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numpy array to scipy.sparse matrix

Given an arbitrary numpy array (ndarray), is there a function or a short way to convert it to a scipy.sparse matrix?

I'd like something that works like:

A = numpy.array([0,1,0],[0,0,0],[1,0,0])
S = to_sparse(A, type="csr_matrix")
like image 359
clstaudt Avatar asked May 21 '12 14:05

clstaudt


2 Answers

I usually do something like

>>> import numpy, scipy.sparse
>>> A = numpy.array([[0,1,0],[0,0,0],[1,0,0]])
>>> Asp = scipy.sparse.csr_matrix(A)
>>> Asp
<3x3 sparse matrix of type '<type 'numpy.int64'>'
    with 2 stored elements in Compressed Sparse Row format>
like image 153
DSM Avatar answered Sep 24 '22 10:09

DSM


A very useful and pertinent example is in the help!

import scipy.sparse as sp
help(sp)

This gives:

Example 2
---------

Construct a matrix in COO format:

>>> from scipy import sparse
>>> from numpy import array
>>> I = array([0,3,1,0])
>>> J = array([0,3,1,2])
>>> V = array([4,5,7,9])
>>> A = sparse.coo_matrix((V,(I,J)),shape=(4,4))

It's also worth noting the various constructors are (again from the help):

    1. csc_matrix: Compressed Sparse Column format
    2. csr_matrix: Compressed Sparse Row format
    3. bsr_matrix: Block Sparse Row format
    4. lil_matrix: List of Lists format
    5. dok_matrix: Dictionary of Keys format
    6. coo_matrix: COOrdinate format (aka IJV, triplet format)
    7. dia_matrix: DIAgonal format

To construct a matrix efficiently, use either lil_matrix (recommended) or
dok_matrix. The lil_matrix class supports basic slicing and fancy
indexing with a similar syntax to NumPy arrays.  

Your example would be as simple as:

S = sp.csr_matrix(A)
like image 34
Hooked Avatar answered Sep 22 '22 10:09

Hooked