├── .gitignore ├── README.md ├── job.py ├── job.sh ├── requirements.txt ├── resources └── config.ini ├── setup.py ├── src ├── __init__.py ├── compute_metric_results.py ├── config.py ├── dataset │ ├── __init__.py │ ├── augmentations │ │ ├── __init__.py │ │ ├── color_augmentations.py │ │ ├── data_normalization.py │ │ └── spatial_augmentations.py │ ├── brats_labels.py │ ├── loaders │ │ ├── __init__.py │ │ ├── batch_sampler.py │ │ └── brats_dataset.py │ ├── patching │ │ ├── __init__.py │ │ ├── binary_distribution.py │ │ ├── centered_crop_patch.py │ │ ├── commons.py │ │ ├── equal_label_distribution.py │ │ ├── no_patch.py │ │ ├── random_distribution.py │ │ └── random_tumor_distribution.py │ ├── patient.py │ ├── train_val_split.py │ └── utils │ │ ├── __init__.py │ │ ├── dataset.py │ │ ├── io_patch.py │ │ ├── nifi_volume.py │ │ └── visualization.py ├── ensemble │ ├── __init__.py │ ├── majority_ensemble.py │ └── mean_ensemble.py ├── inference.py ├── logging_conf.py ├── losses │ ├── __init__.py │ ├── ce_dice_loss.py │ ├── dice_loss.py │ ├── new_losses.py │ ├── region_based_loss.py │ └── utils.py ├── metrics │ ├── __init__.py │ ├── evaluation_metrics.py │ └── training_metrics.py ├── models │ ├── __init__.py │ ├── io_model.py │ ├── unet3d │ │ ├── __init__.py │ │ ├── building_blocks.py │ │ └── unet3d.py │ └── vnet │ │ ├── __init__.py │ │ ├── asymm_vnet.py │ │ └── vnet.py ├── normalize_uncertainty.py ├── post_processing │ ├── __init__.py │ └── post_process.py ├── run_post_processing.py ├── test │ ├── __init__.py │ └── predict.py ├── train.py ├── train │ ├── __init__.py │ ├── subregions.py │ └── trainer.py └── uncertainty │ ├── __init__.py │ ├── filter_by_threshold.py │ ├── test_time_augmentation.py │ ├── test_time_dropout.py │ └── uncertainty.py └── tests ├── __init__.py ├── dataset ├── augmentations │ ├── test_data_normalization.py │ └── test_spatial_augmentations.py ├── loaders │ ├── data_batches.py │ ├── test_brats_dataset.py │ └── test_dataloader.py ├── patching │ ├── common.py │ ├── test_binary_distribution.py │ ├── test_centered_crop_patching.py │ ├── test_commons.py │ ├── test_equal_label_distribution.py │ ├── test_random_distribution.py │ └── test_random_tumor_distribution.py ├── samplers.py └── test_brats_labels.py ├── loader_testing.py ├── losses ├── test_dice_loss.py └── test_new_loss.py └── metrics └── test_evaluation_metrics.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LauraMoraB/BrainTumorSegmentation/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LauraMoraB/BrainTumorSegmentation/HEAD/README.md -------------------------------------------------------------------------------- /job.py: -------------------------------------------------------------------------------- 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