# 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 from batchgenerators.utilities.file_and_folder_operations import maybe_mkdir_p, join # do not modify these unless you know what you are doing my_output_identifier = "nnUNet" default_plans_identifier = "nnUNetPlansv2.1" default_data_identifier = 'nnUNetData_plans_v2.1' default_trainer = "nnUNetTrainerV2" default_cascade_trainer = "nnUNetTrainerV2CascadeFullRes" """ PLEASE READ paths.md FOR INFORMATION TO HOW TO SET THIS UP """ base = os.environ['nnUNet_raw_data_base'] if "nnUNet_raw_data_base" in os.environ.keys() else None preprocessing_output_dir = os.environ['nnUNet_preprocessed'] if "nnUNet_preprocessed" in os.environ.keys() else None network_training_output_dir_base = os.path.join(os.environ['RESULTS_FOLDER']) if "RESULTS_FOLDER" in os.environ.keys() else None if base is not None: nnUNet_raw_data = join(base, "nnUNet_raw_data") nnUNet_cropped_data = join(base, "nnUNet_cropped_data") maybe_mkdir_p(nnUNet_raw_data) maybe_mkdir_p(nnUNet_cropped_data) else: print("nnUNet_raw_data_base is not defined and nnU-Net can only be used on data for which preprocessed files " "are already present on your system. nnU-Net cannot be used for experiment planning and preprocessing like " "this. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up properly.") nnUNet_cropped_data = nnUNet_raw_data = None if preprocessing_output_dir is not None: maybe_mkdir_p(preprocessing_output_dir) else: print("nnUNet_preprocessed is not defined and nnU-Net can not be used for preprocessing " "or training. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up.") preprocessing_output_dir = None if network_training_output_dir_base is not None: network_training_output_dir = join(network_training_output_dir_base, my_output_identifier) maybe_mkdir_p(network_training_output_dir) else: print("RESULTS_FOLDER is not defined and nnU-Net cannot be used for training or " "inference. If this is not intended behavior, please read documentation/setting_up_paths.md for information on how to set this " "up.") network_training_output_dir = None