Source code for allensdk.config.model.formats.hdf5_util

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import h5py
import numpy as np
from scipy.sparse import csr_matrix
import logging


[docs]class Hdf5Util(object): def __init__(self): self.log = logging.getLogger(__name__)
[docs] def read(self, file_path): try: with h5py.File(file_path, 'r') as csr: return csr_matrix((csr['data'][...], csr['indices'][...], csr['indptr'][...])) except Exception: self.log.error( "Couldn't read AllenSDK HDF5 CSR configuration: %s" % file_path) raise
[docs] def write(self, file_path, m): try: with h5py.File(file_path, 'w') as csr: csr.create_dataset('data', data=m.data, dtype=np.uint8) csr.create_dataset('indices', data=m.indices, dtype=np.uint32) csr.create_dataset('indptr', data=m.indptr, dtype=np.uint32) except Exception: self.log.warn( "Couldn't write AllenSDK HDF5 CSR configuration: %s" % file_path) raise