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# Copyright 2021 HIP Applied Computer Vision Lab, Division of Medical Image Computing, German Cancer Research Center
# (DKFZ), Heidelberg, Germany
#
# 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.
from typing import Union
from batchgenerators.utilities.file_and_folder_operations import *
import numpy as np
import re
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'])
except KeyboardInterrupt:
if isfile(npz_file[:-3] + "npy"):
os.remove(npz_file[:-3] + "npy")
if isfile(npz_file[:-4] + "_seg.npy"):
os.remove(npz_file[:-4] + "_seg.npy")
raise KeyboardInterrupt
def get_identifiers_from_splitted_dataset_folder(folder: str, file_ending: str):
files = subfiles(folder, suffix=file_ending, join=False)
# all files must be .nii.gz and have 4 digit channel index
crop = len(file_ending) + 5
files = [i[:-crop] for i in files]
# only unique image ids
files = np.unique(files)
return files
def create_lists_from_splitted_dataset_folder(folder: str, file_ending: str, identifiers: List[str] = None) -> List[List[str]]:
"""
does not rely on dataset.json
"""
if identifiers is None:
identifiers = get_identifiers_from_splitted_dataset_folder(folder, file_ending)
files = subfiles(folder, suffix=file_ending, join=False, sort=True)
list_of_lists = []
for f in identifiers:
p = re.compile(re.escape(f) + r"_\d\d\d\d" + re.escape(file_ending))
list_of_lists.append([join(folder, i) for i in files if p.fullmatch(i)])
return list_of_lists
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