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# Copyright 2020 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 batchgenerators.utilities.file_and_folder_operations import *
from nnunet.configuration import default_num_threads
from nnunet.experiment_planning.utils import split_4d
from nnunet.utilities.file_endings import remove_trailing_slash
def crawl_and_remove_hidden_from_decathlon(folder):
folder = remove_trailing_slash(folder)
assert folder.split('/')[-1].startswith("Task"), "This does not seem to be a decathlon folder. Please give me a " \
"folder that starts with TaskXX and has the subfolders imagesTr, " \
"labelsTr and imagesTs"
subf = subfolders(folder, join=False)
assert 'imagesTr' in subf, "This does not seem to be a decathlon folder. Please give me a " \
"folder that starts with TaskXX and has the subfolders imagesTr, " \
"labelsTr and imagesTs"
assert 'imagesTs' in subf, "This does not seem to be a decathlon folder. Please give me a " \
"folder that starts with TaskXX and has the subfolders imagesTr, " \
"labelsTr and imagesTs"
assert 'labelsTr' in subf, "This does not seem to be a decathlon folder. Please give me a " \
"folder that starts with TaskXX and has the subfolders imagesTr, " \
"labelsTr and imagesTs"
_ = [os.remove(i) for i in subfiles(folder, prefix=".")]
_ = [os.remove(i) for i in subfiles(join(folder, 'imagesTr'), prefix=".")]
_ = [os.remove(i) for i in subfiles(join(folder, 'labelsTr'), prefix=".")]
_ = [os.remove(i) for i in subfiles(join(folder, 'imagesTs'), prefix=".")]
def main():
import argparse
parser = argparse.ArgumentParser(description="The MSD provides data as 4D Niftis with the modality being the first"
" dimension. We think this may be cumbersome for some users and "
"therefore expect 3D niftixs instead, with one file per modality. "
"This utility will convert 4D MSD data into the format nnU-Net "
"expects")
parser.add_argument("-i", help="Input folder. Must point to a TaskXX_TASKNAME folder as downloaded from the MSD "
"website", required=True)
parser.add_argument("-p", required=False, default=default_num_threads, type=int,
help="Use this to specify how many processes are used to run the script. "
"Default is %d" % default_num_threads)
parser.add_argument("-output_task_id", required=False, default=None, type=int,
help="If specified, this will overwrite the task id in the output folder. If unspecified, the "
"task id of the input folder will be used.")
args = parser.parse_args()
crawl_and_remove_hidden_from_decathlon(args.i)
split_4d(args.i, args.p, args.output_task_id)
if __name__ == "__main__":
main()
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