106 lines
3.1 KiB
Python
106 lines
3.1 KiB
Python
# 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()
|