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