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