store_sparse_matrix.py

import tables as tb

from scipy.sparse import lil_matrix

h5 = tb.open_file('sparse.h5', 'a')

data_group = h5.create_group(h5.root, 'data_group')
indices_group = h5.create_group(h5.root, 'indices_group')
indptr_group = h5.create_group(h5.root, 'indptr_group')

for i in xrange(10000):
    name = 'm{:d}'.format(i)
    m = lil_matrix((361, 200000))
    for j in xrange(10):
        m[i % 361, j] = 1
    m = m.tocsr()
    data = m.data
    data_atom = tb.Atom.from_dtype(data.dtype)
    data_store = h5.create_carray(data_group, name, data_atom, data.shape)
    data_store[:] = data

    indices = m.indices
    indices_atom = tb.Atom.from_dtype(indices.dtype)
    indices_store = h5.create_carray(indices_group, name, indices_atom, indices.shape)
    indices_store[:] = indices

    indptr = m.indptr
    indptr_atom = tb.Atom.from_dtype(indptr.dtype)
    indptr_store = h5.create_carray(indptr_group, name, indptr_atom, indptr.shape)
    indptr_store[:] = indptr
h5.close()