Index

A

AbstractDiceLoss (class in functional.losses) active_learning module active_learning_mode

ActiveLearningDataModule (class in datasets.data_module) ActiveLearningPipeline (class in active_learning) add_image() (datasets.bcss_dataset.BCSSDataset method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) architecture

B

batch_padding_collate_fn() (in module datasets.collate) batch_size batch_size_unlabeled_set

BCSSDataModule (class in datasets.bcss_data_module) BCSSDataset (class in datasets.bcss_dataset) BraTSDataModule (class in datasets.brats_data_module) build_stratification_labels() (datasets.bcss_data_module.BCSSDataModule static method)

C

cache_size checkpoint_dir clean_duplicate_scans() (in module query_strategies.utils) ClusteringBasedRepresentativenessSamplingStrategy (class in query_strategies.representativeness_sampling_clustering) CombinedPerEpochMetric (class in metric_tracking.combined_per_epoch_metric) CombinedPerImageMetric (class in metric_tracking.combined_per_image_metric) compute() (functional.metrics.DiceScore method) (functional.metrics.HausdorffDistance method) (functional.metrics.Sensitivity method) (functional.metrics.Specificity method) (metric_tracking.combined_per_epoch_metric.CombinedPerEpochMetric method) (metric_tracking.combined_per_image_metric.CombinedPerImageMetric method) compute_representativeness_scores() (query_strategies.representativeness_sampling_clustering.ClusteringBasedRepresentativenessSamplingStrategy method) (query_strategies.representativeness_sampling_distances.DistanceBasedRepresentativenessSamplingStrategy method) (query_strategies.representativeness_sampling_strategy_base.RepresentativenessSamplingStrategyBase method) (query_strategies.representativeness_sampling_uncertainty.UncertaintyRepresentativenessSamplingStrategy method)

compute_uncertainties() (query_strategies.uncertainty_sampling_strategy.UncertaintySamplingStrategy method) configure_loss() (models.pytorch_model.PytorchModel static method) configure_metrics() (models.pytorch_model.PytorchModel method) configure_optimizers() (models.pytorch_model.PytorchModel method) copy_test_set_to_separate_folder() (in module datasets.bcss_data_module) create_config_files() (in module run_experiments) create_data_module() (in module main) create_model() (in module main) create_query_strategy() (in module main) create_sbatch_jobs_from_config_files() (in module run_experiments) CrossEntropyDiceLoss (class in functional.losses) CrossEntropyLoss (class in functional.losses) current_epoch (models.pytorch_model.PytorchModel property) current_weight() (models.loss_weight_scheduler.LossWeightScheduler method)

D

data_channels() (datasets.bcss_data_module.BCSSDataModule method) (datasets.data_module.ActiveLearningDataModule static method) (datasets.decathlon_data_module.DecathlonDataModule method) data_dir dataset DatasetHooks (class in datasets.dataset_hooks) datasets module datasets.bcss_data_module module datasets.bcss_dataset module datasets.brats_data_module module datasets.collate module datasets.data_module module

datasets.dataset_hooks module datasets.decathlon_data_module module datasets.doubly_shuffled_nifti_dataset module DecathlonDataModule (class in datasets.decathlon_data_module) description dice_score() (in module functional.metrics) DiceLoss (class in functional.losses) DiceScore (class in functional.metrics) dim discover_paths() (datasets.bcss_data_module.BCSSDataModule static method) (datasets.brats_data_module.BraTSDataModule static method) (datasets.decathlon_data_module.DecathlonDataModule static method) distance_to_max_uncertainty() (in module query_strategies.utils) DistanceBasedRepresentativenessSamplingStrategy (class in query_strategies.representativeness_sampling_distances) DoublyShuffledNIfTIDataset (class in datasets.doubly_shuffled_nifti_dataset)

E

entropy() (in module query_strategies.utils) epochs

eval() (models.pytorch_u_net.PytorchUNet method) experiment_name experiment_tags

F

FalsePositiveDiceLoss (class in functional.losses) FalsePositiveLoss (class in functional.losses) flatten_tensors() (in module functional.utils) FocalLoss (class in functional.losses) forward() (functional.losses.AbstractDiceLoss method) (functional.losses.CrossEntropyDiceLoss method) (functional.losses.CrossEntropyLoss method) (functional.losses.DiceLoss method) (functional.losses.FalsePositiveDiceLoss method) (functional.losses.FalsePositiveLoss method) (functional.losses.GeneralizedDiceLoss method) (models.pytorch_u_net.PytorchUNet method) (models.u_net.UNet method)

functional module functional.interpretation module functional.losses module functional.metrics module functional.utils module

G

GeneralizedDiceLoss (class in functional.losses) generate_active_learning_split() (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset static method) generate_grayscale_cam() (functional.interpretation.HeatMaps method) generate_grayscale_logits() (functional.interpretation.HeatMaps method) get_case_id() (datasets.bcss_dataset.BCSSDataset static method) get_dice_loss_module() (functional.losses.AbstractDiceLoss method) (functional.losses.DiceLoss method) (functional.losses.GeneralizedDiceLoss method)

get_images_by_id() (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) get_institute_name() (datasets.bcss_dataset.BCSSDataset static method) get_items_for_logging() (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) get_metric_names() (metric_tracking.combined_per_epoch_metric.CombinedPerEpochMetric method) get_test_metrics() (models.pytorch_model.PytorchModel method) get_train_metrics() (models.pytorch_model.PytorchModel method) get_val_metrics() (models.pytorch_model.PytorchModel method) gpus

H

hausdorff_distance() (in module functional.metrics) HausdorffDistance (class in functional.metrics)

HeatMaps (class in functional.interpretation) heatmaps_per_iteration

I

id_to_class_names() (datasets.bcss_data_module.BCSSDataModule method) (datasets.brats_data_module.BraTSDataModule method) (datasets.data_module.ActiveLearningDataModule method) (datasets.decathlon_data_module.DecathlonDataModule method) image_ids() (datasets.bcss_dataset.BCSSDataset method) (datasets.dataset_hooks.DatasetHooks method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) inference() (inferencing.Inferencer method) inference_image() (inferencing.Inferencer method) inference_scan() (inferencing.Inferencer method)

Inferencer (class in inferencing) inferencing module initial_training_set_size input_dimensionality() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method) InterpolationSamplingStrategy (class in query_strategies.interpolation_sampling_strategy) is_binary() (in module functional.utils) items_to_label iterations

L

label_items() (datasets.bcss_data_module.BCSSDataModule method) (datasets.brats_data_module.BraTSDataModule method) (datasets.data_module.ActiveLearningDataModule method) (datasets.decathlon_data_module.DecathlonDataModule method)

learning_rate loss_config loss_weight_pseudo_labels (models.pytorch_model.PytorchModel property) LossWeightScheduler (class in models.loss_weight_scheduler)

M

main module mask_tensor() (in module functional.utils) metric_tracking module metric_tracking.combined_per_epoch_metric module metric_tracking.combined_per_image_metric module model_selection_criterion models module models.loss_weight_scheduler module models.pytorch_model module models.pytorch_u_net module models.u_net module module active_learning datasets datasets.bcss_data_module datasets.bcss_dataset datasets.brats_data_module datasets.collate datasets.data_module datasets.dataset_hooks datasets.decathlon_data_module datasets.doubly_shuffled_nifti_dataset functional functional.interpretation functional.losses functional.metrics functional.utils inferencing main metric_tracking metric_tracking.combined_per_epoch_metric metric_tracking.combined_per_image_metric models models.loss_weight_scheduler models.pytorch_model models.pytorch_u_net models.u_net query_strategies query_strategies.interpolation_sampling_strategy query_strategies.query_strategy query_strategies.random_sampling_strategy query_strategies.representativeness_sampling_clustering query_strategies.representativeness_sampling_distances query_strategies.representativeness_sampling_strategy_base query_strategies.representativeness_sampling_uncertainty query_strategies.uncertainty_sampling_strategy query_strategies.utils run_experiments

morphological_contour_interpolation() (in module query_strategies.interpolation_sampling_strategy) multi_label() (datasets.bcss_data_module.BCSSDataModule method) (datasets.brats_data_module.BraTSDataModule method) (datasets.data_module.ActiveLearningDataModule method) (datasets.decathlon_data_module.DecathlonDataModule method)

N

normalize() (datasets.bcss_dataset.BCSSDataset static method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset static method) num_classes() (datasets.data_module.ActiveLearningDataModule method) num_levels

num_pseudo_labels() (datasets.bcss_dataset.BCSSDataset method) (datasets.dataset_hooks.DatasetHooks method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) num_workers

O

on_select_item() (query_strategies.representativeness_sampling_clustering.ClusteringBasedRepresentativenessSamplingStrategy method) (query_strategies.representativeness_sampling_strategy_base.RepresentativenessSamplingStrategyBase method)

one_hot_encode() (in module functional.utils) optimizer

P

parameters() (models.pytorch_u_net.PytorchUNet method) precision (models.pytorch_u_net.PytorchUNet attribute) predict() (models.pytorch_model.PytorchModel method) predict_step() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method) prediction_count

prediction_dir prepare_representativeness_computation() (query_strategies.representativeness_sampling_clustering.ClusteringBasedRepresentativenessSamplingStrategy method) (query_strategies.representativeness_sampling_strategy_base.RepresentativenessSamplingStrategyBase method) (query_strategies.representativeness_sampling_uncertainty.UncertaintyRepresentativenessSamplingStrategy method) preprocess_metric_inputs() (in module functional.utils) PytorchModel (class in models.pytorch_model) PytorchUNet (class in models.pytorch_u_net)

Q

query_strategies module query_strategies.interpolation_sampling_strategy module query_strategies.query_strategy module query_strategies.random_sampling_strategy module query_strategies.representativeness_sampling_clustering module

query_strategies.representativeness_sampling_distances module query_strategies.representativeness_sampling_strategy_base module query_strategies.representativeness_sampling_uncertainty module query_strategies.uncertainty_sampling_strategy module query_strategies.utils module QueryStrategy (class in query_strategies.query_strategy)

R

random_state RandomSamplingStrategy (class in query_strategies.random_sampling_strategy) read_mask_for_image() (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) reduce_features() (query_strategies.representativeness_sampling_strategy_base.RepresentativenessSamplingStrategyBase method) reduce_metric() (in module functional.utils) reinforce_type() (datasets.bcss_dataset.BCSSDataset method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) remove_image() (datasets.bcss_dataset.BCSSDataset method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) remove_padding() (in module functional.utils) remove_wandb_cache() (active_learning.ActiveLearningPipeline static method)

RepresentativenessSamplingStrategyBase (class in query_strategies.representativeness_sampling_strategy_base) reset() (functional.metrics.HausdorffDistance method) (metric_tracking.combined_per_epoch_metric.CombinedPerEpochMetric method) (metric_tracking.combined_per_image_metric.CombinedPerImageMetric method) reset_parameters() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method) reset_weights run() (active_learning.ActiveLearningPipeline method) run_active_learning_pipeline() (in module main) run_active_learning_pipeline_from_config() (in module main) run_experiments module

S

SegmentationLoss (class in functional.losses) SegmentationMetric (class in functional.metrics) select_items_to_label() (query_strategies.interpolation_sampling_strategy.InterpolationSamplingStrategy method) (query_strategies.query_strategy.QueryStrategy method) (query_strategies.random_sampling_strategy.RandomSamplingStrategy method) (query_strategies.representativeness_sampling_strategy_base.RepresentativenessSamplingStrategyBase method) (query_strategies.uncertainty_sampling_strategy.UncertaintySamplingStrategy method) select_uncertainty_calculation() (in module query_strategies.utils) SemanticSegmentationTarget (class in functional.interpretation) Sensitivity (class in functional.metrics) sensitivity() (in module functional.metrics) setup() (datasets.data_module.ActiveLearningDataModule method) (models.pytorch_model.PytorchModel method) setup_trainer() (active_learning.ActiveLearningPipeline method)

show_grayscale_heatmap_on_image() (functional.interpretation.HeatMaps static method) signed_distance_interpolation() (in module query_strategies.interpolation_sampling_strategy) single_class_hausdorff_distance() (in module functional.metrics) size() (datasets.bcss_dataset.BCSSDataset method) (datasets.dataset_hooks.DatasetHooks method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) slices_per_image() (datasets.bcss_dataset.BCSSDataset method) (datasets.dataset_hooks.DatasetHooks method) (datasets.doubly_shuffled_nifti_dataset.DoublyShuffledNIfTIDataset method) Specificity (class in functional.metrics) specificity() (in module functional.metrics) start_sbatch_runs() (in module run_experiments) step() (models.loss_weight_scheduler.LossWeightScheduler method) step_loss_weight_pseudo_labels_scheduler() (models.pytorch_model.PytorchModel method)

T

test_dataloader() (datasets.data_module.ActiveLearningDataModule method) test_epoch_end() (models.pytorch_model.PytorchModel method) test_metric_confidence_levels test_metrics test_set_size() (datasets.data_module.ActiveLearningDataModule method) test_step() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method) train() (models.pytorch_u_net.PytorchUNet method) train_dataloader() (datasets.bcss_data_module.BCSSDataModule method) (datasets.brats_data_module.BraTSDataModule method) (datasets.data_module.ActiveLearningDataModule method) (datasets.decathlon_data_module.DecathlonDataModule method) train_metric_confidence_levels train_metrics training (functional.losses.AbstractDiceLoss attribute) (functional.losses.CrossEntropyDiceLoss attribute) (functional.losses.CrossEntropyLoss attribute) (functional.losses.DiceLoss attribute) (functional.losses.FalsePositiveDiceLoss attribute) (functional.losses.FalsePositiveLoss attribute) (functional.losses.FocalLoss attribute) (functional.losses.GeneralizedDiceLoss attribute) (functional.losses.SegmentationLoss attribute) (models.pytorch_model.PytorchModel attribute) (models.pytorch_u_net.PytorchUNet attribute) (models.u_net.UNet attribute)

training_epoch_end() (models.pytorch_model.PytorchModel method) training_set_num_pseudo_labels() (datasets.data_module.ActiveLearningDataModule method) training_set_size() (datasets.data_module.ActiveLearningDataModule method) training_step() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method) type

U

UncertaintyRepresentativenessSamplingStrategy (class in query_strategies.representativeness_sampling_uncertainty) UncertaintySamplingStrategy (class in query_strategies.uncertainty_sampling_strategy) UNet (class in models.u_net) unlabeled_dataloader() (datasets.data_module.ActiveLearningDataModule method) unlabeled_set_size() (datasets.data_module.ActiveLearningDataModule method) update() (functional.metrics.DiceScore method) (functional.metrics.HausdorffDistance method) (functional.metrics.Sensitivity method) (functional.metrics.Specificity method) (metric_tracking.combined_per_epoch_metric.CombinedPerEpochMetric method) (metric_tracking.combined_per_image_metric.CombinedPerImageMetric method)

use_amp (models.pytorch_u_net.PytorchUNet attribute)

V

val_dataloader() (datasets.data_module.ActiveLearningDataModule method) validate_metric_inputs() (in module functional.utils) validation_epoch_end() (models.pytorch_model.PytorchModel method)

validation_set_size() (datasets.data_module.ActiveLearningDataModule method) validation_step() (models.pytorch_model.PytorchModel method) (models.pytorch_u_net.PytorchUNet method)

W

wandb_project_name