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import numpy as np
import os
from batchgenerators.utilities.file_and_folder_operations import isfile, subfiles
import multiprocessing
def _convert_to_npy(npz_file: str, unpack_segmentation: bool = True, overwrite_existing: bool = False) -> None:
# try:
a = np.load(npz_file) # inexpensive, no compression is done here. This just reads metadata
if overwrite_existing or not isfile(npz_file[:-3] + "npy"):
np.save(npz_file[:-3] + "npy", a['data'])
if unpack_segmentation and (overwrite_existing or not isfile(npz_file[:-4] + "_seg.npy")):
np.save(npz_file[:-4] + "_seg.npy", a['seg'])
def unpack_dataset(folder: str, unpack_segmentation: bool = True, overwrite_existing: bool = False,
num_processes: int = 8):
"""
all npz files in this folder belong to the dataset, unpack them all
"""
with multiprocessing.get_context("spawn").Pool(num_processes) as p:
npz_files = subfiles(folder, True, None, ".npz", True)
p.starmap(_convert_to_npy, zip(npz_files,
[unpack_segmentation] * len(npz_files),
[overwrite_existing] * len(npz_files))
)
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