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96 lines
3.0 KiB
96 lines
3.0 KiB
# Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import logging
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import sys
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from pathlib import Path
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from typing import Any
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from typing import Union
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import h5py
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import numpy as np
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def read_hdf5(filename: Union[Path, str], dataset_name: str) -> Any:
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"""Read a dataset from a HDF5 file.
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Args:
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filename (Union[Path, str]):
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Path of the HDF5 file.
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dataset_name (str):
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Name of the dataset to read.
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Returns:
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Any: The retrieved dataset.
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"""
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filename = Path(filename)
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if not filename.exists():
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logging.error(f"There is no such a hdf5 file ({filename}).")
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sys.exit(1)
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hdf5_file = h5py.File(filename, "r")
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if dataset_name not in hdf5_file:
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logging.error(f"There is no such a data in hdf5 file. ({dataset_name})")
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sys.exit(1)
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# [()]: a special syntax of h5py to get the dataset as-is
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hdf5_data = hdf5_file[dataset_name][()]
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hdf5_file.close()
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return hdf5_data
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def write_hdf5(filename: Union[Path, str],
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dataset_name: str,
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write_data: np.ndarray,
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is_overwrite: bool=True) -> None:
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"""Write dataset to HDF5 file.
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Args:
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filename (Union[Path, str]): Path of the HDF5 file.
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dataset_name (str): Name of the dataset to write to.
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write_data (np.ndarrays): The data to write.
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is_overwrite (bool, optional): Whether to overwrite, by default True
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"""
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# convert to numpy array
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filename = Path(filename)
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write_data = np.array(write_data)
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# check folder existence
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filename.parent.mkdir(parents=True, exist_ok=True)
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# check hdf5 existence
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if filename.exists():
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# if already exists, open with r+ mode
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hdf5_file = h5py.File(filename, "r+")
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# check dataset existence
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if dataset_name in hdf5_file:
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if is_overwrite:
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logging.warning("Dataset in hdf5 file already exists. "
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"recreate dataset in hdf5.")
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hdf5_file.__delitem__(dataset_name)
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else:
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logging.error(
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"Dataset in hdf5 file already exists. "
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"if you want to overwrite, please set is_overwrite = True.")
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hdf5_file.close()
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sys.exit(1)
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else:
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# if not exists, open with w mode
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hdf5_file = h5py.File(filename, "w")
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# write data to hdf5
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hdf5_file.create_dataset(dataset_name, data=write_data)
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hdf5_file.flush()
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hdf5_file.close()
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