LICENSE
README.md
pyproject.toml
setup.cfg
tests/test_configurations.py
tests/test_end_to_end.py
tests/test_infinite_random_batch_sampler.py
tests/test_manager.py
tests/test_paths.py
yucca/__init__.py
yucca/paths.py
yucca.egg-info/PKG-INFO
yucca.egg-info/SOURCES.txt
yucca.egg-info/dependency_links.txt
yucca.egg-info/entry_points.txt
yucca.egg-info/requires.txt
yucca.egg-info/top_level.txt
yucca/callbacks/__init__.py
yucca/callbacks/loggers.py
yucca/callbacks/prediction_writer.py
yucca/data/__init__.py
yucca/data/samplers.py
yucca/data/augmentation/YuccaAugmentationComposer.py
yucca/data/augmentation/__init__.py
yucca/data/augmentation/augmentation_presets.py
yucca/data/augmentation/transforms/BiasField.py
yucca/data/augmentation/transforms/Blur.py
yucca/data/augmentation/transforms/Gamma.py
yucca/data/augmentation/transforms/Ghosting.py
yucca/data/augmentation/transforms/Masking.py
yucca/data/augmentation/transforms/Mirror.py
yucca/data/augmentation/transforms/Noise.py
yucca/data/augmentation/transforms/Ringing.py
yucca/data/augmentation/transforms/SimulateLowres.py
yucca/data/augmentation/transforms/Spatial.py
yucca/data/augmentation/transforms/YuccaTransform.py
yucca/data/augmentation/transforms/__init__.py
yucca/data/augmentation/transforms/convert_labels_to_regions.py
yucca/data/augmentation/transforms/copy_image_to_label.py
yucca/data/augmentation/transforms/cropping_and_padding.py
yucca/data/augmentation/transforms/formatting.py
yucca/data/augmentation/transforms/normalize.py
yucca/data/augmentation/transforms/sampling.py
yucca/data/data_modules/YuccaDataModule.py
yucca/data/data_modules/__init__.py
yucca/data/datasets/YuccaCompressedDataset.py
yucca/data/datasets/YuccaDataset.py
yucca/data/datasets/__init__.py
yucca/data/datasets/alternative_datasets/YuccaDataset_1modality.py
yucca/data/datasets/alternative_datasets/__init__.py
yucca/documentation/templates/functional_training.py
yucca/functional/__init__.py
yucca/functional/planning.py
yucca/functional/preprocessing.py
yucca/functional/array_operations/__init__.py
yucca/functional/array_operations/bounding_boxes.py
yucca/functional/array_operations/cropping_and_padding.py
yucca/functional/array_operations/filtering.py
yucca/functional/array_operations/matrix_ops.py
yucca/functional/array_operations/normalization.py
yucca/functional/array_operations/transpose.py
yucca/functional/evaluation/__init__.py
yucca/functional/evaluation/confusion_matrix.py
yucca/functional/evaluation/metrics.py
yucca/functional/evaluation/obj_metrics.py
yucca/functional/evaluation/surface_metrics.py
yucca/functional/evaluation/deepmind_surface_distance/__init__.py
yucca/functional/evaluation/deepmind_surface_distance/lookup_tables.py
yucca/functional/evaluation/deepmind_surface_distance/metrics.py
yucca/functional/testing/__init__.py
yucca/functional/testing/data/__init__.py
yucca/functional/testing/data/array.py
yucca/functional/testing/data/nifti.py
yucca/functional/testing/data/tensor.py
yucca/functional/transforms/__init__.py
yucca/functional/transforms/bias_field.py
yucca/functional/transforms/blur.py
yucca/functional/transforms/croppad.py
yucca/functional/transforms/gamma.py
yucca/functional/transforms/label_transforms.py
yucca/functional/transforms/masking.py
yucca/functional/transforms/motion_ghosting.py
yucca/functional/transforms/noise.py
yucca/functional/transforms/ringing.py
yucca/functional/transforms/sampling.py
yucca/functional/transforms/spatial.py
yucca/functional/utils/__init__.py
yucca/functional/utils/dict.py
yucca/functional/utils/files_and_folders.py
yucca/functional/utils/kwargs.py
yucca/functional/utils/loading.py
yucca/functional/utils/nib_utils.py
yucca/functional/utils/saving.py
yucca/functional/utils/softmax.py
yucca/functional/utils/torch_utils.py
yucca/functional/utils/type_conversions.py
yucca/functional/visualization/__init__.py
yucca/functional/visualization/imshow.py
yucca/lightning_modules/YuccaLightningModule.py
yucca/lightning_modules/YuccaLightningModule_onehot_labels.py
yucca/lightning_modules/__init__.py
yucca/metrics/BoundingBox.py
yucca/metrics/__init__.py
yucca/metrics/training_metrics.py
yucca/networks/__init__.py
yucca/networks/blocks_and_layers/__init__.py
yucca/networks/blocks_and_layers/conv_blocks.py
yucca/networks/blocks_and_layers/conv_layers.py
yucca/networks/blocks_and_layers/norm.py
yucca/networks/networks/DeepLabHeadV3Plus.py
yucca/networks/networks/MedNeXt.py
yucca/networks/networks/MultiResUNet.py
yucca/networks/networks/TinyUNet.py
yucca/networks/networks/UNet.py
yucca/networks/networks/UNetR.py
yucca/networks/networks/UNetRE.py
yucca/networks/networks/UXNet.py
yucca/networks/networks/YuccaNet.py
yucca/networks/networks/__init__.py
yucca/networks/networks/resnet.py
yucca/networks/utils/__init__.py
yucca/networks/utils/get_steps_for_sliding_window.py
yucca/networks/utils/model_memory_estimation.py
yucca/optimization/__init__.py
yucca/optimization/hierarchical_losses.py
yucca/optimization/loss_functions/CE.py
yucca/optimization/loss_functions/Dice.py
yucca/optimization/loss_functions/MSE.py
yucca/optimization/loss_functions/NLL.py
yucca/optimization/loss_functions/__init__.py
yucca/optimization/loss_functions/combined_losses.py
yucca/optimization/loss_functions/deep_supervision.py
yucca/optimization/loss_functions/hierarchical_losses.py
yucca/optimization/loss_functions/nnUNet_losses.py
yucca/optimization/loss_functions/unified_focal_loss.py
yucca/optimization/optimizers/__init__.py
yucca/optimization/schedulers/__init__.py
yucca/optimization/utils/LossTree.py
yucca/optimization/utils/__init__.py
yucca/pipeline/__init__.py
yucca/pipeline/configuration/__init__.py
yucca/pipeline/configuration/configure_callbacks.py
yucca/pipeline/configuration/configure_checkpoint.py
yucca/pipeline/configuration/configure_input_dims.py
yucca/pipeline/configuration/configure_paths.py
yucca/pipeline/configuration/configure_plans.py
yucca/pipeline/configuration/configure_seed.py
yucca/pipeline/configuration/configure_task.py
yucca/pipeline/configuration/split_data.py
yucca/pipeline/evaluation/YuccaEvaluator.py
yucca/pipeline/evaluation/__init__.py
yucca/pipeline/evaluation/challenge_evaluation_scripts/isles_eval.py
yucca/pipeline/evaluation/challenge_preparation_scripts/prepare_decathlon.py
yucca/pipeline/managers/YuccaManager.py
yucca/pipeline/managers/YuccaManagerV2.py
yucca/pipeline/managers/__init__.py
yucca/pipeline/managers/alternative_managers/YuccaManagerV2_labelregions.py
yucca/pipeline/managers/alternative_managers/YuccaManager_NoPatches.py
yucca/pipeline/managers/alternative_managers/YuccaManager_PatchSizeMax.py
yucca/pipeline/managers/alternative_managers/__init__.py
yucca/pipeline/managers/augmentation/YuccaManager_AllAlways.py
yucca/pipeline/managers/augmentation/YuccaManager_BiasField.py
yucca/pipeline/managers/augmentation/YuccaManager_CT.py
yucca/pipeline/managers/augmentation/YuccaManager_Ghosting.py
yucca/pipeline/managers/augmentation/YuccaManager_PreserveRange.py
yucca/pipeline/managers/augmentation/YuccaManager_Ringing.py
yucca/pipeline/managers/augmentation/YuccaManager_SpatialOnly.py
yucca/pipeline/managers/augmentation/YuccaManager_Tester.py
yucca/pipeline/managers/augmentation/__init__.py
yucca/pipeline/managers/dataloading/YuccaManager_Compress.py
yucca/pipeline/managers/dataloading/YuccaManager_Only1Modality.py
yucca/pipeline/managers/dataloading/__init__.py
yucca/pipeline/managers/epochs/YuccaManager_1epoch.py
yucca/pipeline/managers/epochs/__init__.py
yucca/pipeline/managers/losses/YuccaManager_CE.py
yucca/pipeline/managers/losses/YuccaManager_DS.py
yucca/pipeline/managers/losses/__init__.py
yucca/pipeline/managers/lr/YuccaManager_1e5.py
yucca/pipeline/managers/lr/__init__.py
yucca/pipeline/managers/optimizers/YuccaManager_AdamW.py
yucca/pipeline/managers/optimizers/__init__.py
yucca/pipeline/planning/ClassificationPlanner.py
yucca/pipeline/planning/YuccaPlanner.py
yucca/pipeline/planning/YuccaPlannerV2.py
yucca/pipeline/planning/__init__.py
yucca/pipeline/planning/dataset_properties.py
yucca/pipeline/planning/alternative_planners/YuccaPlanner_Compress.py
yucca/pipeline/planning/alternative_planners/YuccaPlanner_MissingModalities.py
yucca/pipeline/planning/alternative_planners/__init__.py
yucca/pipeline/planning/resampling/UnsupervisedPlannerUnitSpacing.py
yucca/pipeline/planning/resampling/YuccaPlanner_1_1_1.py
yucca/pipeline/planning/resampling/YuccaPlanner_1_1_125.py
yucca/pipeline/planning/resampling/YuccaPlanner_224x224.py
yucca/pipeline/planning/resampling/YuccaPlanner_MaxSize.py
yucca/pipeline/planning/resampling/YuccaPlanner_NoResample.py
yucca/pipeline/planning/resampling/__init__.py
yucca/pipeline/preprocessing/ClassificationPreprocessor.py
yucca/pipeline/preprocessing/UnsupervisedPreprocessor.py
yucca/pipeline/preprocessing/YuccaPreprocessor.py
yucca/pipeline/preprocessing/__init__.py
yucca/pipeline/run/__init__.py
yucca/pipeline/run/run_ensemble.py
yucca/pipeline/run/run_evaluation.py
yucca/pipeline/run/run_finetune.py
yucca/pipeline/run/run_inference.py
yucca/pipeline/run/run_preprocessing.py
yucca/pipeline/run/run_task_conversion.py
yucca/pipeline/run/run_training.py
yucca/pipeline/task_conversion/Task000_TEST_CLASSIFICATION.py
yucca/pipeline/task_conversion/Task000_TEST_SEGMENTATION.py
yucca/pipeline/task_conversion/Task000_TEST_UNSUPERVISED.py
yucca/pipeline/task_conversion/Task001_OASIS.py
yucca/pipeline/task_conversion/Task002_LPBA40.py
yucca/pipeline/task_conversion/Task003_Hammers.py
yucca/pipeline/task_conversion/Task004_HarP.py
yucca/pipeline/task_conversion/Task005_ISLES22.py
yucca/pipeline/task_conversion/Task006_WMH_Flair.py
yucca/pipeline/task_conversion/Task007_WMH_T1.py
yucca/pipeline/task_conversion/Task008_WMH.py
yucca/pipeline/task_conversion/Task010_AMOS22.py
yucca/pipeline/task_conversion/Task010_AMOS22TEST.py
yucca/pipeline/task_conversion/Task011_MSSEG1.py
yucca/pipeline/task_conversion/Task012_BraTS21.py
yucca/pipeline/task_conversion/Task013_AutoPET3.py
yucca/pipeline/task_conversion/Task014_MBAS24.py
yucca/pipeline/task_conversion/Task015_AIMS-TBI24.py
yucca/pipeline/task_conversion/Task016_ACDC.py
yucca/pipeline/task_conversion/Task017_BTCV.py
yucca/pipeline/task_conversion/Task018_KITS23.py
yucca/pipeline/task_conversion/Task019_LITS.py
yucca/pipeline/task_conversion/Task020_ATLAS2.py
yucca/pipeline/task_conversion/Task021_Decathlon_BrainTumour.py
yucca/pipeline/task_conversion/Task022_Decathlon_Heart.py
yucca/pipeline/task_conversion/Task023_Decathlon_Liver.py
yucca/pipeline/task_conversion/Task028_Decathlon_HepaticVessel.py
yucca/pipeline/task_conversion/Task031_MSD_BrainTumour.py
yucca/pipeline/task_conversion/Task032_MSD_Heart.py
yucca/pipeline/task_conversion/Task033_MSD_Liver.py
yucca/pipeline/task_conversion/Task034_MSD_Hippocampus.py
yucca/pipeline/task_conversion/Task035_MSD_Prostate.py
yucca/pipeline/task_conversion/Task036_MSD_Lung.py
yucca/pipeline/task_conversion/Task037_MSD_Pancreas.py
yucca/pipeline/task_conversion/Task038_MSD_HepaticVessel.py
yucca/pipeline/task_conversion/Task039_MSD_Spleen.py
yucca/pipeline/task_conversion/Task040_BraTS21_flair.py
yucca/pipeline/task_conversion/Task040_MSD_Colon.py
yucca/pipeline/task_conversion/Task041_BraTS21_t1.py
yucca/pipeline/task_conversion/Task042_BraTS21_t1ce.py
yucca/pipeline/task_conversion/Task043_BraTS21_t2.py
yucca/pipeline/task_conversion/Task100_combine_001_002.py
yucca/pipeline/task_conversion/Task201_PPMI.py
yucca/pipeline/task_conversion/Task202_ISLES22.py
yucca/pipeline/task_conversion/Task203_OASIS3.py
yucca/pipeline/task_conversion/Task204_OASIS4.py
yucca/pipeline/task_conversion/Task205_Hippocampus.py
yucca/pipeline/task_conversion/Task206_BrainTumour.py
yucca/pipeline/task_conversion/Task207_ADNI.py
yucca/pipeline/task_conversion/Task208_WMH.py
yucca/pipeline/task_conversion/Task209_BraTS21.py
yucca/pipeline/task_conversion/Task210_MSSEG1.py
yucca/pipeline/task_conversion/Task241_BR41NS.py
yucca/pipeline/task_conversion/Task245_BRAINS-45K.py
yucca/pipeline/task_conversion/Task298_Combine_supervised.py
yucca/pipeline/task_conversion/Task299_Combine.py
yucca/pipeline/task_conversion/Task501_FetalPlanesDB.py
yucca/pipeline/task_conversion/Task502_tiny_imagenet_200.py
yucca/pipeline/task_conversion/Task701_OASIS_NoLabel.py
yucca/pipeline/task_conversion/Task901_SONAI_NoLabel.py
yucca/pipeline/task_conversion/Task902_SONAI100k_NoLabel.py
yucca/pipeline/task_conversion/Task998_WMH_Dummy_Missing_Modalities.py
yucca/pipeline/task_conversion/__init__.py
yucca/pipeline/task_conversion/template.py
yucca/pipeline/task_conversion/template_combine_imagesTr.py
yucca/pipeline/task_conversion/template_multiprocessing.py
yucca/pipeline/task_conversion/utils.py