Accessing sparse matrix elements

Question

I have a very large sparse matrix of the type 'scipy.sparse.coo.coo_matrix'. I can convert to csr with .tocsr(), however .todense() will not work since the array is too large. I want to be able to extract elements from the matrix as I would do with a regular array, so that I may pass row elements to a function.

For reference, when printed, the matrix looks as follows:

(7, 0)  0.531519363001
(48, 24)    0.400946334437
(70, 6) 0.684460955022
...

The csr format accepts indexing just like dense arrays (though not quite as fast). The coo format does not. For whole rows you many want to do M1=M.tocsr(); row = M1[i,:].A (toarray()) assuming the function expects a dense array. — hpaulj
How would you pull out, for example, the three numbers at the top of my print ((7, 0) 0.531519363001)? I don't know what the .A does in your example, but if I skip that part I get a long row of [0 0 0 ... 0] — Helicity

hpaulj hpaulj · Accepted Answer · 2016-08-08T22:00:18

Make a matrix with 3 elements:

In [550]: M = sparse.coo_matrix(([.5,.4,.6],([0,1,2],[0,5,3])), shape=(5,7))

It's default display (repr(M)):

In [551]: M
Out[551]: 
<5x7 sparse matrix of type '<class 'numpy.float64'>'
    with 3 stored elements in COOrdinate format>

and print display (str(M)) - looks like the input:

In [552]: print(M)
  (0, 0)    0.5
  (1, 5)    0.4
  (2, 3)    0.6

convert to csr format:

In [553]: Mc=M.tocsr()
In [554]: Mc[1,:]   # row 1 is another matrix (1 row):
Out[554]: 
<1x7 sparse matrix of type '<class 'numpy.float64'>'
    with 1 stored elements in Compressed Sparse Row format>

In [555]: Mc[1,:].A    # that row as 2d array
Out[555]: array([[ 0. ,  0. ,  0. ,  0. ,  0. ,  0.4,  0. ]])

In [556]: print(Mc[1,:])    # like 2nd element of M except for row number
  (0, 5)    0.4

Individual element:

In [560]: Mc[1,5]
Out[560]: 0.40000000000000002

The data attributes of these format (if you want to dig further)

In [562]: Mc.data
Out[562]: array([ 0.5,  0.4,  0.6])
In [563]: Mc.indices
Out[563]: array([0, 5, 3], dtype=int32)
In [564]: Mc.indptr
Out[564]: array([0, 1, 2, 3, 3, 3], dtype=int32)
In [565]: M.data
Out[565]: array([ 0.5,  0.4,  0.6])
In [566]: M.col
Out[566]: array([0, 5, 3], dtype=int32)
In [567]: M.row
Out[567]: array([0, 1, 2], dtype=int32)

Accessing sparse matrix elements

1 Answers