# SPDX-FileCopyrightText: 2021 International Photoacoustics Standardisation Consortium (IPASC)
# SPDX-FileCopyrightText: 2021 Computer Assisted Medical Interventions Group, DKFZ
# SPDX-FileCopyrightText: 2021 Janek Gröhl
# SPDX-License-Identifier: MIT
import h5py
from pacfish import PAData
import numpy as np
[docs]def write_data(file_path: str, pa_data: PAData, file_compression: str = None):
"""
Saves a PAData instance into an HDF5 file according to the IPASC consensus format.
Parameters
----------
file_path: str
Path of the file to save the dictionary in.
pa_data: PAData
Instance of the PAData class containing all information
file_compression: str
possible file compression for the hdf5 output file. Possible values are: gzip, lzf and szip.
Return
------
None
This method does not return anything
"""
def recursively_save_dictionaries(file, path, data_dictionary, compression: str = None):
for key, item in data_dictionary.items():
key = str(key)
if not isinstance(item, (list, dict, type(None))):
if isinstance(item, (bytes, int, np.int64, float, str, bool, np.bool_)):
h5file[path + key] = item
else:
if isinstance(item, np.ndarray):
h5file.create_dataset(path + key, data=item, compression=compression)
elif item is None:
h5file[path + key] = "None"
else:
recursively_save_dictionaries(file, path + key + "/", item, file_compression)
with h5py.File(file_path, "w") as h5file:
h5file.create_dataset("binary_time_series_data", data=pa_data.binary_time_series_data)
recursively_save_dictionaries(h5file, "/meta_data/", pa_data.meta_data_acquisition)
recursively_save_dictionaries(h5file, "/meta_data_device/", pa_data.meta_data_device)