numpy.savetxt IndexError: tuple index out of range

Question

I have a numpy array with the following attributes:

print(matrix.shape)
(30000, 1000)

print(matrix)
(0, 208)      0.107297742751
(0, 666)      0.107413554001
(0, 833)      0.090485141939
(0, 616)      0.090485141939
..
..

When I try to write the array to a file I get:

numpy.savetxt('matrix.csv', matrix, delimiter=',')
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-18-412b5d26d905> in <module>()
----> 1 numpy.savetxt('matrix.csv', matrix, delimiter=',')

C:\Anaconda3\lib\site-packages\numpy\lib\npyio.py in savetxt(fname, X, fmt, delimiter, newline, header, footer, comments)
   1042                 ncol = len(X.dtype.descr)
   1043         else:
-> 1044             ncol = X.shape[1]
   1045 
   1046         iscomplex_X = np.iscomplexobj(X)

IndexError: tuple index out of range

What am I doing wrong?

Related: stackoverflow.com/questions/15881817/…

xnx
– xnx

2014-12-06 02:28:30 +00:00
Commented Dec 6, 2014 at 2:28 — xnx
– xnx, Commented Dec 6, 2014 at 2:28
If the answer's there I can't see it.

JeffR
– JeffR

2014-12-06 03:30:38 +00:00
Commented Dec 6, 2014 at 3:30 — JeffR
– JeffR, Commented Dec 6, 2014 at 3:30

Community · Accepted Answer · 2017-05-23 11:51:54Z

2

From the output of print(matrix), it is apparent that matrix is an instance of scipy.sparse.coo_matrix. Such a matrix is not a numpy array; numpy knows nothing about scipy sparse matrices. In particular, numpy.savetxt doesn't handle scipy's sparse matrices.

For a suggestion on how to save a sparse matrix to a text file, see my answer to a different question here: How to format in numpy savetxt such that zeros are saved only as "0"

edited May 23, 2017 at 11:51

CommunityBot

11 silver badge

answered Dec 6, 2014 at 5:02

Warren Weckesser

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