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Fingerprint extraction... |
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Dataset101_FinalSet |
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Using <class 'nnunetv2.imageio.simpleitk_reader_writer.SimpleITKIO'> as reader/writer |
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#################### |
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verify_dataset_integrity Done. |
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If you didn't see any error messages then your dataset is most likely OK! |
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#################### |
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Using <class 'nnunetv2.imageio.simpleitk_reader_writer.SimpleITKIO'> as reader/writer |
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Experiment planning... |
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############################ |
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INFO: You are using the old nnU-Net default planner. We have updated our recommendations. Please consider using those instead! Read more here: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/resenc_presets.md |
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############################ |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 0.89722656 0.89722656]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 497.08737864 497.08737864] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 0.92414336 0.92414336]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 482.60910548 482.60910548] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 0.95186766 0.95186766]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 468.55252959 468.55252959] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 0.98042369 0.98042369]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 454.90536853 454.90536853] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.0098364 1.0098364]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 441.6556976 441.6556976] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.04013149 1.04013149]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 428.79193942 428.79193942] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.07133544 1.07133544]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 416.30285381 416.30285381] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.1034755 1.1034755]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 404.17752797 404.17752797] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.13657977 1.13657977]. |
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Current patch size: (np.int64(112), np.int64(128), np.int64(128)). |
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Current median shape: [391. 392.40536696 392.40536696] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.17067716 1.17067716]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(112)). |
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Current median shape: [391. 380.97608443 380.97608443] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.20579747 1.20579747]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(112)). |
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Current median shape: [391. 369.87969362 369.87969362] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.2419714 1.2419714]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(112)). |
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Current median shape: [391. 359.10649866 359.10649866] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.5 1.27923054 1.27923054]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [391. 348.64708608 348.64708608] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.575 1.31760746 1.31760746]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [379.61165049 338.49231658 338.49231658] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.65225 1.35713568 1.35713568]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [368.55500047 328.63331707 328.63331707] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.7318175 1.39784975 1.39784975]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [357.82038881 319.06147288 319.06147288] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.81377203 1.43978524 1.43978524]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [347.39843574 309.76842027 309.76842027] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.89818519 1.4829788 1.4829788 ]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [337.28003469 300.7460391 300.7460391 ] |
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Attempting to find 3d_lowres config. |
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Current spacing: [2.98513074 1.52746816 1.52746816]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [327.45634436 291.98644573 291.98644573] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.07468466 1.57329221 1.57329221]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [317.91878094 283.48198614 283.48198614] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.1669252 1.62049097 1.62049097]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [308.65901062 275.22522927 275.22522927] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.26193296 1.6691057 1.6691057 ]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [299.66894235 267.20896045 267.20896045] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.35979095 1.71917887 1.71917887]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [290.94072072 259.4261752 259.4261752 ] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.46058468 1.77075424 1.77075424]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [282.46671915 251.87007301 251.87007301] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.56440222 1.82387687 1.82387687]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [274.23953316 244.53405146 244.53405146] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.67133428 1.87859317 1.87859317]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [266.25197394 237.41170045 237.41170045] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.78147431 1.93495097 1.93495097]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [258.49706208 230.49679655 230.49679655] |
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Attempting to find 3d_lowres config. |
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Current spacing: [3.89491854 1.9929995 1.9929995 ]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [250.96802143 223.78329762 223.78329762] |
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Attempting to find 3d_lowres config. |
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Current spacing: [4.0117661 2.05278948 2.05278948]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [243.65827324 217.2653375 217.2653375 ] |
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Attempting to find 3d_lowres config. |
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Current spacing: [4.13211908 2.11437317 2.11437317]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [236.56143033 210.93722087 210.93722087] |
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Attempting to find 3d_lowres config. |
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Current spacing: [4.25608265 2.17780436 2.17780436]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [229.67129158 204.79341832 204.79341832] |
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Attempting to find 3d_lowres config. |
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Current spacing: [4.38376513 2.24313849 2.24313849]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [222.98183648 198.82856148 198.82856148] |
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Attempting to find 3d_lowres config. |
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Current spacing: [4.51527809 2.31043265 2.31043265]. |
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Current patch size: (np.int64(128), np.int64(128), np.int64(128)). |
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Current median shape: [216.48721989 193.03743833 193.03743833] |
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2D U-Net configuration: |
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{'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 12, 'patch_size': (np.int64(512), np.int64(512)), 'median_image_size_in_voxels': array([512., 512.]), 'spacing': array([0.87109375, 0.87109375]), 'normalization_schemes': ['CTNormalization'], 'use_mask_for_norm': [False], 'resampling_fn_data': 'resample_data_or_seg_to_shape', 'resampling_fn_seg': 'resample_data_or_seg_to_shape', 'resampling_fn_data_kwargs': {'is_seg': False, 'order': 3, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'architecture': {'network_class_name': 'dynamic_network_architectures.architectures.unet.PlainConvUNet', 'arch_kwargs': {'n_stages': 8, 'features_per_stage': (32, 64, 128, 256, 512, 512, 512, 512), 'conv_op': 'torch.nn.modules.conv.Conv2d', 'kernel_sizes': ((3, 3), (3, 3), (3, 3), (3, 3), (3, 3), (3, 3), (3, 3), (3, 3)), 'strides': ((1, 1), (2, 2), (2, 2), (2, 2), (2, 2), (2, 2), (2, 2), (2, 2)), 'n_conv_per_stage': (2, 2, 2, 2, 2, 2, 2, 2), 'n_conv_per_stage_decoder': (2, 2, 2, 2, 2, 2, 2), 'conv_bias': True, 'norm_op': 'torch.nn.modules.instancenorm.InstanceNorm2d', 'norm_op_kwargs': {'eps': 1e-05, 'affine': True}, 'dropout_op': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ('conv_op', 'norm_op', 'dropout_op', 'nonlin')}, 'batch_dice': True} |
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Using <class 'nnunetv2.imageio.simpleitk_reader_writer.SimpleITKIO'> as reader/writer |
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3D lowres U-Net configuration: |
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{'data_identifier': 'nnUNetPlans_3d_lowres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': (np.int64(128), np.int64(128), np.int64(128)), 'median_image_size_in_voxels': (216, 193, 193), 'spacing': array([4.51527809, 2.31043265, 2.31043265]), 'normalization_schemes': ['CTNormalization'], 'use_mask_for_norm': [False], 'resampling_fn_data': 'resample_data_or_seg_to_shape', 'resampling_fn_seg': 'resample_data_or_seg_to_shape', 'resampling_fn_data_kwargs': {'is_seg': False, 'order': 3, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'architecture': {'network_class_name': 'dynamic_network_architectures.architectures.unet.PlainConvUNet', 'arch_kwargs': {'n_stages': 6, 'features_per_stage': (32, 64, 128, 256, 320, 320), 'conv_op': 'torch.nn.modules.conv.Conv3d', 'kernel_sizes': ((3, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3)), 'strides': ((1, 1, 1), (2, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2)), 'n_conv_per_stage': (2, 2, 2, 2, 2, 2), 'n_conv_per_stage_decoder': (2, 2, 2, 2, 2), 'conv_bias': True, 'norm_op': 'torch.nn.modules.instancenorm.InstanceNorm3d', 'norm_op_kwargs': {'eps': 1e-05, 'affine': True}, 'dropout_op': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ('conv_op', 'norm_op', 'dropout_op', 'nonlin')}, 'batch_dice': False, 'next_stage': '3d_cascade_fullres'} |
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3D fullres U-Net configuration: |
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{'data_identifier': 'nnUNetPlans_3d_fullres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': (np.int64(112), np.int64(128), np.int64(128)), 'median_image_size_in_voxels': array([391., 512., 512.]), 'spacing': array([2.5 , 0.87109375, 0.87109375]), 'normalization_schemes': ['CTNormalization'], 'use_mask_for_norm': [False], 'resampling_fn_data': 'resample_data_or_seg_to_shape', 'resampling_fn_seg': 'resample_data_or_seg_to_shape', 'resampling_fn_data_kwargs': {'is_seg': False, 'order': 3, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'architecture': {'network_class_name': 'dynamic_network_architectures.architectures.unet.PlainConvUNet', 'arch_kwargs': {'n_stages': 6, 'features_per_stage': (32, 64, 128, 256, 320, 320), 'conv_op': 'torch.nn.modules.conv.Conv3d', 'kernel_sizes': ((1, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3), (3, 3, 3)), 'strides': ((1, 1, 1), (1, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2)), 'n_conv_per_stage': (2, 2, 2, 2, 2, 2), 'n_conv_per_stage_decoder': (2, 2, 2, 2, 2), 'conv_bias': True, 'norm_op': 'torch.nn.modules.instancenorm.InstanceNorm3d', 'norm_op_kwargs': {'eps': 1e-05, 'affine': True}, 'dropout_op': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ('conv_op', 'norm_op', 'dropout_op', 'nonlin')}, 'batch_dice': True} |
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Plans were saved to nnUNet_preprocessed/Dataset101_FinalSet/nnUNetPlans.json |
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Preprocessing... |
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Preprocessing dataset Dataset101_FinalSet |
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Configuration: 2d... |
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Configuration: 3d_fullres... |
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Configuration: 3d_lowres... |
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