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 tbfrom numpy import arrayfrom scipy import sparsedef 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[:] = arrdef 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 npfrom scipy import sparseimport tablesdef 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[:] = arrdef 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