csr.py
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"""Compressed Sparse Row matrix format"""
from __future__ import division, print_function, absolute_import
__docformat__ = "restructuredtext en"
__all__ = ['csr_matrix', 'isspmatrix_csr']
import numpy as np
from scipy._lib.six import xrange
from .base import spmatrix
from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks,
get_csr_submatrix)
from .sputils import upcast, get_index_dtype
from .compressed import _cs_matrix
class csr_matrix(_cs_matrix):
"""
Compressed Sparse Row matrix
This can be instantiated in several ways:
csr_matrix(D)
with a dense matrix or rank-2 ndarray D
csr_matrix(S)
with another sparse matrix S (equivalent to S.tocsr())
csr_matrix((M, N), [dtype])
to construct an empty matrix with shape (M, N)
dtype is optional, defaulting to dtype='d'.
csr_matrix((data, (row_ind, col_ind)), [shape=(M, N)])
where ``data``, ``row_ind`` and ``col_ind`` satisfy the
relationship ``a[row_ind[k], col_ind[k]] = data[k]``.
csr_matrix((data, indices, indptr), [shape=(M, N)])
is the standard CSR representation where the column indices for
row i are stored in ``indices[indptr[i]:indptr[i+1]]`` and their
corresponding 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
Number of stored values, including explicit zeros
data
CSR format data array of the matrix
indices
CSR format index array of the matrix
indptr
CSR format index pointer array of the matrix
has_sorted_indices
Whether indices are sorted
Notes
-----
Sparse matrices can be used in arithmetic operations: they support
addition, subtraction, multiplication, division, and matrix power.
Advantages of the CSR format
- efficient arithmetic operations CSR + CSR, CSR * CSR, etc.
- efficient row slicing
- fast matrix vector products
Disadvantages of the CSR format
- slow column slicing operations (consider CSC)
- changes to the sparsity structure are expensive (consider LIL or DOK)
Examples
--------
>>> import numpy as np
>>> from scipy.sparse import csr_matrix
>>> csr_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])
>>> csr_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])
>>> csr_matrix((data, indices, indptr), shape=(3, 3)).toarray()
array([[1, 0, 2],
[0, 0, 3],
[4, 5, 6]])
As an example of how to construct a CSR matrix incrementally,
the following snippet builds a term-document matrix from texts:
>>> docs = [["hello", "world", "hello"], ["goodbye", "cruel", "world"]]
>>> indptr = [0]
>>> indices = []
>>> data = []
>>> vocabulary = {}
>>> for d in docs:
... for term in d:
... index = vocabulary.setdefault(term, len(vocabulary))
... indices.append(index)
... data.append(1)
... indptr.append(len(indices))
...
>>> csr_matrix((data, indices, indptr), dtype=int).toarray()
array([[2, 1, 0, 0],
[0, 1, 1, 1]])
"""
format = 'csr'
def transpose(self, axes=None, copy=False):
if axes is not None:
raise ValueError(("Sparse matrices do not support "
"an 'axes' parameter because swapping "
"dimensions is the only logical permutation."))
M, N = self.shape
from .csc import csc_matrix
return csc_matrix((self.data, self.indices,
self.indptr), shape=(N, M), copy=copy)
transpose.__doc__ = spmatrix.transpose.__doc__
def tolil(self, copy=False):
from .lil import lil_matrix
lil = lil_matrix(self.shape,dtype=self.dtype)
self.sum_duplicates()
ptr,ind,dat = self.indptr,self.indices,self.data
rows, data = lil.rows, lil.data
for n in xrange(self.shape[0]):
start = ptr[n]
end = ptr[n+1]
rows[n] = ind[start:end].tolist()
data[n] = dat[start:end].tolist()
return lil
tolil.__doc__ = spmatrix.tolil.__doc__
def tocsr(self, copy=False):
if copy:
return self.copy()
else:
return self
tocsr.__doc__ = spmatrix.tocsr.__doc__
def tocsc(self, copy=False):
idx_dtype = get_index_dtype((self.indptr, self.indices),
maxval=max(self.nnz, self.shape[0]))
indptr = np.empty(self.shape[1] + 1, dtype=idx_dtype)
indices = np.empty(self.nnz, dtype=idx_dtype)
data = np.empty(self.nnz, dtype=upcast(self.dtype))
csr_tocsc(self.shape[0], self.shape[1],
self.indptr.astype(idx_dtype),
self.indices.astype(idx_dtype),
self.data,
indptr,
indices,
data)
from .csc import csc_matrix
A = csc_matrix((data, indices, indptr), shape=self.shape)
A.has_sorted_indices = True
return A
tocsc.__doc__ = spmatrix.tocsc.__doc__
def tobsr(self, blocksize=None, copy=True):
from .bsr import bsr_matrix
if blocksize is None:
from .spfuncs import estimate_blocksize
return self.tobsr(blocksize=estimate_blocksize(self))
elif blocksize == (1,1):
arg1 = (self.data.reshape(-1,1,1),self.indices,self.indptr)
return bsr_matrix(arg1, shape=self.shape, copy=copy)
else:
R,C = blocksize
M,N = self.shape
if R < 1 or C < 1 or M % R != 0 or N % C != 0:
raise ValueError('invalid blocksize %s' % blocksize)
blks = csr_count_blocks(M,N,R,C,self.indptr,self.indices)
idx_dtype = get_index_dtype((self.indptr, self.indices),
maxval=max(N//C, blks))
indptr = np.empty(M//R+1, dtype=idx_dtype)
indices = np.empty(blks, dtype=idx_dtype)
data = np.zeros((blks,R,C), dtype=self.dtype)
csr_tobsr(M, N, R, C,
self.indptr.astype(idx_dtype),
self.indices.astype(idx_dtype),
self.data,
indptr, indices, data.ravel())
return bsr_matrix((data,indices,indptr), shape=self.shape)
tobsr.__doc__ = spmatrix.tobsr.__doc__
# these functions are used by the parent class (_cs_matrix)
# to remove redudancy between csc_matrix and csr_matrix
def _swap(self, x):
"""swap the members of x if this is a column-oriented matrix
"""
return x
def __iter__(self):
indptr = np.zeros(2, dtype=self.indptr.dtype)
shape = (1, self.shape[1])
i0 = 0
for i1 in self.indptr[1:]:
indptr[1] = i1 - i0
indices = self.indices[i0:i1]
data = self.data[i0:i1]
yield csr_matrix((data, indices, indptr), shape=shape, copy=True)
i0 = i1
def getrow(self, i):
"""Returns a copy of row i of the matrix, as a (1 x n)
CSR matrix (row vector).
"""
M, N = self.shape
i = int(i)
if i < 0:
i += M
if i < 0 or i >= M:
raise IndexError('index (%d) out of range' % i)
indptr, indices, data = get_csr_submatrix(
M, N, self.indptr, self.indices, self.data, i, i + 1, 0, N)
return csr_matrix((data, indices, indptr), shape=(1, N),
dtype=self.dtype, copy=False)
def getcol(self, i):
"""Returns a copy of column i of the matrix, as a (m x 1)
CSR matrix (column vector).
"""
M, N = self.shape
i = int(i)
if i < 0:
i += N
if i < 0 or i >= N:
raise IndexError('index (%d) out of range' % i)
indptr, indices, data = get_csr_submatrix(
M, N, self.indptr, self.indices, self.data, 0, M, i, i + 1)
return csr_matrix((data, indices, indptr), shape=(M, 1),
dtype=self.dtype, copy=False)
def _get_intXarray(self, row, col):
return self.getrow(row)._minor_index_fancy(col)
def _get_intXslice(self, row, col):
if col.step in (1, None):
return self._get_submatrix(row, col, copy=True)
# TODO: uncomment this once it's faster:
# return self.getrow(row)._minor_slice(col)
M, N = self.shape
start, stop, stride = col.indices(N)
ii, jj = self.indptr[row:row+2]
row_indices = self.indices[ii:jj]
row_data = self.data[ii:jj]
if stride > 0:
ind = (row_indices >= start) & (row_indices < stop)
else:
ind = (row_indices <= start) & (row_indices > stop)
if abs(stride) > 1:
ind &= (row_indices - start) % stride == 0
row_indices = (row_indices[ind] - start) // stride
row_data = row_data[ind]
row_indptr = np.array([0, len(row_indices)])
if stride < 0:
row_data = row_data[::-1]
row_indices = abs(row_indices[::-1])
shape = (1, int(np.ceil(float(stop - start) / stride)))
return csr_matrix((row_data, row_indices, row_indptr), shape=shape,
dtype=self.dtype, copy=False)
def _get_sliceXint(self, row, col):
if row.step in (1, None):
return self._get_submatrix(row, col, copy=True)
return self._major_slice(row)._get_submatrix(minor=col)
def _get_sliceXarray(self, row, col):
return self._major_slice(row)._minor_index_fancy(col)
def _get_arrayXint(self, row, col):
return self._major_index_fancy(row)._get_submatrix(minor=col)
def _get_arrayXslice(self, row, col):
if col.step not in (1, None):
col = np.arange(*col.indices(self.shape[1]))
return self._get_arrayXarray(row, col)
return self._major_index_fancy(row)._get_submatrix(minor=col)
def isspmatrix_csr(x):
"""Is x of csr_matrix type?
Parameters
----------
x
object to check for being a csr matrix
Returns
-------
bool
True if x is a csr matrix, False otherwise
Examples
--------
>>> from scipy.sparse import csr_matrix, isspmatrix_csr
>>> isspmatrix_csr(csr_matrix([[5]]))
True
>>> from scipy.sparse import csc_matrix, csr_matrix, isspmatrix_csc
>>> isspmatrix_csr(csc_matrix([[5]]))
False
"""
return isinstance(x, csr_matrix)