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"""Compressed Block Sparse Row format""" |
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__docformat__ = "restructuredtext en" |
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__all__ = ['bsr_array', 'bsr_matrix', 'isspmatrix_bsr'] |
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from warnings import warn |
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import numpy as np |
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from scipy._lib._util import copy_if_needed |
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from ._matrix import spmatrix |
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from ._data import _data_matrix, _minmax_mixin |
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from ._compressed import _cs_matrix |
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from ._base import issparse, _formats, _spbase, sparray |
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from ._sputils import (isshape, getdtype, getdata, to_native, upcast, |
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check_shape) |
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from . import _sparsetools |
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from ._sparsetools import (bsr_matvec, bsr_matvecs, csr_matmat_maxnnz, |
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bsr_matmat, bsr_transpose, bsr_sort_indices, |
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bsr_tocsr) |
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class _bsr_base(_cs_matrix, _minmax_mixin): |
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_format = 'bsr' |
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def __init__(self, arg1, shape=None, dtype=None, copy=False, |
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blocksize=None, *, maxprint=None): |
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_data_matrix.__init__(self, arg1, maxprint=maxprint) |
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if issparse(arg1): |
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if arg1.format == self.format and copy: |
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arg1 = arg1.copy() |
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else: |
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arg1 = arg1.tobsr(blocksize=blocksize) |
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self.indptr, self.indices, self.data, self._shape = ( |
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arg1.indptr, arg1.indices, arg1.data, arg1._shape |
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) |
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elif isinstance(arg1,tuple): |
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if isshape(arg1): |
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self._shape = check_shape(arg1) |
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M,N = self.shape |
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if blocksize is None: |
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blocksize = (1,1) |
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else: |
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if not isshape(blocksize): |
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raise ValueError(f'invalid blocksize={blocksize}') |
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blocksize = tuple(blocksize) |
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self.data = np.zeros((0,) + blocksize, getdtype(dtype, default=float)) |
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R,C = blocksize |
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if (M % R) != 0 or (N % C) != 0: |
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raise ValueError('shape must be multiple of blocksize') |
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idx_dtype = self._get_index_dtype(maxval=max(M//R, N//C, R, C)) |
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self.indices = np.zeros(0, dtype=idx_dtype) |
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self.indptr = np.zeros(M//R + 1, dtype=idx_dtype) |
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elif len(arg1) == 2: |
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coo = self._coo_container(arg1, dtype=dtype, shape=shape) |
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bsr = coo.tobsr(blocksize=blocksize) |
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self.indptr, self.indices, self.data, self._shape = ( |
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bsr.indptr, bsr.indices, bsr.data, bsr._shape |
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) |
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elif len(arg1) == 3: |
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(data, indices, indptr) = arg1 |
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maxval = 1 |
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if shape is not None: |
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maxval = max(shape) |
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if blocksize is not None: |
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maxval = max(maxval, max(blocksize)) |
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idx_dtype = self._get_index_dtype((indices, indptr), maxval=maxval, |
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check_contents=True) |
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if not copy: |
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copy = copy_if_needed |
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self.indices = np.array(indices, copy=copy, dtype=idx_dtype) |
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self.indptr = np.array(indptr, copy=copy, dtype=idx_dtype) |
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self.data = getdata(data, copy=copy, dtype=dtype) |
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if self.data.ndim != 3: |
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raise ValueError( |
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f'BSR data must be 3-dimensional, got shape={self.data.shape}' |
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) |
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if blocksize is not None: |
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if not isshape(blocksize): |
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raise ValueError(f'invalid blocksize={blocksize}') |
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if tuple(blocksize) != self.data.shape[1:]: |
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raise ValueError( |
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f'mismatching blocksize={blocksize}' |
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f' vs {self.data.shape[1:]}' |
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) |
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else: |
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raise ValueError('unrecognized bsr_array constructor usage') |
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else: |
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try: |
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arg1 = np.asarray(arg1) |
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except Exception as e: |
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raise ValueError("unrecognized form for " |
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f"{self.format}_matrix constructor") from e |
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if isinstance(self, sparray) and arg1.ndim != 2: |
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raise ValueError(f"BSR arrays don't support {arg1.ndim}D input. Use 2D") |
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arg1 = self._coo_container(arg1, dtype=dtype).tobsr(blocksize=blocksize) |
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self.indptr, self.indices, self.data, self._shape = ( |
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arg1.indptr, arg1.indices, arg1.data, arg1._shape |
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) |
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if shape is not None: |
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self._shape = check_shape(shape) |
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else: |
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if self.shape is None: |
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try: |
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M = len(self.indptr) - 1 |
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N = self.indices.max() + 1 |
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except Exception as e: |
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raise ValueError('unable to infer matrix dimensions') from e |
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else: |
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R,C = self.blocksize |
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self._shape = check_shape((M*R,N*C)) |
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if self.shape is None: |
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if shape is None: |
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raise ValueError('need to infer shape') |
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else: |
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self._shape = check_shape(shape) |
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if dtype is not None: |
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self.data = self.data.astype(getdtype(dtype, self.data), copy=False) |
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self.check_format(full_check=False) |
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def check_format(self, full_check=True): |
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"""Check whether the array/matrix respects the BSR format. |
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Parameters |
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---------- |
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full_check : bool, optional |
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If `True`, run rigorous check, scanning arrays for valid values. |
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Note that activating those check might copy arrays for casting, |
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modifying indices and index pointers' inplace. |
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If `False`, run basic checks on attributes. O(1) operations. |
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Default is `True`. |
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""" |
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M,N = self.shape |
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R,C = self.blocksize |
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if self.indptr.dtype.kind != 'i': |
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warn(f"indptr array has non-integer dtype ({self.indptr.dtype.name})", |
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stacklevel=2) |
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if self.indices.dtype.kind != 'i': |
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warn(f"indices array has non-integer dtype ({self.indices.dtype.name})", |
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stacklevel=2) |
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if self.indices.ndim != 1 or self.indptr.ndim != 1: |
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raise ValueError("indices, and indptr should be 1-D") |
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if self.data.ndim != 3: |
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raise ValueError("data should be 3-D") |
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if (len(self.indptr) != M//R + 1): |
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raise ValueError("index pointer size (%d) should be (%d)" % |
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(len(self.indptr), M//R + 1)) |
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if (self.indptr[0] != 0): |
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raise ValueError("index pointer should start with 0") |
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if (len(self.indices) != len(self.data)): |
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raise ValueError("indices and data should have the same size") |
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if (self.indptr[-1] > len(self.indices)): |
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raise ValueError("Last value of index pointer should be less than " |
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"the size of index and data arrays") |
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self.prune() |
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if full_check: |
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if self.nnz > 0: |
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if self.indices.max() >= N//C: |
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raise ValueError("column index values must be < %d (now max %d)" |
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% (N//C, self.indices.max())) |
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if self.indices.min() < 0: |
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raise ValueError("column index values must be >= 0") |
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if np.diff(self.indptr).min() < 0: |
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raise ValueError("index pointer values must form a " |
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"non-decreasing sequence") |
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idx_dtype = self._get_index_dtype((self.indices, self.indptr)) |
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self.indptr = np.asarray(self.indptr, dtype=idx_dtype) |
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self.indices = np.asarray(self.indices, dtype=idx_dtype) |
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self.data = to_native(self.data) |
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@property |
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def blocksize(self) -> tuple: |
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"""Block size of the matrix.""" |
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return self.data.shape[1:] |
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def _getnnz(self, axis=None): |
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if axis is not None: |
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raise NotImplementedError("_getnnz over an axis is not implemented " |
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"for BSR format") |
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R, C = self.blocksize |
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return int(self.indptr[-1]) * R * C |
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_getnnz.__doc__ = _spbase._getnnz.__doc__ |
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def count_nonzero(self, axis=None): |
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if axis is not None: |
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raise NotImplementedError( |
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"count_nonzero over axis is not implemented for BSR format." |
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) |
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return np.count_nonzero(self._deduped_data()) |
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count_nonzero.__doc__ = _spbase.count_nonzero.__doc__ |
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def __repr__(self): |
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_, fmt = _formats[self.format] |
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sparse_cls = 'array' if isinstance(self, sparray) else 'matrix' |
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b = 'x'.join(str(x) for x in self.blocksize) |
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return ( |
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f"<{fmt} sparse {sparse_cls} of dtype '{self.dtype}'\n" |
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f"\twith {self.nnz} stored elements (blocksize={b}) and shape {self.shape}>" |
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) |
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def diagonal(self, k=0): |
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rows, cols = self.shape |
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if k <= -rows or k >= cols: |
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return np.empty(0, dtype=self.data.dtype) |
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R, C = self.blocksize |
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y = np.zeros(min(rows + min(k, 0), cols - max(k, 0)), |
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dtype=upcast(self.dtype)) |
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_sparsetools.bsr_diagonal(k, rows // R, cols // C, R, C, |
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self.indptr, self.indices, |
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np.ravel(self.data), y) |
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return y |
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diagonal.__doc__ = _spbase.diagonal.__doc__ |
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def __getitem__(self,key): |
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raise NotImplementedError |
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def __setitem__(self,key,val): |
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raise NotImplementedError |
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def _add_dense(self, other): |
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return self.tocoo(copy=False)._add_dense(other) |
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def _matmul_vector(self, other): |
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M,N = self.shape |
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R,C = self.blocksize |
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result = np.zeros(self.shape[0], dtype=upcast(self.dtype, other.dtype)) |
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bsr_matvec(M//R, N//C, R, C, |
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self.indptr, self.indices, self.data.ravel(), |
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other, result) |
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return result |
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def _matmul_multivector(self,other): |
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R,C = self.blocksize |
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M,N = self.shape |
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n_vecs = other.shape[1] |
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result = np.zeros((M,n_vecs), dtype=upcast(self.dtype,other.dtype)) |
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bsr_matvecs(M//R, N//C, n_vecs, R, C, |
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self.indptr, self.indices, self.data.ravel(), |
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other.ravel(), result.ravel()) |
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return result |
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def _matmul_sparse(self, other): |
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M, K1 = self.shape |
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K2, N = other.shape |
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R,n = self.blocksize |
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if other.format == "bsr": |
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C = other.blocksize[1] |
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else: |
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C = 1 |
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if other.format == "csr" and n == 1: |
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other = other.tobsr(blocksize=(n,C), copy=False) |
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else: |
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other = other.tobsr(blocksize=(n,C)) |
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idx_dtype = self._get_index_dtype((self.indptr, self.indices, |
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other.indptr, other.indices)) |
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bnnz = csr_matmat_maxnnz(M//R, N//C, |
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self.indptr.astype(idx_dtype), |
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self.indices.astype(idx_dtype), |
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other.indptr.astype(idx_dtype), |
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other.indices.astype(idx_dtype)) |
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idx_dtype = self._get_index_dtype((self.indptr, self.indices, |
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other.indptr, other.indices), |
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maxval=bnnz) |
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indptr = np.empty(self.indptr.shape, dtype=idx_dtype) |
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indices = np.empty(bnnz, dtype=idx_dtype) |
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data = np.empty(R*C*bnnz, dtype=upcast(self.dtype,other.dtype)) |
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bsr_matmat(bnnz, M//R, N//C, R, C, n, |
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self.indptr.astype(idx_dtype), |
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self.indices.astype(idx_dtype), |
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np.ravel(self.data), |
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other.indptr.astype(idx_dtype), |
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other.indices.astype(idx_dtype), |
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np.ravel(other.data), |
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indptr, |
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indices, |
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data) |
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data = data.reshape(-1,R,C) |
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return self._bsr_container( |
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(data, indices, indptr), shape=(M, N), blocksize=(R, C) |
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) |
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def tobsr(self, blocksize=None, copy=False): |
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"""Convert this array/matrix into Block Sparse Row Format. |
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With copy=False, the data/indices may be shared between this |
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array/matrix and the resultant bsr_array/bsr_matrix. |
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If blocksize=(R, C) is provided, it will be used for determining |
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block size of the bsr_array/bsr_matrix. |
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""" |
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if blocksize not in [None, self.blocksize]: |
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return self.tocsr().tobsr(blocksize=blocksize) |
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if copy: |
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return self.copy() |
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else: |
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return self |
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def tocsr(self, copy=False): |
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M, N = self.shape |
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R, C = self.blocksize |
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nnz = self.nnz |
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idx_dtype = self._get_index_dtype((self.indptr, self.indices), |
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maxval=max(nnz, N)) |
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indptr = np.empty(M + 1, dtype=idx_dtype) |
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indices = np.empty(nnz, dtype=idx_dtype) |
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data = np.empty(nnz, dtype=upcast(self.dtype)) |
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bsr_tocsr(M // R, |
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N // C, |
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R, C, |
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self.indptr.astype(idx_dtype, copy=False), |
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self.indices.astype(idx_dtype, copy=False), |
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self.data, |
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indptr, |
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indices, |
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data) |
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return self._csr_container((data, indices, indptr), shape=self.shape) |
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tocsr.__doc__ = _spbase.tocsr.__doc__ |
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def tocsc(self, copy=False): |
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return self.tocsr(copy=False).tocsc(copy=copy) |
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tocsc.__doc__ = _spbase.tocsc.__doc__ |
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def tocoo(self, copy=True): |
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"""Convert this array/matrix to COOrdinate format. |
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When copy=False the data array will be shared between |
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this array/matrix and the resultant coo_array/coo_matrix. |
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""" |
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M,N = self.shape |
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R,C = self.blocksize |
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indptr_diff = np.diff(self.indptr) |
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if indptr_diff.dtype.itemsize > np.dtype(np.intp).itemsize: |
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indptr_diff_limited = indptr_diff.astype(np.intp) |
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if np.any(indptr_diff_limited != indptr_diff): |
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raise ValueError("Matrix too big to convert") |
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indptr_diff = indptr_diff_limited |
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idx_dtype = self._get_index_dtype(maxval=max(M, N)) |
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row = (R * np.arange(M//R, dtype=idx_dtype)).repeat(indptr_diff) |
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row = row.repeat(R*C).reshape(-1,R,C) |
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row += np.tile(np.arange(R, dtype=idx_dtype).reshape(-1,1), (1,C)) |
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row = row.reshape(-1) |
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col = ((C * self.indices).astype(idx_dtype, copy=False) |
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.repeat(R*C).reshape(-1,R,C)) |
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col += np.tile(np.arange(C, dtype=idx_dtype), (R,1)) |
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col = col.reshape(-1) |
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data = self.data.reshape(-1) |
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if copy: |
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data = data.copy() |
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return self._coo_container( |
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(data, (row, col)), shape=self.shape |
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) |
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def toarray(self, order=None, out=None): |
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return self.tocoo(copy=False).toarray(order=order, out=out) |
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toarray.__doc__ = _spbase.toarray.__doc__ |
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def transpose(self, axes=None, copy=False): |
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if axes is not None and axes != (1, 0): |
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raise ValueError("Sparse matrices do not support " |
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"an 'axes' parameter because swapping " |
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"dimensions is the only logical permutation.") |
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R, C = self.blocksize |
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M, N = self.shape |
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NBLK = self.nnz//(R*C) |
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if self.nnz == 0: |
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return self._bsr_container((N, M), blocksize=(C, R), |
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dtype=self.dtype, copy=copy) |
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indptr = np.empty(N//C + 1, dtype=self.indptr.dtype) |
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indices = np.empty(NBLK, dtype=self.indices.dtype) |
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data = np.empty((NBLK, C, R), dtype=self.data.dtype) |
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bsr_transpose(M//R, N//C, R, C, |
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self.indptr, self.indices, self.data.ravel(), |
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indptr, indices, data.ravel()) |
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return self._bsr_container((data, indices, indptr), |
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shape=(N, M), copy=copy) |
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transpose.__doc__ = _spbase.transpose.__doc__ |
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def eliminate_zeros(self): |
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"""Remove zero elements in-place.""" |
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if not self.nnz: |
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return |
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R,C = self.blocksize |
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M,N = self.shape |
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mask = (self.data != 0).reshape(-1,R*C).sum(axis=1) |
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nonzero_blocks = mask.nonzero()[0] |
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self.data[:len(nonzero_blocks)] = self.data[nonzero_blocks] |
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_sparsetools.csr_eliminate_zeros(M//R, N//C, self.indptr, |
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self.indices, mask) |
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self.prune() |
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def sum_duplicates(self): |
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"""Eliminate duplicate array/matrix entries by adding them together |
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|
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The is an *in place* operation |
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""" |
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if self.has_canonical_format: |
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return |
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self.sort_indices() |
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R, C = self.blocksize |
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M, N = self.shape |
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n_row = M // R |
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nnz = 0 |
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row_end = 0 |
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for i in range(n_row): |
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jj = row_end |
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row_end = self.indptr[i+1] |
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while jj < row_end: |
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j = self.indices[jj] |
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x = self.data[jj] |
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jj += 1 |
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while jj < row_end and self.indices[jj] == j: |
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x += self.data[jj] |
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jj += 1 |
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self.indices[nnz] = j |
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self.data[nnz] = x |
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nnz += 1 |
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self.indptr[i+1] = nnz |
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self.prune() |
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self.has_canonical_format = True |
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def sort_indices(self): |
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"""Sort the indices of this array/matrix *in place* |
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""" |
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if self.has_sorted_indices: |
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return |
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|
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R,C = self.blocksize |
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M,N = self.shape |
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bsr_sort_indices(M//R, N//C, R, C, self.indptr, self.indices, self.data.ravel()) |
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self.has_sorted_indices = True |
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|
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def prune(self): |
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"""Remove empty space after all non-zero elements. |
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""" |
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|
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R,C = self.blocksize |
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M,N = self.shape |
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|
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if len(self.indptr) != M//R + 1: |
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raise ValueError("index pointer has invalid length") |
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|
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bnnz = self.indptr[-1] |
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|
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if len(self.indices) < bnnz: |
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raise ValueError("indices array has too few elements") |
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if len(self.data) < bnnz: |
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raise ValueError("data array has too few elements") |
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self.data = self.data[:bnnz] |
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self.indices = self.indices[:bnnz] |
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def _binopt(self, other, op, in_shape=None, out_shape=None): |
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"""Apply the binary operation fn to two sparse matrices.""" |
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other = self.__class__(other, blocksize=self.blocksize) |
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fn = getattr(_sparsetools, self.format + op + self.format) |
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R,C = self.blocksize |
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|
|
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) |
|
|
|
|
|
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) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
def _broadcast_to(self, shape, copy=False): |
|
return _spbase._broadcast_to(self, shape, copy) |
|
|
|
|
|
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) |
|
|
|
|
|
|
|
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. |
|
|
|
**Limitations** |
|
|
|
Block Sparse Row format sparse arrays do not support slicing. |
|
|
|
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. |
|
|
|
**Limitations** |
|
|
|
Block Sparse Row format sparse matrices do not support slicing. |
|
|
|
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]]) |
|
|
|
""" |
|
|
|
|