# 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 nnunet.utilities.folder_names import get_output_folder_name def get_datasets(): configurations_all = { "Task01_BrainTumour": ("3d_fullres", "2d"), "Task02_Heart": ("3d_fullres", "2d",), "Task03_Liver": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task04_Hippocampus": ("3d_fullres", "2d",), "Task05_Prostate": ("3d_fullres", "2d",), "Task06_Lung": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task07_Pancreas": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task08_HepaticVessel": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task09_Spleen": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task10_Colon": ("3d_cascade_fullres", "3d_fullres", "3d_lowres", "2d"), "Task48_KiTS_clean": ("3d_cascade_fullres", "3d_lowres", "3d_fullres", "2d"), "Task27_ACDC": ("3d_fullres", "2d",), "Task24_Promise": ("3d_fullres", "2d",), "Task35_ISBILesionSegmentation": ("3d_fullres", "2d",), "Task38_CHAOS_Task_3_5_Variant2": ("3d_fullres", "2d",), "Task29_LITS": ("3d_cascade_fullres", "3d_lowres", "2d", "3d_fullres",), "Task17_AbdominalOrganSegmentation": ("3d_cascade_fullres", "3d_lowres", "2d", "3d_fullres",), "Task55_SegTHOR": ("3d_cascade_fullres", "3d_lowres", "3d_fullres", "2d",), "Task56_VerSe": ("3d_cascade_fullres", "3d_lowres", "3d_fullres", "2d",), } return configurations_all def get_commands(configurations, regular_trainer="nnUNetTrainerV2", cascade_trainer="nnUNetTrainerV2CascadeFullRes", plans="nnUNetPlansv2.1"): node_pool = ["hdf18-gpu%02.0d" % i for i in range(1, 21)] + ["hdf19-gpu%02.0d" % i for i in range(1, 8)] + ["hdf19-gpu%02.0d" % i for i in range(11, 16)] ctr = 0 for task in configurations: models = configurations[task] for m in models: if m == "3d_cascade_fullres": trainer = cascade_trainer else: trainer = regular_trainer folder = get_output_folder_name(m, task, trainer, plans, overwrite_training_output_dir="/datasets/datasets_fabian/results/nnUNet") node = node_pool[ctr % len(node_pool)] print("bsub -m %s -q gputest -L /bin/bash \"source ~/.bashrc && python postprocessing/" "consolidate_postprocessing.py -f" % node, folder, "\"") ctr += 1