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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.
import os
import shutil
from batchgenerators.utilities.file_and_folder_operations import subdirs, subfiles
def crawl_and_copy(current_folder, out_folder, prefix="fabian_", suffix="ummary.json"):
"""
This script will run recursively through all subfolders of current_folder and copy all files that end with
suffix with some automatically generated prefix into out_folder
:param current_folder:
:param out_folder:
:param prefix:
:return:
"""
s = subdirs(current_folder, join=False)
f = subfiles(current_folder, join=False)
f = [i for i in f if i.endswith(suffix)]
if current_folder.find("fold0") != -1:
for fl in f:
shutil.copy(os.path.join(current_folder, fl), os.path.join(out_folder, prefix+fl))
for su in s:
if prefix == "":
add = su
else:
add = "__" + su
crawl_and_copy(os.path.join(current_folder, su), out_folder, prefix=prefix+add)
if __name__ == "__main__":
from nnunet.paths import network_training_output_dir
output_folder = "/home/fabian/PhD/results/nnUNetV2/leaderboard"
crawl_and_copy(network_training_output_dir, output_folder)
from nnunet.evaluation.add_mean_dice_to_json import run_in_folder
run_in_folder(output_folder)
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