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import os
import h5py
from queue import Empty
import multiprocessing
def get_hdf5_group_keys(file_path, data_path=None):
"""Note: segmentation faults seem to be caused only when iterating the HDF5 root.
"""
os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
with h5py.File(file_path, mode="r") as group:
if data_path:
group = group[data_path]
else:
group = group["/"] # to preserve the order
return list(group.keys())
def safe_hdf5_group_keys(file_path, data_path=None):
return run_in_subprocess(
get_hdf5_group_keys, file_path, data_path=data_path, default=list()
)
def run_in_subprocess(target, *args, context=None, default=None, **kwargs):
ctx = multiprocessing.get_context(context)
queue = ctx.Queue(maxsize=1)
p = ctx.Process(
target=subprocess_main,
args=(queue, target) + args,
kwargs=kwargs,
)
p.start()
try:
p.join()
try:
return queue.get(block=False)
except Empty:
return default
finally:
try:
p.kill()
except AttributeError:
p.terminate()
def subprocess_main(queue, method, *args, **kwargs):
queue.put(method(*args, **kwargs))
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