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']) np.save(npz_file[:-4] + "_global.npy", a['data_global']) np.save(npz_file[:-4] + "_global_seg.npy", a['seg_global']) 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)) )