How to save a dictionary of scipy sparse csr matrices?

Asked Feb 06 '18 at 21:31

Active Feb 06 '18 at 21:31

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I've seen this question, but I'm having trouble with using save_npz.

I have a dictionary of scipy sparse csr matrices called adj_mat_time_t.

I'm trying to save it to a file via:

scipy.sparse.save_npz('binary_adj_mats.npz', adj_mat_time_t)

The error:

Traceback (most recent call last):
    ...
  File "my_prog.py", line 400...
    scipy.sparse.save_npz('binary_adj_mats.npz', adj_mat_time_t)
  File "/user/pkgs/anaconda2/lib/python2.7/site-packages/scipy/sparse/_matrix_io.py", line 64, in save_npz
    arrays_dict = dict(format=matrix.format.encode('ascii'),
AttributeError: 'dict' object has no attribute 'format'

I'm working with scipy version 1.0.0

How can I fix this?

edited Jun 20 '20 at 09:12

Community

asked Feb 06 '18 at 21:31

StatsSorceress

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`save_npz` is designed to work with a single sparse matrix. It does not handle a list or dictionary of matrices. You'll have to do your own iteration. – hpaulj Feb 06 '18 at 22:08
@hpaulj Okay. Would you be willing to code up an example as a solution? – StatsSorceress Feb 06 '18 at 22:10
That's basic Python file and dictionary operations. – hpaulj Feb 06 '18 at 22:12
Okay, but dictionaries aren't serializable as far as I know, so `json` isn't a solution. Should I try to pickle this? – StatsSorceress Feb 06 '18 at 22:14
What I mean is that if you are going to use `save_npz` you have write each matrix to a separate file. You could alternatively try the MATLAB format, `savemat`. – hpaulj Feb 06 '18 at 22:23
Ooh, that would mean more than 12,000 files! Not an option, I'm afraid. According to this question (https://stackoverflow.com/questions/9232751/saving-and-loading-python-dict-with-savemat-results-in-error), `savemat` does not preserve the nature of a dictionary. Any other ideas? – StatsSorceress Feb 06 '18 at 22:25
why not just pickle this dictionary? – MaxU - stand with Ukraine Feb 06 '18 at 22:41
That's what I ended up doing. Thanks guys. – StatsSorceress Feb 06 '18 at 23:27

How to save a dictionary of scipy sparse csr matrices?

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