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CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/data_augmentation/nnUNetTrainerV2_noMirroring.py | # 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://w... | 2,489 | 45.111111 | 118 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_lReLU_biasInSegOutput.py | # 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://w... | 2,288 | 47.702128 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_allConv3x3.py | # 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://w... | 2,727 | 43.721311 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_lReLU_convlReLUIN.py | # 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://w... | 2,318 | 48.340426 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_NoNormalization.py | # 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://w... | 2,256 | 47.021277 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_BN.py | # 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://w... | 2,473 | 43.178571 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_ReLU.py | # 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://w... | 2,180 | 46.413043 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_ResencUNet.py | # 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://w... | 5,977 | 57.038835 | 134 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_ReLU_convReLUIN.py | # 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://w... | 2,285 | 47.638298 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_NoNormalization_lr1en3.py | # 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://w... | 1,293 | 48.769231 | 117 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_GN.py | # 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://w... | 2,379 | 45.666667 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_softDeepSupervision.py | # 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://w... | 6,237 | 47.734375 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_GeLU.py | # 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://w... | 2,829 | 37.767123 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_ReLU_biasInSegOutput.py | # 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://w... | 2,258 | 47.06383 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_3ConvPerStage.py | # 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://w... | 2,271 | 47.340426 | 117 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_noDeepSupervision.py | # 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://w... | 8,908 | 52.668675 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_LReLU_slope_2en1.py | # 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://w... | 2,221 | 47.304348 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_Mish.py | # 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://w... | 2,228 | 45.4375 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_3ConvPerStage_samefilters.py | # 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://w... | 2,214 | 47.152174 | 117 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/architectural_variants/nnUNetTrainerV2_FRN.py | # 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://w... | 2,430 | 43.2 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/miscellaneous/nnUNetTrainerV2_fullEvals.py | # 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://w... | 9,982 | 49.933673 | 132 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/cascade/nnUNetTrainerV2CascadeFullRes_shorter.py | # 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://w... | 1,324 | 49.961538 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/cascade/nnUNetTrainerV2CascadeFullRes_shorter_lowerLR.py | # 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://w... | 1,363 | 49.518519 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/cascade/nnUNetTrainerV2CascadeFullRes_lowerLR.py | # 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://w... | 1,321 | 49.846154 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/cascade/nnUNetTrainerV2CascadeFullRes_DAVariants.py | # 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://w... | 4,283 | 47.681818 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_ForceBD.py | # 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://w... | 1,180 | 46.24 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_CEGDL.py | # 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://w... | 1,331 | 50.230769 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_Dice.py | # 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://w... | 1,936 | 52.805556 | 131 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_Dice_squared.py | # 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://w... | 1,462 | 51.25 | 138 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_DiceTopK10.py | # 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://w... | 1,382 | 50.222222 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_graduallyTransitionFromCEToDice.py | # 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://w... | 2,667 | 44.220339 | 131 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_TopK10.py | # 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://w... | 1,514 | 44.909091 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_ForceSD.py | # 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://w... | 1,181 | 46.28 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_Dice_lr1en3.py | # 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://w... | 1,743 | 48.828571 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_CE.py | # 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://w... | 1,276 | 52.208333 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_Loss_MCC.py | # 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://w... | 1,943 | 50.157895 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/network_training/nnUNet_variants/loss_function/nnUNetTrainerV2_focalLoss.py | # 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://w... | 6,748 | 30.834906 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/learning_rate/poly_lr.py | # 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://w... | 807 | 43.888889 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/data_augmentation/custom_transforms.py | # 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://w... | 4,821 | 37.887097 | 124 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/data_augmentation/pyramid_augmentations.py | # 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://w... | 9,007 | 46.661376 | 156 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/data_augmentation/default_data_augmentation.py | # 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://w... | 34,196 | 53.7152 | 120 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/data_augmentation/downsampling.py | # 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://w... | 4,164 | 38.292453 | 132 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/data_augmentation/__init__.py | from __future__ import absolute_import
from . import * | 54 | 26.5 | 38 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/cascade_stuff/predict_next_stage.py | # 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://w... | 6,245 | 44.926471 | 119 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/cascade_stuff/__init__.py | from __future__ import absolute_import
from . import * | 54 | 26.5 | 38 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/optimizer/ranger.py | ############
# https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer
# This code was taken from the repo above and was not created by me (Fabian)! Full credit goes to the original authors
############
import math
import torch
from torch.optim.optimizer import Optimizer
class Ranger(Optimizer):
def __init_... | 6,465 | 41.261438 | 132 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/loss_functions/dice_loss.py | # 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://w... | 14,049 | 31.903981 | 121 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/loss_functions/TopK_loss.py | # 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://w... | 1,364 | 39.147059 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/loss_functions/crossentropy.py | from torch import nn, Tensor
class RobustCrossEntropyLoss(nn.CrossEntropyLoss):
"""
this is just a compatibility layer because my target tensor is float and has an extra dimension
"""
def forward(self, input: Tensor, target: Tensor) -> Tensor:
if len(target.shape) == len(input.shape):
... | 438 | 35.583333 | 99 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/loss_functions/deep_supervision.py | # 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://w... | 1,679 | 37.181818 | 117 | py |
CoTr | CoTr-main/nnUNet/nnunet/training/loss_functions/__init__.py | from __future__ import absolute_import
from . import * | 54 | 26.5 | 38 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task017_BeyondCranialVaultAbdominalOrganSegmentation.py | # 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://w... | 5,387 | 36.158621 | 123 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task055_SegTHOR.py | # 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://w... | 3,462 | 33.979798 | 142 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task058_ISBI_EM_SEG.py | # 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://w... | 4,263 | 39.609524 | 128 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task082_BraTS_2020.py | # 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://w... | 32,886 | 42.790945 | 426 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task032_BraTS_2018.py | # 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://w... | 6,634 | 36.485876 | 120 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task076_Fluo_N3DH_SIM.py | # 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://w... | 12,344 | 38.440895 | 143 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task089_Fluo-N2DH-SIM.py | # 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://w... | 11,972 | 40.286207 | 121 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task064_KiTS_labelsFixed.py | # 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://w... | 3,012 | 34.447059 | 142 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task035_ISBI_MSLesionSegmentationChallenge.py | # 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://w... | 6,987 | 41.871166 | 203 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task027_AutomaticCardiacDetectionChallenge.py | # 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://w... | 4,754 | 43.858491 | 154 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task029_LiverTumorSegmentationChallenge.py | # 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://w... | 4,535 | 35.878049 | 123 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task069_CovidSeg.py | import shutil
from batchgenerators.utilities.file_and_folder_operations import *
import SimpleITK as sitk
from nnunet.paths import nnUNet_raw_data
if __name__ == '__main__':
#data is available at http://medicalsegmentation.com/covid19/
download_dir = '/home/fabian/Downloads'
task_id = 69
task_name = ... | 2,507 | 35.347826 | 142 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task075_Fluo_C3DH_A549_ManAndSim.py | # 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://w... | 5,610 | 39.65942 | 119 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task065_KiTS_NicksLabels.py | # 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://w... | 3,196 | 35.329545 | 142 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task024_Promise2012.py | # 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://w... | 3,287 | 39.097561 | 152 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task040_KiTS.py | # 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://w... | 9,159 | 37.008299 | 252 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task114_heart_MNMs.py | from collections import OrderedDict
from batchgenerators.utilities.file_and_folder_operations import *
import shutil
import numpy as np
from numpy.random.mtrand import RandomState
import subprocess
from multiprocessing import pool
import pandas as pd
def get_mnms_data(data_root):
files_raw = []
files_gt = []... | 11,023 | 43.813008 | 194 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task062_NIHPancreas.py | # 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://w... | 3,238 | 34.988889 | 142 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task037_038_Chaos_Challenge.py | # 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://w... | 20,639 | 43.772234 | 278 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task056_VerSe2019.py | # 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://w... | 7,616 | 43.028902 | 157 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task061_CREMI.py | # 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://w... | 6,124 | 40.952055 | 126 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/__init__.py | from __future__ import absolute_import
from . import * | 55 | 17.666667 | 38 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task056_Verse_normalize_orientation.py | # 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://w... | 3,396 | 33.313131 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task059_EPFL_EM_MITO_SEG.py | # 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://w... | 4,324 | 42.686869 | 128 | py |
CoTr | CoTr-main/nnUNet/nnunet/dataset_conversion/Task043_BraTS_2019.py | # 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://w... | 6,075 | 35.824242 | 120 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/generic_UNet_DP.py | # 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://w... | 6,839 | 53.72 | 131 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/neural_network.py | # 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://w... | 43,801 | 51.964933 | 137 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/initialization.py | # 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://w... | 1,673 | 41.923077 | 158 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/generic_UNet.py | # 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://w... | 20,989 | 45.644444 | 180 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/generic_modular_residual_UNet.py | # 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://w... | 24,392 | 46.829412 | 125 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/__init__.py | from __future__ import absolute_import
from . import * | 54 | 26.5 | 38 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/generic_modular_UNet.py | # 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://w... | 19,951 | 41.451064 | 136 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/custom_modules/helperModules.py | # 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://w... | 1,051 | 34.066667 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/custom_modules/conv_blocks.py | # 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://w... | 9,127 | 38.860262 | 143 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/custom_modules/feature_response_normalization.py | # 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://w... | 1,547 | 34.181818 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/network_architecture/custom_modules/mish.py | ############
# https://github.com/lessw2020/mish/blob/master/mish.py
# This code was taken from the repo above and was not created by me (Fabian)! Full credit goes to the original authors
############
import torch
import torch.nn as nn
import torch.nn.functional as F
# Mish - "Mish: A Self Regularized Non-Monotonic... | 730 | 29.458333 | 118 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/file_conversions.py | from typing import Tuple, List
from skimage import io
import SimpleITK as sitk
import numpy as np
import tifffile
def convert_2d_image_to_nifti(filename: str, output_name: str, spacing=(999, 1, 1), transform=None, is_seg: bool = False) -> None:
"""
Reads an image (must be a format that it recognized by skimag... | 4,314 | 38.587156 | 136 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/sitk_stuff.py | # 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://w... | 908 | 36.875 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/recursive_delete_npz.py | # 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://w... | 1,554 | 39.921053 | 118 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/one_hot_encoding.py | # 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://w... | 990 | 38.64 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/file_endings.py | # 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://w... | 1,130 | 35.483871 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/nd_softmax.py | # 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://w... | 801 | 35.454545 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/tensor_utilities.py | # 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://w... | 1,624 | 28.545455 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/folder_names.py | # 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://w... | 1,810 | 36.729167 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/to_torch.py | # 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://w... | 1,167 | 35.5 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/task_name_id_conversion.py | # 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://w... | 3,514 | 50.691176 | 133 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/random_stuff.py | # 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://w... | 794 | 35.136364 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/distributed.py | # 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://w... | 3,172 | 34.255556 | 114 | py |
CoTr | CoTr-main/nnUNet/nnunet/utilities/__init__.py | from __future__ import absolute_import
from . import * | 54 | 26.5 | 38 | py |
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