How can I save a very large MATLAB sparse matrix to a text file?

Question

I have a 30000x14000 sparse matrix in MATLAB (version 7), which I need to use in another program. Calling save won't write this as ASCII (not supported). Calling full() on this monster results in an Out of Memory error.
How do I export it?

Answer 1

You can use find to get index & value vectors:

[i,j,val] = find(data)
data_dump = [i,j,val]

You can recreate data from data_dump with spconvert, which is meant to "Import from sparse matrix external format" (so I guess it's a good export format):

data = spconvert( data_dump )

You can save to ascii with:

save -ascii data.txt data_dump

But this dumps indices as double, you can write it out more nicely with fopen/fprintf/fclose:

fid = fopen('data.txt','w')
fprintf( fid,'%d %d %f\n', transpose(data_dump) )
fclose(fid)

Hope this helps.

Answer 2

Save the sparse matrix as a .mat file. Then, in the other program, use a suitable library to read the .mat file.

For instance, if the other program is written in Python, you can use the scipy.io.mio.loadmat function, which supports sparse arrays and gives you a sparse numpy matrix.