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

# Allen Institute Software License - This software license is the 2-clause BSD
# license plus a third clause that prohibits redistribution for commercial
# purposes without further permission.
#
# Copyright 2017. Allen Institute. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Redistributions for commercial purposes are not permitted without the
# Allen Institute's written permission.
# For purposes of this license, commercial purposes is the incorporation of the
# Allen Institute's software into anything for which you will charge fees or
# other compensation. Contact terms@alleninstitute.org for commercial licensing
# opportunities.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
import h5py
import numpy as np
from scipy.sparse import csr_matrix
import logging


class Hdf5Util(object):

    def __init__(self):
        self.log = logging.getLogger(__name__)

    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

    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