peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/scipy
/sparse
/_bsr.py
"""Compressed Block Sparse Row format""" | |
__docformat__ = "restructuredtext en" | |
__all__ = ['bsr_array', 'bsr_matrix', 'isspmatrix_bsr'] | |
from warnings import warn | |
import numpy as np | |
from scipy._lib._util import copy_if_needed | |
from ._matrix import spmatrix | |
from ._data import _data_matrix, _minmax_mixin | |
from ._compressed import _cs_matrix | |
from ._base import issparse, _formats, _spbase, sparray | |
from ._sputils import (isshape, getdtype, getdata, to_native, upcast, | |
check_shape) | |
from . import _sparsetools | |
from ._sparsetools import (bsr_matvec, bsr_matvecs, csr_matmat_maxnnz, | |
bsr_matmat, bsr_transpose, bsr_sort_indices, | |
bsr_tocsr) | |
class _bsr_base(_cs_matrix, _minmax_mixin): | |
_format = 'bsr' | |
def __init__(self, arg1, shape=None, dtype=None, copy=False, blocksize=None): | |
_data_matrix.__init__(self) | |
if issparse(arg1): | |
if arg1.format == self.format and copy: | |
arg1 = arg1.copy() | |
else: | |
arg1 = arg1.tobsr(blocksize=blocksize) | |
self.indptr, self.indices, self.data, self._shape = ( | |
arg1.indptr, arg1.indices, arg1.data, arg1._shape | |
) | |
elif isinstance(arg1,tuple): | |
if isshape(arg1): | |
# it's a tuple of matrix dimensions (M,N) | |
self._shape = check_shape(arg1) | |
M,N = self.shape | |
# process blocksize | |
if blocksize is None: | |
blocksize = (1,1) | |
else: | |
if not isshape(blocksize): | |
raise ValueError('invalid blocksize=%s' % blocksize) | |
blocksize = tuple(blocksize) | |
self.data = np.zeros((0,) + blocksize, getdtype(dtype, default=float)) | |
R,C = blocksize | |
if (M % R) != 0 or (N % C) != 0: | |
raise ValueError('shape must be multiple of blocksize') | |
# Select index dtype large enough to pass array and | |
# scalar parameters to sparsetools | |
idx_dtype = self._get_index_dtype(maxval=max(M//R, N//C, R, C)) | |
self.indices = np.zeros(0, dtype=idx_dtype) | |
self.indptr = np.zeros(M//R + 1, dtype=idx_dtype) | |
elif len(arg1) == 2: | |
# (data,(row,col)) format | |
coo = self._coo_container(arg1, dtype=dtype, shape=shape) | |
bsr = coo.tobsr(blocksize=blocksize) | |
self.indptr, self.indices, self.data, self._shape = ( | |
bsr.indptr, bsr.indices, bsr.data, bsr._shape | |
) | |
elif len(arg1) == 3: | |
# (data,indices,indptr) format | |
(data, indices, indptr) = arg1 | |
# Select index dtype large enough to pass array and | |
# scalar parameters to sparsetools | |
maxval = 1 | |
if shape is not None: | |
maxval = max(shape) | |
if blocksize is not None: | |
maxval = max(maxval, max(blocksize)) | |
idx_dtype = self._get_index_dtype((indices, indptr), maxval=maxval, | |
check_contents=True) | |
if not copy: | |
copy = copy_if_needed | |
self.indices = np.array(indices, copy=copy, dtype=idx_dtype) | |
self.indptr = np.array(indptr, copy=copy, dtype=idx_dtype) | |
self.data = getdata(data, copy=copy, dtype=dtype) | |
if self.data.ndim != 3: | |
raise ValueError( | |
f'BSR data must be 3-dimensional, got shape={self.data.shape}' | |
) | |
if blocksize is not None: | |
if not isshape(blocksize): | |
raise ValueError(f'invalid blocksize={blocksize}') | |
if tuple(blocksize) != self.data.shape[1:]: | |
raise ValueError('mismatching blocksize={} vs {}'.format( | |
blocksize, self.data.shape[1:])) | |
else: | |
raise ValueError('unrecognized bsr_array constructor usage') | |
else: | |
# must be dense | |
try: | |
arg1 = np.asarray(arg1) | |
except Exception as e: | |
raise ValueError("unrecognized form for" | |
" %s_matrix constructor" % self.format) from e | |
arg1 = self._coo_container( | |
arg1, dtype=dtype | |
).tobsr(blocksize=blocksize) | |
self.indptr, self.indices, self.data, self._shape = ( | |
arg1.indptr, arg1.indices, arg1.data, arg1._shape | |
) | |
if shape is not None: | |
self._shape = check_shape(shape) | |
else: | |
if self.shape is None: | |
# shape not already set, try to infer dimensions | |
try: | |
M = len(self.indptr) - 1 | |
N = self.indices.max() + 1 | |
except Exception as e: | |
raise ValueError('unable to infer matrix dimensions') from e | |
else: | |
R,C = self.blocksize | |
self._shape = check_shape((M*R,N*C)) | |
if self.shape is None: | |
if shape is None: | |
# TODO infer shape here | |
raise ValueError('need to infer shape') | |
else: | |
self._shape = check_shape(shape) | |
if dtype is not None: | |
self.data = self.data.astype(dtype, copy=False) | |
self.check_format(full_check=False) | |
def check_format(self, full_check=True): | |
"""Check whether the array/matrix respects the BSR format. | |
Parameters | |
---------- | |
full_check : bool, optional | |
If `True`, run rigorous check, scanning arrays for valid values. | |
Note that activating those check might copy arrays for casting, | |
modifying indices and index pointers' inplace. | |
If `False`, run basic checks on attributes. O(1) operations. | |
Default is `True`. | |
""" | |
M,N = self.shape | |
R,C = self.blocksize | |
# index arrays should have integer data types | |
if self.indptr.dtype.kind != 'i': | |
warn(f"indptr array has non-integer dtype ({self.indptr.dtype.name})", | |
stacklevel=2) | |
if self.indices.dtype.kind != 'i': | |
warn(f"indices array has non-integer dtype ({self.indices.dtype.name})", | |
stacklevel=2) | |
# check array shapes | |
if self.indices.ndim != 1 or self.indptr.ndim != 1: | |
raise ValueError("indices, and indptr should be 1-D") | |
if self.data.ndim != 3: | |
raise ValueError("data should be 3-D") | |
# check index pointer | |
if (len(self.indptr) != M//R + 1): | |
raise ValueError("index pointer size (%d) should be (%d)" % | |
(len(self.indptr), M//R + 1)) | |
if (self.indptr[0] != 0): | |
raise ValueError("index pointer should start with 0") | |
# check index and data arrays | |
if (len(self.indices) != len(self.data)): | |
raise ValueError("indices and data should have the same size") | |
if (self.indptr[-1] > len(self.indices)): | |
raise ValueError("Last value of index pointer should be less than " | |
"the size of index and data arrays") | |
self.prune() | |
if full_check: | |
# check format validity (more expensive) | |
if self.nnz > 0: | |
if self.indices.max() >= N//C: | |
raise ValueError("column index values must be < %d (now max %d)" | |
% (N//C, self.indices.max())) | |
if self.indices.min() < 0: | |
raise ValueError("column index values must be >= 0") | |
if np.diff(self.indptr).min() < 0: | |
raise ValueError("index pointer values must form a " | |
"non-decreasing sequence") | |
idx_dtype = self._get_index_dtype((self.indices, self.indptr)) | |
self.indptr = np.asarray(self.indptr, dtype=idx_dtype) | |
self.indices = np.asarray(self.indices, dtype=idx_dtype) | |
self.data = to_native(self.data) | |
# if not self.has_sorted_indices(): | |
# warn('Indices were not in sorted order. Sorting indices.') | |
# self.sort_indices(check_first=False) | |
def blocksize(self) -> tuple: | |
"""Block size of the matrix.""" | |
return self.data.shape[1:] | |
def _getnnz(self, axis=None): | |
if axis is not None: | |
raise NotImplementedError("_getnnz over an axis is not implemented " | |
"for BSR format") | |
R,C = self.blocksize | |
return int(self.indptr[-1] * R * C) | |
_getnnz.__doc__ = _spbase._getnnz.__doc__ | |
def __repr__(self): | |
_, fmt = _formats[self.format] | |
sparse_cls = 'array' if isinstance(self, sparray) else 'matrix' | |
shape_str = 'x'.join(str(x) for x in self.shape) | |
blksz = 'x'.join(str(x) for x in self.blocksize) | |
return ( | |
f"<{shape_str} sparse {sparse_cls} of type '{self.dtype.type}'\n" | |
f"\twith {self.nnz} stored elements (blocksize = {blksz}) in {fmt} format>" | |
) | |
def diagonal(self, k=0): | |
rows, cols = self.shape | |
if k <= -rows or k >= cols: | |
return np.empty(0, dtype=self.data.dtype) | |
R, C = self.blocksize | |
y = np.zeros(min(rows + min(k, 0), cols - max(k, 0)), | |
dtype=upcast(self.dtype)) | |
_sparsetools.bsr_diagonal(k, rows // R, cols // C, R, C, | |
self.indptr, self.indices, | |
np.ravel(self.data), y) | |
return y | |
diagonal.__doc__ = _spbase.diagonal.__doc__ | |
########################## | |
# NotImplemented methods # | |
########################## | |
def __getitem__(self,key): | |
raise NotImplementedError | |
def __setitem__(self,key,val): | |
raise NotImplementedError | |
###################### | |
# Arithmetic methods # | |
###################### | |
def _add_dense(self, other): | |
return self.tocoo(copy=False)._add_dense(other) | |
def _matmul_vector(self, other): | |
M,N = self.shape | |
R,C = self.blocksize | |
result = np.zeros(self.shape[0], dtype=upcast(self.dtype, other.dtype)) | |
bsr_matvec(M//R, N//C, R, C, | |
self.indptr, self.indices, self.data.ravel(), | |
other, result) | |
return result | |
def _matmul_multivector(self,other): | |
R,C = self.blocksize | |
M,N = self.shape | |
n_vecs = other.shape[1] # number of column vectors | |
result = np.zeros((M,n_vecs), dtype=upcast(self.dtype,other.dtype)) | |
bsr_matvecs(M//R, N//C, n_vecs, R, C, | |
self.indptr, self.indices, self.data.ravel(), | |
other.ravel(), result.ravel()) | |
return result | |
def _matmul_sparse(self, other): | |
M, K1 = self.shape | |
K2, N = other.shape | |
R,n = self.blocksize | |
# convert to this format | |
if other.format == "bsr": | |
C = other.blocksize[1] | |
else: | |
C = 1 | |
if other.format == "csr" and n == 1: | |
other = other.tobsr(blocksize=(n,C), copy=False) # lightweight conversion | |
else: | |
other = other.tobsr(blocksize=(n,C)) | |
idx_dtype = self._get_index_dtype((self.indptr, self.indices, | |
other.indptr, other.indices)) | |
bnnz = csr_matmat_maxnnz(M//R, N//C, | |
self.indptr.astype(idx_dtype), | |
self.indices.astype(idx_dtype), | |
other.indptr.astype(idx_dtype), | |
other.indices.astype(idx_dtype)) | |
idx_dtype = self._get_index_dtype((self.indptr, self.indices, | |
other.indptr, other.indices), | |
maxval=bnnz) | |
indptr = np.empty(self.indptr.shape, dtype=idx_dtype) | |
indices = np.empty(bnnz, dtype=idx_dtype) | |
data = np.empty(R*C*bnnz, dtype=upcast(self.dtype,other.dtype)) | |
bsr_matmat(bnnz, M//R, N//C, R, C, n, | |
self.indptr.astype(idx_dtype), | |
self.indices.astype(idx_dtype), | |
np.ravel(self.data), | |
other.indptr.astype(idx_dtype), | |
other.indices.astype(idx_dtype), | |
np.ravel(other.data), | |
indptr, | |
indices, | |
data) | |
data = data.reshape(-1,R,C) | |
# TODO eliminate zeros | |
return self._bsr_container( | |
(data, indices, indptr), shape=(M, N), blocksize=(R, C) | |
) | |
###################### | |
# Conversion methods # | |
###################### | |
def tobsr(self, blocksize=None, copy=False): | |
"""Convert this array/matrix into Block Sparse Row Format. | |
With copy=False, the data/indices may be shared between this | |
array/matrix and the resultant bsr_array/bsr_matrix. | |
If blocksize=(R, C) is provided, it will be used for determining | |
block size of the bsr_array/bsr_matrix. | |
""" | |
if blocksize not in [None, self.blocksize]: | |
return self.tocsr().tobsr(blocksize=blocksize) | |
if copy: | |
return self.copy() | |
else: | |
return self | |
def tocsr(self, copy=False): | |
M, N = self.shape | |
R, C = self.blocksize | |
nnz = self.nnz | |
idx_dtype = self._get_index_dtype((self.indptr, self.indices), | |
maxval=max(nnz, N)) | |
indptr = np.empty(M + 1, dtype=idx_dtype) | |
indices = np.empty(nnz, dtype=idx_dtype) | |
data = np.empty(nnz, dtype=upcast(self.dtype)) | |
bsr_tocsr(M // R, # n_brow | |
N // C, # n_bcol | |
R, C, | |
self.indptr.astype(idx_dtype, copy=False), | |
self.indices.astype(idx_dtype, copy=False), | |
self.data, | |
indptr, | |
indices, | |
data) | |
return self._csr_container((data, indices, indptr), shape=self.shape) | |
tocsr.__doc__ = _spbase.tocsr.__doc__ | |
def tocsc(self, copy=False): | |
return self.tocsr(copy=False).tocsc(copy=copy) | |
tocsc.__doc__ = _spbase.tocsc.__doc__ | |
def tocoo(self, copy=True): | |
"""Convert this array/matrix to COOrdinate format. | |
When copy=False the data array will be shared between | |
this array/matrix and the resultant coo_array/coo_matrix. | |
""" | |
M,N = self.shape | |
R,C = self.blocksize | |
indptr_diff = np.diff(self.indptr) | |
if indptr_diff.dtype.itemsize > np.dtype(np.intp).itemsize: | |
# Check for potential overflow | |
indptr_diff_limited = indptr_diff.astype(np.intp) | |
if np.any(indptr_diff_limited != indptr_diff): | |
raise ValueError("Matrix too big to convert") | |
indptr_diff = indptr_diff_limited | |
idx_dtype = self._get_index_dtype(maxval=max(M, N)) | |
row = (R * np.arange(M//R, dtype=idx_dtype)).repeat(indptr_diff) | |
row = row.repeat(R*C).reshape(-1,R,C) | |
row += np.tile(np.arange(R, dtype=idx_dtype).reshape(-1,1), (1,C)) | |
row = row.reshape(-1) | |
col = ((C * self.indices).astype(idx_dtype, copy=False) | |
.repeat(R*C).reshape(-1,R,C)) | |
col += np.tile(np.arange(C, dtype=idx_dtype), (R,1)) | |
col = col.reshape(-1) | |
data = self.data.reshape(-1) | |
if copy: | |
data = data.copy() | |
return self._coo_container( | |
(data, (row, col)), shape=self.shape | |
) | |
def toarray(self, order=None, out=None): | |
return self.tocoo(copy=False).toarray(order=order, out=out) | |
toarray.__doc__ = _spbase.toarray.__doc__ | |
def transpose(self, axes=None, copy=False): | |
if axes is not None and axes != (1, 0): | |
raise ValueError("Sparse matrices do not support " | |
"an 'axes' parameter because swapping " | |
"dimensions is the only logical permutation.") | |
R, C = self.blocksize | |
M, N = self.shape | |
NBLK = self.nnz//(R*C) | |
if self.nnz == 0: | |
return self._bsr_container((N, M), blocksize=(C, R), | |
dtype=self.dtype, copy=copy) | |
indptr = np.empty(N//C + 1, dtype=self.indptr.dtype) | |
indices = np.empty(NBLK, dtype=self.indices.dtype) | |
data = np.empty((NBLK, C, R), dtype=self.data.dtype) | |
bsr_transpose(M//R, N//C, R, C, | |
self.indptr, self.indices, self.data.ravel(), | |
indptr, indices, data.ravel()) | |
return self._bsr_container((data, indices, indptr), | |
shape=(N, M), copy=copy) | |
transpose.__doc__ = _spbase.transpose.__doc__ | |
############################################################## | |
# methods that examine or modify the internal data structure # | |
############################################################## | |
def eliminate_zeros(self): | |
"""Remove zero elements in-place.""" | |
if not self.nnz: | |
return # nothing to do | |
R,C = self.blocksize | |
M,N = self.shape | |
mask = (self.data != 0).reshape(-1,R*C).sum(axis=1) # nonzero blocks | |
nonzero_blocks = mask.nonzero()[0] | |
self.data[:len(nonzero_blocks)] = self.data[nonzero_blocks] | |
# modifies self.indptr and self.indices *in place* | |
_sparsetools.csr_eliminate_zeros(M//R, N//C, self.indptr, | |
self.indices, mask) | |
self.prune() | |
def sum_duplicates(self): | |
"""Eliminate duplicate array/matrix entries by adding them together | |
The is an *in place* operation | |
""" | |
if self.has_canonical_format: | |
return | |
self.sort_indices() | |
R, C = self.blocksize | |
M, N = self.shape | |
# port of _sparsetools.csr_sum_duplicates | |
n_row = M // R | |
nnz = 0 | |
row_end = 0 | |
for i in range(n_row): | |
jj = row_end | |
row_end = self.indptr[i+1] | |
while jj < row_end: | |
j = self.indices[jj] | |
x = self.data[jj] | |
jj += 1 | |
while jj < row_end and self.indices[jj] == j: | |
x += self.data[jj] | |
jj += 1 | |
self.indices[nnz] = j | |
self.data[nnz] = x | |
nnz += 1 | |
self.indptr[i+1] = nnz | |
self.prune() # nnz may have changed | |
self.has_canonical_format = True | |
def sort_indices(self): | |
"""Sort the indices of this array/matrix *in place* | |
""" | |
if self.has_sorted_indices: | |
return | |
R,C = self.blocksize | |
M,N = self.shape | |
bsr_sort_indices(M//R, N//C, R, C, self.indptr, self.indices, self.data.ravel()) | |
self.has_sorted_indices = True | |
def prune(self): | |
"""Remove empty space after all non-zero elements. | |
""" | |
R,C = self.blocksize | |
M,N = self.shape | |
if len(self.indptr) != M//R + 1: | |
raise ValueError("index pointer has invalid length") | |
bnnz = self.indptr[-1] | |
if len(self.indices) < bnnz: | |
raise ValueError("indices array has too few elements") | |
if len(self.data) < bnnz: | |
raise ValueError("data array has too few elements") | |
self.data = self.data[:bnnz] | |
self.indices = self.indices[:bnnz] | |
# utility functions | |
def _binopt(self, other, op, in_shape=None, out_shape=None): | |
"""Apply the binary operation fn to two sparse matrices.""" | |
# Ideally we'd take the GCDs of the blocksize dimensions | |
# and explode self and other to match. | |
other = self.__class__(other, blocksize=self.blocksize) | |
# e.g. bsr_plus_bsr, etc. | |
fn = getattr(_sparsetools, self.format + op + self.format) | |
R,C = self.blocksize | |
max_bnnz = len(self.data) + len(other.data) | |
idx_dtype = self._get_index_dtype((self.indptr, self.indices, | |
other.indptr, other.indices), | |
maxval=max_bnnz) | |
indptr = np.empty(self.indptr.shape, dtype=idx_dtype) | |
indices = np.empty(max_bnnz, dtype=idx_dtype) | |
bool_ops = ['_ne_', '_lt_', '_gt_', '_le_', '_ge_'] | |
if op in bool_ops: | |
data = np.empty(R*C*max_bnnz, dtype=np.bool_) | |
else: | |
data = np.empty(R*C*max_bnnz, dtype=upcast(self.dtype,other.dtype)) | |
fn(self.shape[0]//R, self.shape[1]//C, R, C, | |
self.indptr.astype(idx_dtype), | |
self.indices.astype(idx_dtype), | |
self.data, | |
other.indptr.astype(idx_dtype), | |
other.indices.astype(idx_dtype), | |
np.ravel(other.data), | |
indptr, | |
indices, | |
data) | |
actual_bnnz = indptr[-1] | |
indices = indices[:actual_bnnz] | |
data = data[:R*C*actual_bnnz] | |
if actual_bnnz < max_bnnz/2: | |
indices = indices.copy() | |
data = data.copy() | |
data = data.reshape(-1,R,C) | |
return self.__class__((data, indices, indptr), shape=self.shape) | |
# needed by _data_matrix | |
def _with_data(self,data,copy=True): | |
"""Returns a matrix with the same sparsity structure as self, | |
but with different data. By default the structure arrays | |
(i.e. .indptr and .indices) are copied. | |
""" | |
if copy: | |
return self.__class__((data,self.indices.copy(),self.indptr.copy()), | |
shape=self.shape,dtype=data.dtype) | |
else: | |
return self.__class__((data,self.indices,self.indptr), | |
shape=self.shape,dtype=data.dtype) | |
# # these functions are used by the parent class | |
# # to remove redundancy between bsc_matrix and bsr_matrix | |
# def _swap(self,x): | |
# """swap the members of x if this is a column-oriented matrix | |
# """ | |
# return (x[0],x[1]) | |
def isspmatrix_bsr(x): | |
"""Is `x` of a bsr_matrix type? | |
Parameters | |
---------- | |
x | |
object to check for being a bsr matrix | |
Returns | |
------- | |
bool | |
True if `x` is a bsr matrix, False otherwise | |
Examples | |
-------- | |
>>> from scipy.sparse import bsr_array, bsr_matrix, csr_matrix, isspmatrix_bsr | |
>>> isspmatrix_bsr(bsr_matrix([[5]])) | |
True | |
>>> isspmatrix_bsr(bsr_array([[5]])) | |
False | |
>>> isspmatrix_bsr(csr_matrix([[5]])) | |
False | |
""" | |
return isinstance(x, bsr_matrix) | |
# This namespace class separates array from matrix with isinstance | |
class bsr_array(_bsr_base, sparray): | |
""" | |
Block Sparse Row format sparse array. | |
This can be instantiated in several ways: | |
bsr_array(D, [blocksize=(R,C)]) | |
where D is a 2-D ndarray. | |
bsr_array(S, [blocksize=(R,C)]) | |
with another sparse array or matrix S (equivalent to S.tobsr()) | |
bsr_array((M, N), [blocksize=(R,C), dtype]) | |
to construct an empty sparse array with shape (M, N) | |
dtype is optional, defaulting to dtype='d'. | |
bsr_array((data, ij), [blocksize=(R,C), shape=(M, N)]) | |
where ``data`` and ``ij`` satisfy ``a[ij[0, k], ij[1, k]] = data[k]`` | |
bsr_array((data, indices, indptr), [shape=(M, N)]) | |
is the standard BSR representation where the block column | |
indices for row i are stored in ``indices[indptr[i]:indptr[i+1]]`` | |
and their corresponding block values are stored in | |
``data[ indptr[i]: indptr[i+1] ]``. If the shape parameter is not | |
supplied, the array dimensions are inferred from the index arrays. | |
Attributes | |
---------- | |
dtype : dtype | |
Data type of the array | |
shape : 2-tuple | |
Shape of the array | |
ndim : int | |
Number of dimensions (this is always 2) | |
nnz | |
size | |
data | |
BSR format data array of the array | |
indices | |
BSR format index array of the array | |
indptr | |
BSR format index pointer array of the array | |
blocksize | |
Block size | |
has_sorted_indices : bool | |
Whether indices are sorted | |
has_canonical_format : bool | |
T | |
Notes | |
----- | |
Sparse arrays can be used in arithmetic operations: they support | |
addition, subtraction, multiplication, division, and matrix power. | |
**Summary of BSR format** | |
The Block Sparse Row (BSR) format is very similar to the Compressed | |
Sparse Row (CSR) format. BSR is appropriate for sparse matrices with dense | |
sub matrices like the last example below. Such sparse block matrices often | |
arise in vector-valued finite element discretizations. In such cases, BSR is | |
considerably more efficient than CSR and CSC for many sparse arithmetic | |
operations. | |
**Blocksize** | |
The blocksize (R,C) must evenly divide the shape of the sparse array (M,N). | |
That is, R and C must satisfy the relationship ``M % R = 0`` and | |
``N % C = 0``. | |
If no blocksize is specified, a simple heuristic is applied to determine | |
an appropriate blocksize. | |
**Canonical Format** | |
In canonical format, there are no duplicate blocks and indices are sorted | |
per row. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import bsr_array | |
>>> bsr_array((3, 4), dtype=np.int8).toarray() | |
array([[0, 0, 0, 0], | |
[0, 0, 0, 0], | |
[0, 0, 0, 0]], dtype=int8) | |
>>> row = np.array([0, 0, 1, 2, 2, 2]) | |
>>> col = np.array([0, 2, 2, 0, 1, 2]) | |
>>> data = np.array([1, 2, 3 ,4, 5, 6]) | |
>>> bsr_array((data, (row, col)), shape=(3, 3)).toarray() | |
array([[1, 0, 2], | |
[0, 0, 3], | |
[4, 5, 6]]) | |
>>> indptr = np.array([0, 2, 3, 6]) | |
>>> indices = np.array([0, 2, 2, 0, 1, 2]) | |
>>> data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2) | |
>>> bsr_array((data,indices,indptr), shape=(6, 6)).toarray() | |
array([[1, 1, 0, 0, 2, 2], | |
[1, 1, 0, 0, 2, 2], | |
[0, 0, 0, 0, 3, 3], | |
[0, 0, 0, 0, 3, 3], | |
[4, 4, 5, 5, 6, 6], | |
[4, 4, 5, 5, 6, 6]]) | |
""" | |
class bsr_matrix(spmatrix, _bsr_base): | |
""" | |
Block Sparse Row format sparse matrix. | |
This can be instantiated in several ways: | |
bsr_matrix(D, [blocksize=(R,C)]) | |
where D is a 2-D ndarray. | |
bsr_matrix(S, [blocksize=(R,C)]) | |
with another sparse array or matrix S (equivalent to S.tobsr()) | |
bsr_matrix((M, N), [blocksize=(R,C), dtype]) | |
to construct an empty sparse matrix with shape (M, N) | |
dtype is optional, defaulting to dtype='d'. | |
bsr_matrix((data, ij), [blocksize=(R,C), shape=(M, N)]) | |
where ``data`` and ``ij`` satisfy ``a[ij[0, k], ij[1, k]] = data[k]`` | |
bsr_matrix((data, indices, indptr), [shape=(M, N)]) | |
is the standard BSR representation where the block column | |
indices for row i are stored in ``indices[indptr[i]:indptr[i+1]]`` | |
and their corresponding block values are stored in | |
``data[ indptr[i]: indptr[i+1] ]``. If the shape parameter is not | |
supplied, the matrix dimensions are inferred from the index arrays. | |
Attributes | |
---------- | |
dtype : dtype | |
Data type of the matrix | |
shape : 2-tuple | |
Shape of the matrix | |
ndim : int | |
Number of dimensions (this is always 2) | |
nnz | |
size | |
data | |
BSR format data array of the matrix | |
indices | |
BSR format index array of the matrix | |
indptr | |
BSR format index pointer array of the matrix | |
blocksize | |
Block size | |
has_sorted_indices : bool | |
Whether indices are sorted | |
has_canonical_format : bool | |
T | |
Notes | |
----- | |
Sparse matrices can be used in arithmetic operations: they support | |
addition, subtraction, multiplication, division, and matrix power. | |
**Summary of BSR format** | |
The Block Sparse Row (BSR) format is very similar to the Compressed | |
Sparse Row (CSR) format. BSR is appropriate for sparse matrices with dense | |
sub matrices like the last example below. Such sparse block matrices often | |
arise in vector-valued finite element discretizations. In such cases, BSR is | |
considerably more efficient than CSR and CSC for many sparse arithmetic | |
operations. | |
**Blocksize** | |
The blocksize (R,C) must evenly divide the shape of the sparse matrix (M,N). | |
That is, R and C must satisfy the relationship ``M % R = 0`` and | |
``N % C = 0``. | |
If no blocksize is specified, a simple heuristic is applied to determine | |
an appropriate blocksize. | |
**Canonical Format** | |
In canonical format, there are no duplicate blocks and indices are sorted | |
per row. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.sparse import bsr_matrix | |
>>> bsr_matrix((3, 4), dtype=np.int8).toarray() | |
array([[0, 0, 0, 0], | |
[0, 0, 0, 0], | |
[0, 0, 0, 0]], dtype=int8) | |
>>> row = np.array([0, 0, 1, 2, 2, 2]) | |
>>> col = np.array([0, 2, 2, 0, 1, 2]) | |
>>> data = np.array([1, 2, 3 ,4, 5, 6]) | |
>>> bsr_matrix((data, (row, col)), shape=(3, 3)).toarray() | |
array([[1, 0, 2], | |
[0, 0, 3], | |
[4, 5, 6]]) | |
>>> indptr = np.array([0, 2, 3, 6]) | |
>>> indices = np.array([0, 2, 2, 0, 1, 2]) | |
>>> data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2) | |
>>> bsr_matrix((data,indices,indptr), shape=(6, 6)).toarray() | |
array([[1, 1, 0, 0, 2, 2], | |
[1, 1, 0, 0, 2, 2], | |
[0, 0, 0, 0, 3, 3], | |
[0, 0, 0, 0, 3, 3], | |
[4, 4, 5, 5, 6, 6], | |
[4, 4, 5, 5, 6, 6]]) | |
""" | |