Storing numpy sparse matrix in HDF5 (PyTables)

The answer by DaveP is almost right... but can cause problems for very sparse matrices: if the last column(s) or row(s) are empty, they are dropped. So to be sure that everything works, the "shape" attribute must be stored too.

This is the code I regularly use:

import tables as tb
from numpy import array
from scipy import sparse

def store_sparse_mat(m, name, store='store.h5'):
    msg = "This code only works for csr matrices"
    assert(m.__class__ == sparse.csr.csr_matrix), msg
    with tb.openFile(store,'a') as f:
        for par in ('data', 'indices', 'indptr', 'shape'):
            full_name = '%s_%s' % (name, par)
            try:
                n = getattr(f.root, full_name)
                n._f_remove()
            except AttributeError:
                pass

            arr = array(getattr(m, par))
            atom = tb.Atom.from_dtype(arr.dtype)
            ds = f.createCArray(f.root, full_name, atom, arr.shape)
            ds[:] = arr

def load_sparse_mat(name, store='store.h5'):
    with tb.openFile(store) as f:
        pars = []
        for par in ('data', 'indices', 'indptr', 'shape'):
            pars.append(getattr(f.root, '%s_%s' % (name, par)).read())
    m = sparse.csr_matrix(tuple(pars[:3]), shape=pars[3])
    return m

It is trivial to adapt it to csc matrices.

A CSR matrix can be fully reconstructed from its data, indices and indptr attributes. These are just regular numpy arrays, so there should be no problem storing them as 3 separate arrays in pytables, then passing them back to the constructor of csr_matrix. See the scipy docs.

Edit: Pietro's answer has pointed out that the shape member should also be stored

I have updated Pietro Battiston's excellent answer for Python 3.6 and PyTables 3.x, as some PyTables function names have changed in the upgrade from 2.x.

import numpy as np
from scipy import sparse
import tables

def store_sparse_mat(M, name, filename='store.h5'):
    """
    Store a csr matrix in HDF5

    Parameters
    ----------
    M : scipy.sparse.csr.csr_matrix
        sparse matrix to be stored

    name: str
        node prefix in HDF5 hierarchy

    filename: str
        HDF5 filename
    """
    assert(M.__class__ == sparse.csr.csr_matrix), 'M must be a csr matrix'
    with tables.open_file(filename, 'a') as f:
        for attribute in ('data', 'indices', 'indptr', 'shape'):
            full_name = f'{name}_{attribute}'

            # remove existing nodes
            try:  
                n = getattr(f.root, full_name)
                n._f_remove()
            except AttributeError:
                pass

            # add nodes
            arr = np.array(getattr(M, attribute))
            atom = tables.Atom.from_dtype(arr.dtype)
            ds = f.create_carray(f.root, full_name, atom, arr.shape)
            ds[:] = arr

def load_sparse_mat(name, filename='store.h5'):
    """
    Load a csr matrix from HDF5

    Parameters
    ----------
    name: str
        node prefix in HDF5 hierarchy

    filename: str
        HDF5 filename

    Returns
    ----------
    M : scipy.sparse.csr.csr_matrix
        loaded sparse matrix
    """
    with tables.open_file(filename) as f:

        # get nodes
        attributes = []
        for attribute in ('data', 'indices', 'indptr', 'shape'):
            attributes.append(getattr(f.root, f'{name}_{attribute}').read())

    # construct sparse matrix
    M = sparse.csr_matrix(tuple(attributes[:3]), shape=attributes[3])
    return M