbers | |
import math | |
import numpy as np | |
from scipy._lib._util import check_random_state, rng_integers | |
from ._sputils import upcast, get_index_dtype, isscalarlike | |
from ._sparsetools import csr_hstack | |
from ._bsr import bsr_matrix, bsr_array | |
from ._coo import coo_matrix, coo_array | |
from ._csc import csc_matrix, csc_array | |
from ._csr import csr_matrix, csr_array | |
from ._dia import dia_matrix, dia_array | |
from ._base import issparse, sparray | |
def spdiags(data, diags, m=None, n=None, format=None): | |
""" | |
Return a sparse matrix from diagonals. | |
Parameters | |
---------- | |
data : array_like | |
Matrix diagonals stored row-wise | |
diags : sequence of int or an int | |
Diagonals to set: | |
* k = 0 the main diagonal | |
* k > 0 the kth upper diagonal | |
* k < 0 the kth lower diagonal | |
m, n : int, tuple, optional | |
Shape of the result. If `n` is None and `m` is a given tuple, | |
the shape is this tuple. If omitted, the matrix is square and | |
its shape is len(data[0]). | |
format : str, optional | |
Format of the result. By default (format=None) an appropriate sparse | |
matrix format is returned. This choice is subject to change. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``diags_array`` to take advantage | |
of the sparse array functionality. | |
See Also | |
-------- | |
diags_array : more convenient form of this function | |
diags : matrix version of diags_array | |
dia_matrix : the sparse DIAgonal format. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import spdiags | |
>>> data = np.array([[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]]) | |
>>> diags = np.array([0, -1, 2]) | |
>>> spdiags(data, diags, 4, 4).toarray() | |
array([[1, 0, 3, 0], | |
[1, 2, 0, 4], | |
[0, 2, 3, 0], | |
[0, 0, 3, 4]]) | |
""" | |
if m is None and n is None: | |
m = n = len(data[0]) | |
elif n is None: | |
m, n = m | |
return dia_matrix((data, diags), shape=(m, n)).asformat(format) | |
def diags_array(diagonals, /, *, offsets=0, shape=None, format=None, dtype=None): | |
""" | |
Construct a sparse array from diagonals. | |
Parameters | |
---------- | |
diagonals : sequence of array_like | |
Sequence of arrays containing the array diagonals, | |
corresponding to `offsets`. | |
offsets : sequence of int or an int, optional | |
Diagonals to set: | |
- k = 0 the main diagonal (default) | |
- k > 0 the kth upper diagonal | |
- k < 0 the kth lower diagonal | |
shape : tuple of int, optional | |
Shape of the result. If omitted, a square array large enough | |
to contain the diagonals is returned. | |
format : {"dia", "csr", "csc", "lil", ...}, optional | |
Matrix format of the result. By default (format=None) an | |
appropriate sparse array format is returned. This choice is | |
subject to change. | |
dtype : dtype, optional | |
Data type of the array. | |
Notes | |
----- | |
The result from `diags_array` is the sparse equivalent of:: | |
np.diag(diagonals[0], offsets[0]) | |
+ ... | |
+ np.diag(diagonals[k], offsets[k]) | |
Repeated diagonal offsets are disallowed. | |
.. versionadded:: 1.11 | |
Examples | |
-------- | |
>>> from scipy.sparse import diags_array | |
>>> diagonals = [[1, 2, 3, 4], [1, 2, 3], [1, 2]] | |
>>> diags_array(diagonals, offsets=[0, -1, 2]).toarray() | |
array([[1, 0, 1, 0], | |
[1, 2, 0, 2], | |
[0, 2, 3, 0], | |
[0, 0, 3, 4]]) | |
Broadcasting of scalars is supported (but shape needs to be | |
specified): | |
>>> diags_array([1, -2, 1], offsets=[-1, 0, 1], shape=(4, 4)).toarray() | |
array([[-2., 1., 0., 0.], | |
[ 1., -2., 1., 0.], | |
[ 0., 1., -2., 1.], | |
[ 0., 0., 1., -2.]]) | |
If only one diagonal is wanted (as in `numpy.diag`), the following | |
works as well: | |
>>> diags_array([1, 2, 3], offsets=1).toarray() | |
array([[ 0., 1., 0., 0.], | |
[ 0., 0., 2., 0.], | |
[ 0., 0., 0., 3.], | |
[ 0., 0., 0., 0.]]) | |
""" | |
# if offsets is not a sequence, assume that there's only one diagonal | |
if isscalarlike(offsets): | |
# now check that there's actually only one diagonal | |
if len(diagonals) == 0 or isscalarlike(diagonals[0]): | |
diagonals = [np.atleast_1d(diagonals)] | |
else: | |
raise ValueError("Different number of diagonals and offsets.") | |
else: | |
diagonals = list(map(np.atleast_1d, diagonals)) | |
offsets = np.atleast_1d(offsets) | |
# Basic check | |
if len(diagonals) != len(offsets): | |
raise ValueError("Different number of diagonals and offsets.") | |
# Determine shape, if omitted | |
if shape is None: | |
m = len(diagonals[0]) + abs(int(offsets[0])) | |
shape = (m, m) | |
# Determine data type, if omitted | |
if dtype is None: | |
dtype = np.common_type(*diagonals) | |
# Construct data array | |
m, n = shape | |
M = max([min(m + offset, n - offset) + max(0, offset) | |
for offset in offsets]) | |
M = max(0, M) | |
data_arr = np.zeros((len(offsets), M), dtype=dtype) | |
K = min(m, n) | |
for j, diagonal in enumerate(diagonals): | |
offset = offsets[j] | |
k = max(0, offset) | |
length = min(m + offset, n - offset, K) | |
if length < 0: | |
raise ValueError("Offset %d (index %d) out of bounds" % (offset, j)) | |
try: | |
data_arr[j, k:k+length] = diagonal[...,:length] | |
except ValueError as e: | |
if len(diagonal) != length and len(diagonal) != 1: | |
raise ValueError( | |
"Diagonal length (index %d: %d at offset %d) does not " | |
"agree with array size (%d, %d)." % ( | |
j, len(diagonal), offset, m, n)) from e | |
raise | |
return dia_array((data_arr, offsets), shape=(m, n)).asformat(format) | |
def diags(diagonals, offsets=0, shape=None, format=None, dtype=None): | |
""" | |
Construct a sparse matrix from diagonals. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``diags_array`` to take advantage | |
of the sparse array functionality. | |
Parameters | |
---------- | |
diagonals : sequence of array_like | |
Sequence of arrays containing the matrix diagonals, | |
corresponding to `offsets`. | |
offsets : sequence of int or an int, optional | |
Diagonals to set: | |
- k = 0 the main diagonal (default) | |
- k > 0 the kth upper diagonal | |
- k < 0 the kth lower diagonal | |
shape : tuple of int, optional | |
Shape of the result. If omitted, a square matrix large enough | |
to contain the diagonals is returned. | |
format : {"dia", "csr", "csc", "lil", ...}, optional | |
Matrix format of the result. By default (format=None) an | |
appropriate sparse matrix format is returned. This choice is | |
subject to change. | |
dtype : dtype, optional | |
Data type of the matrix. | |
See Also | |
-------- | |
spdiags : construct matrix from diagonals | |
diags_array : construct sparse array instead of sparse matrix | |
Notes | |
----- | |
This function differs from `spdiags` in the way it handles | |
off-diagonals. | |
The result from `diags` is the sparse equivalent of:: | |
np.diag(diagonals[0], offsets[0]) | |
+ ... | |
+ np.diag(diagonals[k], offsets[k]) | |
Repeated diagonal offsets are disallowed. | |
.. versionadded:: 0.11 | |
Examples | |
-------- | |
>>> from scipy.sparse import diags | |
>>> diagonals = [[1, 2, 3, 4], [1, 2, 3], [1, 2]] | |
>>> diags(diagonals, [0, -1, 2]).toarray() | |
array([[1, 0, 1, 0], | |
[1, 2, 0, 2], | |
[0, 2, 3, 0], | |
[0, 0, 3, 4]]) | |
Broadcasting of scalars is supported (but shape needs to be | |
specified): | |
>>> diags([1, -2, 1], [-1, 0, 1], shape=(4, 4)).toarray() | |
array([[-2., 1., 0., 0.], | |
[ 1., -2., 1., 0.], | |
[ 0., 1., -2., 1.], | |
[ 0., 0., 1., -2.]]) | |
If only one diagonal is wanted (as in `numpy.diag`), the following | |
works as well: | |
>>> diags([1, 2, 3], 1).toarray() | |
array([[ 0., 1., 0., 0.], | |
[ 0., 0., 2., 0.], | |
[ 0., 0., 0., 3.], | |
[ 0., 0., 0., 0.]]) | |
""" | |
A = diags_array(diagonals, offsets=offsets, shape=shape, dtype=dtype) | |
return dia_matrix(A).asformat(format) | |
def identity(n, dtype='d', format=None): | |
"""Identity matrix in sparse format | |
Returns an identity matrix with shape (n,n) using a given | |
sparse format and dtype. This differs from `eye_array` in | |
that it has a square shape with ones only on the main diagonal. | |
It is thus the multiplicative identity. `eye_array` allows | |
rectangular shapes and the diagonal can be offset from the main one. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``eye_array`` to take advantage | |
of the sparse array functionality. | |
Parameters | |
---------- | |
n : int | |
Shape of the identity matrix. | |
dtype : dtype, optional | |
Data type of the matrix | |
format : str, optional | |
Sparse format of the result, e.g., format="csr", etc. | |
Examples | |
-------- | |
>>> import scipy as sp | |
>>> sp.sparse.identity(3).toarray() | |
array([[ 1., 0., 0.], | |
[ 0., 1., 0.], | |
[ 0., 0., 1.]]) | |
>>> sp.sparse.identity(3, dtype='int8', format='dia') | |
<3x3 sparse matrix of type '<class 'numpy.int8'>' | |
with 3 stored elements (1 diagonals) in DIAgonal format> | |
>>> sp.sparse.eye_array(3, dtype='int8', format='dia') | |
<3x3 sparse array of type '<class 'numpy.int8'>' | |
with 3 stored elements (1 diagonals) in DIAgonal format> | |
""" | |
return eye(n, n, dtype=dtype, format=format) | |
def eye_array(m, n=None, *, k=0, dtype=float, format=None): | |
"""Identity matrix in sparse array format | |
Return a sparse array with ones on diagonal. | |
Specifically a sparse array (m x n) where the kth diagonal | |
is all ones and everything else is zeros. | |
Parameters | |
---------- | |
m : int or tuple of ints | |
Number of rows requested. | |
n : int, optional | |
Number of columns. Default: `m`. | |
k : int, optional | |
Diagonal to place ones on. Default: 0 (main diagonal). | |
dtype : dtype, optional | |
Data type of the array | |
format : str, optional (default: "dia") | |
Sparse format of the result, e.g., format="csr", etc. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import scipy as sp | |
>>> sp.sparse.eye_array(3).toarray() | |
array([[ 1., 0., 0.], | |
[ 0., 1., 0.], | |
[ 0., 0., 1.]]) | |
>>> sp.sparse.eye_array(3, dtype=np.int8) | |
<3x3 sparse array of type '<class 'numpy.int8'>' | |
with 3 stored elements (1 diagonals) in DIAgonal format> | |
""" | |
# TODO: delete next 15 lines [combine with _eye()] once spmatrix removed | |
return _eye(m, n, k, dtype, format) | |
def _eye(m, n, k, dtype, format, as_sparray=True): | |
if as_sparray: | |
csr_sparse = csr_array | |
csc_sparse = csc_array | |
coo_sparse = coo_array | |
diags_sparse = diags_array | |
else: | |
csr_sparse = csr_matrix | |
csc_sparse = csc_matrix | |
coo_sparse = coo_matrix | |
diags_sparse = diags | |
if n is None: | |
n = m | |
m, n = int(m), int(n) | |
if m == n and k == 0: | |
# fast branch for special formats | |
if format in ['csr', 'csc']: | |
idx_dtype = get_index_dtype(maxval=n) | |
indptr = np.arange(n+1, dtype=idx_dtype) | |
indices = np.arange(n, dtype=idx_dtype) | |
data = np.ones(n, dtype=dtype) | |
cls = {'csr': csr_sparse, 'csc': csc_sparse}[format] | |
return cls((data, indices, indptr), (n, n)) | |
elif format == 'coo': | |
idx_dtype = get_index_dtype(maxval=n) | |
row = np.arange(n, dtype=idx_dtype) | |
col = np.arange(n, dtype=idx_dtype) | |
data = np.ones(n, dtype=dtype) | |
return coo_sparse((data, (row, col)), (n, n)) | |
data = np.ones((1, max(0, min(m + k, n))), dtype=dtype) | |
return diags_sparse(data, offsets=[k], shape=(m, n), dtype=dtype).asformat(format) | |
def eye(m, n=None, k=0, dtype=float, format=None): | |
"""Sparse matrix with ones on diagonal | |
Returns a sparse matrix (m x n) where the kth diagonal | |
is all ones and everything else is zeros. | |
Parameters | |
---------- | |
m : int | |
Number of rows in the matrix. | |
n : int, optional | |
Number of columns. Default: `m`. | |
k : int, optional | |
Diagonal to place ones on. Default: 0 (main diagonal). | |
dtype : dtype, optional | |
Data type of the matrix. | |
format : str, optional | |
Sparse format of the result, e.g., format="csr", etc. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``eye_array`` to take advantage | |
of the sparse array functionality. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import scipy as sp | |
>>> sp.sparse.eye(3).toarray() | |
array([[ 1., 0., 0.], | |
[ 0., 1., 0.], | |
[ 0., 0., 1.]]) | |
>>> sp.sparse.eye(3, dtype=np.int8) | |
<3x3 sparse matrix of type '<class 'numpy.int8'>' | |
with 3 stored elements (1 diagonals) in DIAgonal format> | |
""" | |
return _eye(m, n, k, dtype, format, False) | |
def kron(A, B, format=None): | |
"""kronecker product of sparse matrices A and B | |
Parameters | |
---------- | |
A : sparse or dense matrix | |
first matrix of the product | |
B : sparse or dense matrix | |
second matrix of the product | |
format : str, optional (default: 'bsr' or 'coo') | |
format of the result (e.g. "csr") | |
If None, choose 'bsr' for relatively dense array and 'coo' for others | |
Returns | |
------- | |
kronecker product in a sparse format. | |
Returns a sparse matrix unless either A or B is a | |
sparse array in which case returns a sparse array. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import scipy as sp | |
>>> A = sp.sparse.csr_array(np.array([[0, 2], [5, 0]])) | |
>>> B = sp.sparse.csr_array(np.array([[1, 2], [3, 4]])) | |
>>> sp.sparse.kron(A, B).toarray() | |
array([[ 0, 0, 2, 4], | |
[ 0, 0, 6, 8], | |
[ 5, 10, 0, 0], | |
[15, 20, 0, 0]]) | |
>>> sp.sparse.kron(A, [[1, 2], [3, 4]]).toarray() | |
array([[ 0, 0, 2, 4], | |
[ 0, 0, 6, 8], | |
[ 5, 10, 0, 0], | |
[15, 20, 0, 0]]) | |
""" | |
# TODO: delete next 10 lines and replace _sparse with _array when spmatrix removed | |
if isinstance(A, sparray) or isinstance(B, sparray): | |
# convert to local variables | |
bsr_sparse = bsr_array | |
csr_sparse = csr_array | |
coo_sparse = coo_array | |
else: # use spmatrix | |
bsr_sparse = bsr_matrix | |
csr_sparse = csr_matrix | |
coo_sparse = coo_matrix | |
B = coo_sparse(B) | |
# B is fairly dense, use BSR | |
if (format is None or format == "bsr") and 2*B.nnz >= B.shape[0] * B.shape[1]: | |
A = csr_sparse(A,copy=True) | |
output_shape = (A.shape[0]*B.shape[0], A.shape[1]*B.shape[1]) | |
if A.nnz == 0 or B.nnz == 0: | |
# kronecker product is the zero matrix | |
return coo_sparse(output_shape).asformat(format) | |
B = B.toarray() | |
data = A.data.repeat(B.size).reshape(-1,B.shape[0],B.shape[1]) | |
data = data * B | |
return bsr_sparse((data,A.indices,A.indptr), shape=output_shape) | |
else: | |
# use COO | |
A = coo_sparse(A) | |
output_shape = (A.shape[0]*B.shape[0], A.shape[1]*B.shape[1]) | |
if A.nnz == 0 or B.nnz == 0: | |
# kronecker product is the zero matrix | |
return coo_sparse(output_shape).asformat(format) | |
# expand entries of a into blocks | |
row = A.row.repeat(B.nnz) | |
col = A.col.repeat(B.nnz) | |
data = A.data.repeat(B.nnz) | |
if max(A.shape[0]*B.shape[0], A.shape[1]*B.shape[1]) > np.iinfo('int32').max: | |
row = row.astype(np.int64) | |
col = col.astype(np.int64) | |
row *= B.shape[0] | |
col *= B.shape[1] | |
# increment block indices | |
row,col = row.reshape(-1,B.nnz),col.reshape(-1,B.nnz) | |
row += B.row | |
col += B.col | |
row,col = row.reshape(-1),col.reshape(-1) | |
# compute block entries | |
data = data.reshape(-1,B.nnz) * B.data | |
data = data.reshape(-1) | |
return coo_sparse((data,(row,col)), shape=output_shape).asformat(format) | |
def kronsum(A, B, format=None): | |
"""kronecker sum of square sparse matrices A and B | |
Kronecker sum of two sparse matrices is a sum of two Kronecker | |
products kron(I_n,A) + kron(B,I_m) where A has shape (m,m) | |
and B has shape (n,n) and I_m and I_n are identity matrices | |
of shape (m,m) and (n,n), respectively. | |
Parameters | |
---------- | |
A | |
square matrix | |
B | |
square matrix | |
format : str | |
format of the result (e.g. "csr") | |
Returns | |
------- | |
kronecker sum in a sparse matrix format | |
""" | |
# TODO: delete next 8 lines and replace _sparse with _array when spmatrix removed | |
if isinstance(A, sparray) or isinstance(B, sparray): | |
# convert to local variables | |
coo_sparse = coo_array | |
identity_sparse = eye_array | |
else: | |
coo_sparse = coo_matrix | |
identity_sparse = identity | |
A = coo_sparse(A) | |
B = coo_sparse(B) | |
if A.shape[0] != A.shape[1]: | |
raise ValueError('A is not square') | |
if B.shape[0] != B.shape[1]: | |
raise ValueError('B is not square') | |
dtype = upcast(A.dtype, B.dtype) | |
I_n = identity_sparse(A.shape[0], dtype=dtype) | |
I_m = identity_sparse(B.shape[0], dtype=dtype) | |
L = kron(I_m, A, format='coo') | |
R = kron(B, I_n, format='coo') | |
return (L + R).asformat(format) | |
def _compressed_sparse_stack(blocks, axis, return_spmatrix): | |
""" | |
Stacking fast path for CSR/CSC matrices or arrays | |
(i) vstack for CSR, (ii) hstack for CSC. | |
""" | |
other_axis = 1 if axis == 0 else 0 | |
data = np.concatenate([b.data for b in blocks]) | |
constant_dim = blocks[0].shape[other_axis] | |
idx_dtype = get_index_dtype(arrays=[b.indptr for b in blocks], | |
maxval=max(data.size, constant_dim)) | |
indices = np.empty(data.size, dtype=idx_dtype) | |
indptr = np.empty(sum(b.shape[axis] for b in blocks) + 1, dtype=idx_dtype) | |
last_indptr = idx_dtype(0) | |
sum_dim = 0 | |
sum_indices = 0 | |
for b in blocks: | |
if b.shape[other_axis] != constant_dim: | |
raise ValueError(f'incompatible dimensions for axis {other_axis}') | |
indices[sum_indices:sum_indices+b.indices.size] = b.indices | |
sum_indices += b.indices.size | |
idxs = slice(sum_dim, sum_dim + b.shape[axis]) | |
indptr[idxs] = b.indptr[:-1] | |
indptr[idxs] += last_indptr | |
sum_dim += b.shape[axis] | |
last_indptr += b.indptr[-1] | |
indptr[-1] = last_indptr | |
# TODO remove this if-structure when sparse matrices removed | |
if return_spmatrix: | |
if axis == 0: | |
return csr_matrix((data, indices, indptr), | |
shape=(sum_dim, constant_dim)) | |
else: | |
return csc_matrix((data, indices, indptr), | |
shape=(constant_dim, sum_dim)) | |
if axis == 0: | |
return csr_array((data, indices, indptr), | |
shape=(sum_dim, constant_dim)) | |
else: | |
return csc_array((data, indices, indptr), | |
shape=(constant_dim, sum_dim)) | |
def _stack_along_minor_axis(blocks, axis): | |
""" | |
Stacking fast path for CSR/CSC matrices along the minor axis | |
(i) hstack for CSR, (ii) vstack for CSC. | |
""" | |
n_blocks = len(blocks) | |
if n_blocks == 0: | |
raise ValueError('Missing block matrices') | |
if n_blocks == 1: | |
return blocks[0] | |
# check for incompatible dimensions | |
other_axis = 1 if axis == 0 else 0 | |
other_axis_dims = {b.shape[other_axis] for b in blocks} | |
if len(other_axis_dims) > 1: | |
raise ValueError(f'Mismatching dimensions along axis {other_axis}: ' | |
f'{other_axis_dims}') | |
constant_dim, = other_axis_dims | |
# Do the stacking | |
indptr_list = [b.indptr for b in blocks] | |
data_cat = np.concatenate([b.data for b in blocks]) | |
# Need to check if any indices/indptr, would be too large post- | |
# concatenation for np.int32: | |
# - The max value of indices is the output array's stacking-axis length - 1 | |
# - The max value in indptr is the number of non-zero entries. This is | |
# exceedingly unlikely to require int64, but is checked out of an | |
# abundance of caution. | |
sum_dim = sum(b.shape[axis] for b in blocks) | |
nnz = sum(len(b.indices) for b in blocks) | |
idx_dtype = get_index_dtype(maxval=max(sum_dim - 1, nnz)) | |
stack_dim_cat = np.array([b.shape[axis] for b in blocks], dtype=idx_dtype) | |
if data_cat.size > 0: | |
indptr_cat = np.concatenate(indptr_list).astype(idx_dtype) | |
indices_cat = (np.concatenate([b.indices for b in blocks]) | |
.astype(idx_dtype)) | |
indptr = np.empty(constant_dim + 1, dtype=idx_dtype) | |
indices = np.empty_like(indices_cat) | |
data = np.empty_like(data_cat) | |
csr_hstack(n_blocks, constant_dim, stack_dim_cat, | |
indptr_cat, indices_cat, data_cat, | |
indptr, indices, data) | |
else: | |
indptr = np.zeros(constant_dim + 1, dtype=idx_dtype) | |
indices = np.empty(0, dtype=idx_dtype) | |
data = np.empty(0, dtype=data_cat.dtype) | |
if axis == 0: | |
return blocks[0]._csc_container((data, indices, indptr), | |
shape=(sum_dim, constant_dim)) | |
else: | |
return blocks[0]._csr_container((data, indices, indptr), | |
shape=(constant_dim, sum_dim)) | |
def hstack(blocks, format=None, dtype=None): | |
""" | |
Stack sparse matrices horizontally (column wise) | |
Parameters | |
---------- | |
blocks | |
sequence of sparse matrices with compatible shapes | |
format : str | |
sparse format of the result (e.g., "csr") | |
by default an appropriate sparse matrix format is returned. | |
This choice is subject to change. | |
dtype : dtype, optional | |
The data-type of the output matrix. If not given, the dtype is | |
determined from that of `blocks`. | |
Returns | |
------- | |
new_array : sparse matrix or array | |
If any block in blocks is a sparse array, return a sparse array. | |
Otherwise return a sparse matrix. | |
If you want a sparse array built from blocks that are not sparse | |
arrays, use `block(hstack(blocks))` or convert one block | |
e.g. `blocks[0] = csr_array(blocks[0])`. | |
See Also | |
-------- | |
vstack : stack sparse matrices vertically (row wise) | |
Examples | |
-------- | |
>>> from scipy.sparse import coo_matrix, hstack | |
>>> A = coo_matrix([[1, 2], [3, 4]]) | |
>>> B = coo_matrix([[5], [6]]) | |
>>> hstack([A,B]).toarray() | |
array([[1, 2, 5], | |
[3, 4, 6]]) | |
""" | |
blocks = np.asarray(blocks, dtype='object') | |
if any(isinstance(b, sparray) for b in blocks.flat): | |
return _block([blocks], format, dtype) | |
else: | |
return _block([blocks], format, dtype, return_spmatrix=True) | |
def vstack(blocks, format=None, dtype=None): | |
""" | |
Stack sparse arrays vertically (row wise) | |
Parameters | |
---------- | |
blocks | |
sequence of sparse arrays with compatible shapes | |
format : str, optional | |
sparse format of the result (e.g., "csr") | |
by default an appropriate sparse array format is returned. | |
This choice is subject to change. | |
dtype : dtype, optional | |
The data-type of the output array. If not given, the dtype is | |
determined from that of `blocks`. | |
Returns | |
------- | |
new_array : sparse matrix or array | |
If any block in blocks is a sparse array, return a sparse array. | |
Otherwise return a sparse matrix. | |
If you want a sparse array built from blocks that are not sparse | |
arrays, use `block(vstack(blocks))` or convert one block | |
e.g. `blocks[0] = csr_array(blocks[0])`. | |
See Also | |
-------- | |
hstack : stack sparse matrices horizontally (column wise) | |
Examples | |
-------- | |
>>> from scipy.sparse import coo_array, vstack | |
>>> A = coo_array([[1, 2], [3, 4]]) | |
>>> B = coo_array([[5, 6]]) | |
>>> vstack([A, B]).toarray() | |
array([[1, 2], | |
[3, 4], | |
[5, 6]]) | |
""" | |
blocks = np.asarray(blocks, dtype='object') | |
if any(isinstance(b, sparray) for b in blocks.flat): | |
return _block([[b] for b in blocks], format, dtype) | |
else: | |
return _block([[b] for b in blocks], format, dtype, return_spmatrix=True) | |
def bmat(blocks, format=None, dtype=None): | |
""" | |
Build a sparse array or matrix from sparse sub-blocks | |
Note: `block_array` is preferred over `bmat`. They are the same function | |
except that `bmat` can return a deprecated sparse matrix. | |
`bmat` returns a coo_matrix if none of the inputs are a sparse array. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``block_array`` to take advantage | |
of the sparse array functionality. | |
Parameters | |
---------- | |
blocks : array_like | |
Grid of sparse matrices with compatible shapes. | |
An entry of None implies an all-zero matrix. | |
format : {'bsr', 'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}, optional | |
The sparse format of the result (e.g. "csr"). By default an | |
appropriate sparse matrix format is returned. | |
This choice is subject to change. | |
dtype : dtype, optional | |
The data-type of the output matrix. If not given, the dtype is | |
determined from that of `blocks`. | |
Returns | |
------- | |
bmat : sparse matrix or array | |
If any block in blocks is a sparse array, return a sparse array. | |
Otherwise return a sparse matrix. | |
If you want a sparse array built from blocks that are not sparse | |
arrays, use `block_array()`. | |
See Also | |
-------- | |
block_array | |
Examples | |
-------- | |
>>> from scipy.sparse import coo_array, bmat | |
>>> A = coo_array([[1, 2], [3, 4]]) | |
>>> B = coo_array([[5], [6]]) | |
>>> C = coo_array([[7]]) | |
>>> bmat([[A, B], [None, C]]).toarray() | |
array([[1, 2, 5], | |
[3, 4, 6], | |
[0, 0, 7]]) | |
>>> bmat([[A, None], [None, C]]).toarray() | |
array([[1, 2, 0], | |
[3, 4, 0], | |
[0, 0, 7]]) | |
""" | |
blocks = np.asarray(blocks, dtype='object') | |
if any(isinstance(b, sparray) for b in blocks.flat): | |
return _block(blocks, format, dtype) | |
else: | |
return _block(blocks, format, dtype, return_spmatrix=True) | |
def block_array(blocks, *, format=None, dtype=None): | |
""" | |
Build a sparse array from sparse sub-blocks | |
Parameters | |
---------- | |
blocks : array_like | |
Grid of sparse arrays with compatible shapes. | |
An entry of None implies an all-zero array. | |
format : {'bsr', 'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}, optional | |
The sparse format of the result (e.g. "csr"). By default an | |
appropriate sparse array format is returned. | |
This choice is subject to change. | |
dtype : dtype, optional | |
The data-type of the output array. If not given, the dtype is | |
determined from that of `blocks`. | |
Returns | |
------- | |
block : sparse array | |
See Also | |
-------- | |
block_diag : specify blocks along the main diagonals | |
diags : specify (possibly offset) diagonals | |
Examples | |
-------- | |
>>> from scipy.sparse import coo_array, block_array | |
>>> A = coo_array([[1, 2], [3, 4]]) | |
>>> B = coo_array([[5], [6]]) | |
>>> C = coo_array([[7]]) | |
>>> block_array([[A, B], [None, C]]).toarray() | |
array([[1, 2, 5], | |
[3, 4, 6], | |
[0, 0, 7]]) | |
>>> block_array([[A, None], [None, C]]).toarray() | |
array([[1, 2, 0], | |
[3, 4, 0], | |
[0, 0, 7]]) | |
""" | |
return _block(blocks, format, dtype) | |
def _block(blocks, format, dtype, return_spmatrix=False): | |
blocks = np.asarray(blocks, dtype='object') | |
if blocks.ndim != 2: | |
raise ValueError('blocks must be 2-D') | |
M,N = blocks.shape | |
# check for fast path cases | |
if (format in (None, 'csr') and | |
all(issparse(b) and b.format == 'csr' for b in blocks.flat) | |
): | |
if N > 1: | |
# stack along columns (axis 1): must have shape (M, 1) | |
blocks = [[_stack_along_minor_axis(blocks[b, :], 1)] for b in range(M)] | |
blocks = np.asarray(blocks, dtype='object') | |
# stack along rows (axis 0): | |
A = _compressed_sparse_stack(blocks[:, 0], 0, return_spmatrix) | |
if dtype is not None: | |
A = A.astype(dtype) | |
return A | |
elif (format in (None, 'csc') and | |
all(issparse(b) and b.format == 'csc' for b in blocks.flat) | |
): | |
if M > 1: | |
# stack along rows (axis 0): must have shape (1, N) | |
blocks = [[_stack_along_minor_axis(blocks[:, b], 0) for b in range(N)]] | |
blocks = np.asarray(blocks, dtype='object') | |
# stack along columns (axis 1): | |
A = _compressed_sparse_stack(blocks[0, :], 1, return_spmatrix) | |
if dtype is not None: | |
A = A.astype(dtype) | |
return A | |
block_mask = np.zeros(blocks.shape, dtype=bool) | |
brow_lengths = np.zeros(M, dtype=np.int64) | |
bcol_lengths = np.zeros(N, dtype=np.int64) | |
# convert everything to COO format | |
for i in range(M): | |
for j in range(N): | |
if blocks[i,j] is not None: | |
A = coo_array(blocks[i,j]) | |
blocks[i,j] = A | |
block_mask[i,j] = True | |
if brow_lengths[i] == 0: | |
brow_lengths[i] = A.shape[0] | |
elif brow_lengths[i] != A.shape[0]: | |
msg = (f'blocks[{i},:] has incompatible row dimensions. ' | |
f'Got blocks[{i},{j}].shape[0] == {A.shape[0]}, ' | |
f'expected {brow_lengths[i]}.') | |
raise ValueError(msg) | |
if bcol_lengths[j] == 0: | |
bcol_lengths[j] = A.shape[1] | |
elif bcol_lengths[j] != A.shape[1]: | |
msg = (f'blocks[:,{j}] has incompatible column ' | |
f'dimensions. ' | |
f'Got blocks[{i},{j}].shape[1] == {A.shape[1]}, ' | |
f'expected {bcol_lengths[j]}.') | |
raise ValueError(msg) | |
nnz = sum(block.nnz for block in blocks[block_mask]) | |
if dtype is None: | |
all_dtypes = [blk.dtype for blk in blocks[block_mask]] | |
dtype = upcast(*all_dtypes) if all_dtypes else None | |
row_offsets = np.append(0, np.cumsum(brow_lengths)) | |
col_offsets = np.append(0, np.cumsum(bcol_lengths)) | |
shape = (row_offsets[-1], col_offsets[-1]) | |
data = np.empty(nnz, dtype=dtype) | |
idx_dtype = get_index_dtype(maxval=max(shape)) | |
row = np.empty(nnz, dtype=idx_dtype) | |
col = np.empty(nnz, dtype=idx_dtype) | |
nnz = 0 | |
ii, jj = np.nonzero(block_mask) | |
for i, j in zip(ii, jj): | |
B = blocks[i, j] | |
idx = slice(nnz, nnz + B.nnz) | |
data[idx] = B.data | |
np.add(B.row, row_offsets[i], out=row[idx], dtype=idx_dtype) | |
np.add(B.col, col_offsets[j], out=col[idx], dtype=idx_dtype) | |
nnz += B.nnz | |
if return_spmatrix: | |
return coo_matrix((data, (row, col)), shape=shape).asformat(format) | |
return coo_array((data, (row, col)), shape=shape).asformat(format) | |
def block_diag(mats, format=None, dtype=None): | |
""" | |
Build a block diagonal sparse matrix or array from provided matrices. | |
Parameters | |
---------- | |
mats : sequence of matrices or arrays | |
Input matrices or arrays. | |
format : str, optional | |
The sparse format of the result (e.g., "csr"). If not given, the result | |
is returned in "coo" format. | |
dtype : dtype specifier, optional | |
The data-type of the output. If not given, the dtype is | |
determined from that of `blocks`. | |
Returns | |
------- | |
res : sparse matrix or array | |
If at least one input is a sparse array, the output is a sparse array. | |
Otherwise the output is a sparse matrix. | |
Notes | |
----- | |
.. versionadded:: 0.11.0 | |
See Also | |
-------- | |
block_array | |
diags_array | |
Examples | |
-------- | |
>>> from scipy.sparse import coo_array, block_diag | |
>>> A = coo_array([[1, 2], [3, 4]]) | |
>>> B = coo_array([[5], [6]]) | |
>>> C = coo_array([[7]]) | |
>>> block_diag((A, B, C)).toarray() | |
array([[1, 2, 0, 0], | |
[3, 4, 0, 0], | |
[0, 0, 5, 0], | |
[0, 0, 6, 0], | |
[0, 0, 0, 7]]) | |
""" | |
if any(isinstance(a, sparray) for a in mats): | |
container = coo_array | |
else: | |
container = coo_matrix | |
row = [] | |
col = [] | |
data = [] | |
r_idx = 0 | |
c_idx = 0 | |
for a in mats: | |
if isinstance(a, (list, numbers.Number)): | |
a = coo_array(np.atleast_2d(a)) | |
if issparse(a): | |
a = a.tocoo() | |
nrows, ncols = a._shape_as_2d | |
row.append(a.row + r_idx) | |
col.append(a.col + c_idx) | |
data.append(a.data) | |
else: | |
nrows, ncols = a.shape | |
a_row, a_col = np.divmod(np.arange(nrows*ncols), ncols) | |
row.append(a_row + r_idx) | |
col.append(a_col + c_idx) | |
data.append(a.ravel()) | |
r_idx += nrows | |
c_idx += ncols | |
row = np.concatenate(row) | |
col = np.concatenate(col) | |
data = np.concatenate(data) | |
return container((data, (row, col)), | |
shape=(r_idx, c_idx), | |
dtype=dtype).asformat(format) | |
def random_array(shape, *, density=0.01, format='coo', dtype=None, | |
random_state=None, data_sampler=None): | |
"""Return a sparse array of uniformly random numbers in [0, 1) | |
Returns a sparse array with the given shape and density | |
where values are generated uniformly randomly in the range [0, 1). | |
.. warning:: | |
Since numpy 1.17, passing a ``np.random.Generator`` (e.g. | |
``np.random.default_rng``) for ``random_state`` will lead to much | |
faster execution times. | |
A much slower implementation is used by default for backwards | |
compatibility. | |
Parameters | |
---------- | |
shape : int or tuple of ints | |
shape of the array | |
density : real, optional (default: 0.01) | |
density of the generated matrix: density equal to one means a full | |
matrix, density of 0 means a matrix with no non-zero items. | |
format : str, optional (default: 'coo') | |
sparse matrix format. | |
dtype : dtype, optional (default: np.float64) | |
type of the returned matrix values. | |
random_state : {None, int, `Generator`, `RandomState`}, optional | |
A random number generator to determine nonzero structure. We recommend using | |
a `numpy.random.Generator` manually provided for every call as it is much | |
faster than RandomState. | |
- If `None` (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
- If an int, a new ``Generator`` instance is used, | |
seeded with the int. | |
- If a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
This random state will be used for sampling `indices` (the sparsity | |
structure), and by default for the data values too (see `data_sampler`). | |
data_sampler : callable, optional (default depends on dtype) | |
Sampler of random data values with keyword arg `size`. | |
This function should take a single keyword argument `size` specifying | |
the length of its returned ndarray. It is used to generate the nonzero | |
values in the matrix after the locations of those values are chosen. | |
By default, uniform [0, 1) random values are used unless `dtype` is | |
an integer (default uniform integers from that dtype) or | |
complex (default uniform over the unit square in the complex plane). | |
For these, the `random_state` rng is used e.g. `rng.uniform(size=size)`. | |
Returns | |
------- | |
res : sparse array | |
Examples | |
-------- | |
Passing a ``np.random.Generator`` instance for better performance: | |
>>> import numpy as np | |
>>> import scipy as sp | |
>>> rng = np.random.default_rng() | |
Default sampling uniformly from [0, 1): | |
>>> S = sp.sparse.random_array((3, 4), density=0.25, random_state=rng) | |
Providing a sampler for the values: | |
>>> rvs = sp.stats.poisson(25, loc=10).rvs | |
>>> S = sp.sparse.random_array((3, 4), density=0.25, | |
... random_state=rng, data_sampler=rvs) | |
>>> S.toarray() | |
array([[ 36., 0., 33., 0.], # random | |
[ 0., 0., 0., 0.], | |
[ 0., 0., 36., 0.]]) | |
Building a custom distribution. | |
This example builds a squared normal from np.random: | |
>>> def np_normal_squared(size=None, random_state=rng): | |
... return random_state.standard_normal(size) ** 2 | |
>>> S = sp.sparse.random_array((3, 4), density=0.25, random_state=rng, | |
... data_sampler=np_normal_squared) | |
Or we can build it from sp.stats style rvs functions: | |
>>> def sp_stats_normal_squared(size=None, random_state=rng): | |
... std_normal = sp.stats.distributions.norm_gen().rvs | |
... return std_normal(size=size, random_state=random_state) ** 2 | |
>>> S = sp.sparse.random_array((3, 4), density=0.25, random_state=rng, | |
... data_sampler=sp_stats_normal_squared) | |
Or we can subclass sp.stats rv_continous or rv_discrete: | |
>>> class NormalSquared(sp.stats.rv_continuous): | |
... def _rvs(self, size=None, random_state=rng): | |
... return random_state.standard_normal(size) ** 2 | |
>>> X = NormalSquared() | |
>>> Y = X().rvs | |
>>> S = sp.sparse.random_array((3, 4), density=0.25, | |
... random_state=rng, data_sampler=Y) | |
""" | |
# Use the more efficient RNG by default. | |
if random_state is None: | |
random_state = np.random.default_rng() | |
data, ind = _random(shape, density, format, dtype, random_state, data_sampler) | |
return coo_array((data, ind), shape=shape).asformat(format) | |
def _random(shape, density=0.01, format=None, dtype=None, | |
random_state=None, data_sampler=None): | |
if density < 0 or density > 1: | |
raise ValueError("density expected to be 0 <= density <= 1") | |
tot_prod = math.prod(shape) # use `math` for when prod is >= 2**64 | |
# Number of non zero values | |
size = int(round(density * tot_prod)) | |
rng = check_random_state(random_state) | |
if data_sampler is None: | |
if np.issubdtype(dtype, np.integer): | |
def data_sampler(size): | |
return rng_integers(rng, | |
np.iinfo(dtype).min, | |
np.iinfo(dtype).max, | |
size, | |
dtype=dtype) | |
elif np.issubdtype(dtype, np.complexfloating): | |
def data_sampler(size): | |
return (rng.uniform(size=size) + | |
rng.uniform(size=size) * 1j) | |
else: | |
data_sampler = rng.uniform | |
# rng.choice uses int64 if first arg is an int | |
if tot_prod < np.iinfo(np.int64).max: | |
raveled_ind = rng.choice(tot_prod, size=size, replace=False) | |
ind = np.unravel_index(raveled_ind, shape=shape, order='F') | |
else: | |
# for ravel indices bigger than dtype max, use sets to remove duplicates | |
ndim = len(shape) | |
seen = set() | |
while len(seen) < size: | |
dsize = size - len(seen) | |
seen.update(map(tuple, rng_integers(rng, shape, size=(dsize, ndim)))) | |
ind = tuple(np.array(list(seen)).T) | |
# size kwarg allows eg data_sampler=partial(np.random.poisson, lam=5) | |
vals = data_sampler(size=size).astype(dtype, copy=False) | |
return vals, ind | |
def random(m, n, density=0.01, format='coo', dtype=None, | |
random_state=None, data_rvs=None): | |
"""Generate a sparse matrix of the given shape and density with randomly | |
distributed values. | |
.. warning:: | |
Since numpy 1.17, passing a ``np.random.Generator`` (e.g. | |
``np.random.default_rng``) for ``random_state`` will lead to much | |
faster execution times. | |
A much slower implementation is used by default for backwards | |
compatibility. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``random_array`` to take advantage of the | |
sparse array functionality. | |
Parameters | |
---------- | |
m, n : int | |
shape of the matrix | |
density : real, optional | |
density of the generated matrix: density equal to one means a full | |
matrix, density of 0 means a matrix with no non-zero items. | |
format : str, optional | |
sparse matrix format. | |
dtype : dtype, optional | |
type of the returned matrix values. | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
- If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
- If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
- If `seed` is already a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
This random state will be used for sampling the sparsity structure, but | |
not necessarily for sampling the values of the structurally nonzero | |
entries of the matrix. | |
data_rvs : callable, optional | |
Samples a requested number of random values. | |
This function should take a single argument specifying the length | |
of the ndarray that it will return. The structurally nonzero entries | |
of the sparse random matrix will be taken from the array sampled | |
by this function. By default, uniform [0, 1) random values will be | |
sampled using the same random state as is used for sampling | |
the sparsity structure. | |
Returns | |
------- | |
res : sparse matrix | |
See Also | |
-------- | |
random_array : constructs sparse arrays instead of sparse matrices | |
Examples | |
-------- | |
Passing a ``np.random.Generator`` instance for better performance: | |
>>> import scipy as sp | |
>>> import numpy as np | |
>>> rng = np.random.default_rng() | |
>>> S = sp.sparse.random(3, 4, density=0.25, random_state=rng) | |
Providing a sampler for the values: | |
>>> rvs = sp.stats.poisson(25, loc=10).rvs | |
>>> S = sp.sparse.random(3, 4, density=0.25, random_state=rng, data_rvs=rvs) | |
>>> S.toarray() | |
array([[ 36., 0., 33., 0.], # random | |
[ 0., 0., 0., 0.], | |
[ 0., 0., 36., 0.]]) | |
Building a custom distribution. | |
This example builds a squared normal from np.random: | |
>>> def np_normal_squared(size=None, random_state=rng): | |
... return random_state.standard_normal(size) ** 2 | |
>>> S = sp.sparse.random(3, 4, density=0.25, random_state=rng, | |
... data_rvs=np_normal_squared) | |
Or we can build it from sp.stats style rvs functions: | |
>>> def sp_stats_normal_squared(size=None, random_state=rng): | |
... std_normal = sp.stats.distributions.norm_gen().rvs | |
... return std_normal(size=size, random_state=random_state) ** 2 | |
>>> S = sp.sparse.random(3, 4, density=0.25, random_state=rng, | |
... data_rvs=sp_stats_normal_squared) | |
Or we can subclass sp.stats rv_continous or rv_discrete: | |
>>> class NormalSquared(sp.stats.rv_continuous): | |
... def _rvs(self, size=None, random_state=rng): | |
... return random_state.standard_normal(size) ** 2 | |
>>> X = NormalSquared() | |
>>> Y = X() # get a frozen version of the distribution | |
>>> S = sp.sparse.random(3, 4, density=0.25, random_state=rng, data_rvs=Y.rvs) | |
""" | |
if n is None: | |
n = m | |
m, n = int(m), int(n) | |
# make keyword syntax work for data_rvs e.g. data_rvs(size=7) | |
if data_rvs is not None: | |
def data_rvs_kw(size): | |
return data_rvs(size) | |
else: | |
data_rvs_kw = None | |
vals, ind = _random((m, n), density, format, dtype, random_state, data_rvs_kw) | |
return coo_matrix((vals, ind), shape=(m, n)).asformat(format) | |
def rand(m, n, density=0.01, format="coo", dtype=None, random_state=None): | |
"""Generate a sparse matrix of the given shape and density with uniformly | |
distributed values. | |
.. warning:: | |
This function returns a sparse matrix -- not a sparse array. | |
You are encouraged to use ``random_array`` to take advantage | |
of the sparse array functionality. | |
Parameters | |
---------- | |
m, n : int | |
shape of the matrix | |
density : real, optional | |
density of the generated matrix: density equal to one means a full | |
matrix, density of 0 means a matrix with no non-zero items. | |
format : str, optional | |
sparse matrix format. | |
dtype : dtype, optional | |
type of the returned matrix values. | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
Returns | |
------- | |
res : sparse matrix | |
Notes | |
----- | |
Only float types are supported for now. | |
See Also | |
-------- | |
random : Similar function allowing a custom random data sampler | |
random_array : Similar to random() but returns a sparse array | |
Examples | |
-------- | |
>>> from scipy.sparse import rand | |
>>> matrix = rand(3, 4, density=0.25, format="csr", random_state=42) | |
>>> matrix | |
<3x4 sparse matrix of type '<class 'numpy.float64'>' | |
with 3 stored elements in Compressed Sparse Row format> | |
>>> matrix.toarray() | |
array([[0.05641158, 0. , 0. , 0.65088847], # random | |
[0. , 0. , 0. , 0.14286682], | |
[0. , 0. , 0. , 0. ]]) | |
""" | |
return random(m, n, density, format, dtype, random_state) | |