Index

A

add_arguments_to_parser() (cli.common.CommonCLI method) (cli.common.I2RInternshipCommonCLI method) (scripts.attention_unet.ResidualAttentionCLI method) (scripts.cine.CineCLI method) (scripts.four_stream.FourStreamAttentionCLI method) (scripts.lge.LGECLI method) (scripts.three_stream.ThreeStreamAttentionCLI method) (scripts.tscsenet.TSCSECLI method) (scripts.two_plus_one.TwoPlusOneCLI method) AFFINE (models.fusion.stn.utils.SpatialTransformerType attribute) AffineTransformer (class in models.fusion.stn.utils) allow_zero_length_dataloader_with_multiple_devices (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute)

alpha (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) AttentionLayer (class in models.attention.model) average (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMJaccardIndex attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMJaccardIndex attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute)

B

batch_size (dataset.dataset.DefaultDatasetProtocol attribute) (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) bce2d() (metrics.JointEdgeSegLoss method) (metrics.loss.JointEdgeSegLoss method) before_instantiate_classes() (cli.common.CommonCLI method) (scripts.attention_unet.ResidualAttentionCLI method) (scripts.four_stream.FourStreamAttentionCLI method) (scripts.three_stream.ThreeStreamAttentionCLI method)

BERTModule (class in models.fusion.model) beta (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) BetterProgressBar (class in utils.global_progress_bar) BINARY_CLASS_3_MODE (utils.types.ClassificationMode attribute) BinaryMJaccardIndex (class in metrics.jaccard) BLANK (utils.types.DummyPredictMode attribute)

C

calc_uncertainty() (in module models.attention.urr.utils) check_input_shape() (models.attention.segmentation_model.ResidualAttentionUnet method) (models.fusion.model.FourStreamVisionModule method) (models.fusion.model.ThreeStreamVisionModule method) CineBaselineDataModule (class in scripts.cine) CineCLI (class in scripts.cine) CineDataset (class in dataset) (class in dataset.dataset) class_occurrences (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) class_weights (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) classes (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) ClassificationMode (class in utils.types) cli module cli.common module CommonCLI (class in cli.common) CommonModelMixin (class in models.common) compress_2() (in module models.two_plus_one) compress_dilated() (in module models.two_plus_one) compute() (metrics.dice.GeneralizedDiceScoreVariant method) (metrics.GeneralizedDiceScoreVariant method) (metrics.hausdorff.HausdorffDistanceVariant method) (metrics.HausdorffDistanceVariant method) (metrics.jaccard.BinaryMJaccardIndex method) (metrics.jaccard.MulticlassMJaccardIndex method) (metrics.jaccard.MultilabelMJaccardIndex method) (metrics.MulticlassMF1Score method) (metrics.MulticlassMJaccardIndex method) (metrics.MulticlassMPrecision method) (metrics.MulticlassMRecall method) (metrics.MultilabelMF1Score method) (metrics.MultilabelMJaccardIndex method) (metrics.MultilabelMPrecision method) (metrics.MultilabelMRecall method) (metrics.precision_recall.MulticlassMF1Score method) (metrics.precision_recall.MulticlassMPrecision method) (metrics.precision_recall.MulticlassMRecall method) (metrics.precision_recall.MultilabelMF1Score method) (metrics.precision_recall.MultilabelMPrecision method) (metrics.precision_recall.MultilabelMRecall method)

compute_theta() (models.fusion.stn.model.STN method) concatenate_imgs() (in module dataset.dataset) configure_columns() (utils.global_progress_bar.BetterProgressBar method) configure_optimizers() (in module utils.utils) (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method) confmat (metrics.MulticlassMJaccardIndex attribute) (metrics.MultilabelMJaccardIndex attribute) count (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) cuda_optical_flow() (in module dataset.optical_flow)

D

dataset module dataset.dataset module dataset.optical_flow module de_transform (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1] default_arguments (cli.common.CommonCLI attribute) DefaultDatasetProtocol (class in dataset.dataset) DefaultTransformsMixin (class in dataset.dataset) dense_optical_flow() (in module dataset.optical_flow) dice_metrics (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1] DIFFEOMORPHIC (models.fusion.stn.utils.SpatialTransformerType attribute) DiffeomorphicTransformer (class in models.fusion.stn.utils)

DILATED (models.two_plus_one.TemporalConvolutionalType attribute) DilatedOneD (class in models.two_plus_one) distance_metric (metrics.HausdorffDistanceVariant attribute) dl_classification_mode (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1] dummy_predict (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) DummyPredictMode (class in utils.types) dump_memory_snapshot (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

E

edge_attention() (metrics.JointEdgeSegLoss method) (metrics.loss.JointEdgeSegLoss method) Embeddings (class in models.transunet) encoder (models.attention.segmentation_model.ResidualAttentionUnet property) (models.fusion.segmentation_model.FourStreamAttentionUnet property)

ENCODER_OUTPUT_SHAPES (in module models.common) eval_classification_mode (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1]

F

flat_conv (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) fn (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) forward() (metrics.infarct.InfarctHeuristics method) (metrics.InfarctHeuristics method) (metrics.JointEdgeSegLoss method) (metrics.loss.JointEdgeSegLoss method) (metrics.loss.StructureLoss method) (metrics.loss.WeightedDiceLoss method) (metrics.StructureLoss method) (metrics.WeightedDiceLoss method) (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.model.AttentionLayer method) (models.attention.model.SpatialAttentionBlock method) (models.attention.ResidualAttentionLightningModule method) (models.attention.segmentation_model.ResidualAttentionUnet method) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule method) (models.attention.urr.model.RegionRefiner method) (models.attention.urr.segmentation_model.UnetDecoderURR method) (models.attention.urr.segmentation_model.UnetPlusPlusDecoderURR method) (models.attention.urr.segmentation_model.URRDecoder method) (models.attention.urr.segmentation_model.URRResidualAttentionUnet method) (models.attention.urr.URRResidualAttentionLightningModule method) (models.attention.urr.URRResidualAttentionUnet method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.fusion.model.BERTModule method) (models.fusion.model.FourStreamVisionModule method) (models.fusion.model.FusionLayer method) (models.fusion.model.PositionalEncoding method) (models.fusion.model.ThreeStreamVisionModule method) (models.fusion.segmentation_model.FourStreamAttentionUnet method) (models.fusion.segmentation_model.ThreeStreamAttentionUnet method) (models.fusion.stn.model.SpatialTransformer method) (models.fusion.stn.model.STN method) (models.fusion.stn.utils.AffineTransformer method) (models.fusion.stn.utils.DiffeomorphicTransformer method) (models.two_plus_one.DilatedOneD method) (models.two_plus_one.OneD method) (models.two_plus_one.Temporal3DConv method) (models.two_plus_one.TwoPlusOneUnet method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnet method)

forward_localiser() (models.fusion.stn.model.STN method) FourStreamAttentionCLI (class in scripts.four_stream) FourStreamAttentionLightningModule (class in models.fusion.lightning_module) FourStreamAttentionUnet (class in models.fusion.segmentation_model) FourStreamDataModule (class in scripts.four_stream) FourStreamDataset (class in dataset) (class in dataset.dataset) FourStreamVisionModule (class in models.fusion.model) fp (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) full_state_update (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute) FusionLayer (class in models.fusion.model)

G

GeneralizedDiceScoreVariant (class in metrics) (class in metrics.dice) get_accumulate_grad_batches() (in module utils.utils) get_best_macro_avg_dice_class_2_3_filename() (in module utils.utils) get_best_weighted_avg_dice_filename() (in module utils.utils) get_checkpoint_filename() (in module utils.utils) get_class() (models.two_plus_one.TemporalConvolutionalType method) get_class_weights() (in module dataset.dataset) get_classification_mode() (in module utils.utils) get_default_transforms() (dataset.dataset.DefaultTransformsMixin class method) (dataset.dataset.FourStreamDataset class method) (dataset.dataset.ResidualTwoPlusOneDataset class method) (dataset.dataset.ThreeStreamDataset class method) (dataset.FourStreamDataset class method) (dataset.ResidualTwoPlusOneDataset class method) (dataset.ThreeStreamDataset class method)

get_last_checkpoint_filename() (in module utils.utils) get_loading_mode() (in module utils.utils) get_model_type() (in module utils.utils) get_output_dir_from_ckpt_path() (in module utils.prediction_writer) get_residual_mode() (in module utils.utils) get_temporal_conv_type() (in module models.two_plus_one) get_trainval_data_subsets() (in module dataset) (in module dataset.dataset) get_trainval_dataloaders() (in module dataset.dataset) get_transforms() (in module utils.utils) get_version_name() (in module utils.utils) GREYSCALE (utils.types.LoadingMode attribute) GROUND_TRUTH (utils.types.DummyPredictMode attribute)

H

hausdorff_distance_variant() (in module metrics) (in module metrics.hausdorff) hausdorff_metrics (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute)

HausdorffDistanceVariant (class in metrics) (class in metrics.hausdorff) higher_is_better (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute)

I

I2RInternshipCommonCLI (class in cli.common) IGNORE_EMPTY_CLASS (utils.types.MetricMode attribute) img_dir (dataset.dataset.DefaultDatasetProtocol attribute) in_channels (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) INCLUDE_EMPTY_CLASS (utils.types.MetricMode attribute) infarct_area (metrics.infarct.InfarctResults attribute), [1] (metrics.InfarctResults attribute), [1] infarct_metrics (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) InfarctArea (class in metrics) InfarctAreaRatio (class in metrics) InfarctHeuristics (class in metrics) (class in metrics.infarct)

InfarctPredictionWriter (class in metrics) InfarctResults (class in metrics) (class in metrics.infarct) InfarctSpan (class in metrics) InfarctTransmuralities (class in metrics) InfarctVisualisation (class in metrics.infarct) init_localiser() (models.fusion.stn.model.STN method) init_model_weights() (models.fusion.stn.model.STN method) init_transformer() (in module models.fusion.stn.utils) initialize() (models.attention.segmentation_model.ResidualAttentionUnet method) (models.fusion.segmentation_model.FourStreamAttentionUnet method) (models.fusion.segmentation_model.ThreeStreamAttentionUnet method) (models.two_plus_one.TwoPlusOneUnet method) (models.two_stream.TwoStreamUnet method) input_format (metrics.HausdorffDistanceVariant attribute) InverseNormalize (class in utils.types) is_close() (metrics.infarct.InfarctResults method) (metrics.InfarctResults method) is_differentiable (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute)

J

JointEdgeSegLoss (class in metrics) (class in metrics.loss)

L

learning_rate (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) LGEBaselineDataModule (class in scripts.lge) LGECLI (class in scripts.lge) LGEDataset (class in dataset) (class in dataset.dataset) LightningGradualWarmupScheduler (class in utils.utils) LightningUnetWrapper (class in models.default_unet) load_train_indices() (in module dataset.dataset) loading_mode (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

LoadingMode (class in utils.types) log_metrics() (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.common.CommonModelMixin method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method)

M

macro_avg_metric (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) MaskImageWriter (class in utils.prediction_writer) max_refresh (utils.global_progress_bar.RemainingTimeColumn attribute) MetricMode (class in utils.types) metrics module metrics.dice module metrics.hausdorff module metrics.infarct module metrics.jaccard module metrics.logging module metrics.loss module metrics.precision_recall module metrics.utils module mF1_running (metrics.MulticlassMF1Score attribute) (metrics.MultilabelMF1Score attribute) (metrics.precision_recall.MulticlassMF1Score attribute) (metrics.precision_recall.MultilabelMF1Score attribute) mJaccard_running (metrics.jaccard.BinaryMJaccardIndex attribute) (metrics.jaccard.MulticlassMJaccardIndex attribute) (metrics.jaccard.MultilabelMJaccardIndex attribute) (metrics.MulticlassMJaccardIndex attribute) (metrics.MultilabelMJaccardIndex attribute) model (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1] model_type (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1] models module models.attention module models.attention.lightning_module module models.attention.model module models.attention.segmentation_model module models.attention.urr module models.attention.urr.lightning_module module models.attention.urr.model module models.attention.urr.segmentation_model module models.attention.urr.utils module models.attention.utils module models.common module models.default_unet module models.fusion module models.fusion.lightning_module module models.fusion.model module models.fusion.segmentation_model module models.fusion.stn module models.fusion.stn.model module models.fusion.stn.utils module models.transunet module models.two_plus_one module models.two_stream module ModelType (class in utils.types) module cli cli.common dataset dataset.dataset dataset.optical_flow metrics metrics.dice metrics.hausdorff metrics.infarct metrics.jaccard metrics.logging metrics.loss metrics.precision_recall metrics.utils models models.attention models.attention.lightning_module models.attention.model models.attention.segmentation_model models.attention.urr models.attention.urr.lightning_module models.attention.urr.model models.attention.urr.segmentation_model models.attention.urr.utils models.attention.utils models.common models.default_unet models.fusion models.fusion.lightning_module models.fusion.model models.fusion.segmentation_model models.fusion.stn models.fusion.stn.model models.fusion.stn.utils models.transunet models.two_plus_one models.two_stream scripts scripts.attention_unet scripts.cine scripts.four_stream scripts.lge scripts.optuna scripts.three_stream scripts.tscsenet scripts.two_plus_one scripts.urr_attention_unet utils utils.global_progress_bar utils.logging utils.prediction_writer utils.types utils.utils

mPrecision_running (metrics.MulticlassMPrecision attribute) (metrics.MultilabelMPrecision attribute) (metrics.precision_recall.MulticlassMPrecision attribute) (metrics.precision_recall.MultilabelMPrecision attribute) mRecall_running (metrics.MulticlassMRecall attribute) (metrics.MultilabelMRecall attribute) (metrics.precision_recall.MulticlassMRecall attribute) (metrics.precision_recall.MultilabelMRecall attribute) multi_frame (cli.common.CommonCLI attribute) (scripts.lge.LGECLI attribute) MULTICLASS_1_2_MODE (utils.types.ClassificationMode attribute) MULTICLASS_MODE (utils.types.ClassificationMode attribute) MulticlassMF1Score (class in metrics) (class in metrics.precision_recall) MulticlassMJaccardIndex (class in metrics) (class in metrics.jaccard) MulticlassMPrecision (class in metrics) (class in metrics.precision_recall) MulticlassMRecall (class in metrics) (class in metrics.precision_recall) multidim_average (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) MULTILABEL_MODE (utils.types.ClassificationMode attribute) MultilabelMF1Score (class in metrics) (class in metrics.precision_recall) MultilabelMJaccardIndex (class in metrics) (class in metrics.jaccard) MultilabelMPrecision (class in metrics) (class in metrics.precision_recall) MultilabelMRecall (class in metrics) (class in metrics.precision_recall) multiplier (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

N

NONE (utils.types.DummyPredictMode attribute) NormaliseImageFramesByHistogram (class in dataset.dataset) num_classes() (utils.types.ClassificationMode method) num_frames (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

O

O1 (models.attention.urr.utils.URRSource attribute) O3 (models.attention.urr.utils.URRSource attribute) on_test_epoch_end() (models.common.CommonModelMixin method) on_train_end() (models.common.CommonModelMixin method) on_train_epoch_end() (models.common.CommonModelMixin method) on_train_start() (models.common.CommonModelMixin method) (models.default_unet.LightningUnetWrapper method) on_validation_epoch_end() (models.common.CommonModelMixin method) OneD (class in models.two_plus_one) OPTICAL_FLOW_CPU (utils.types.ResidualMode attribute) OPTICAL_FLOW_GPU (utils.types.ResidualMode attribute) optimizer (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

optimizer_kwargs (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) ORIGINAL (models.two_plus_one.TemporalConvolutionalType attribute) other_metrics (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute), [1]

P

per_class_metric (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) plot_lower_bound (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute) PositionalEncoding (class in models.fusion.model) predict() (models.attention.segmentation_model.ResidualAttentionUnet method) (models.two_plus_one.TwoPlusOneUnet method) predict_dataloader() (scripts.attention_unet.ResidualTwoPlusOneDataModule method) (scripts.cine.CineBaselineDataModule method) (scripts.four_stream.FourStreamDataModule method) (scripts.lge.LGEBaselineDataModule method) (scripts.three_stream.ThreeStreamDataModule method) (scripts.two_plus_one.TwoPlusOneDataModule method)

predict_step() (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule method) (models.attention.urr.URRResidualAttentionLightningModule method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method) prepare_data_per_node (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute)

R

ratio (metrics.infarct.InfarctResults attribute), [1] (metrics.InfarctResults attribute), [1] RegionRefiner (class in models.attention.urr.model) RemainingTimeColumn (class in utils.global_progress_bar) RemoveBlackLevelLiftByHistogram (class in dataset.dataset) RemoveBlackLevelLiftByMin (class in dataset.dataset) render() (utils.global_progress_bar.RemainingTimeColumn method) residual_mode (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

ResidualAttentionCLI (class in scripts.attention_unet) ResidualAttentionLightningModule (class in models.attention) (class in models.attention.lightning_module) ResidualAttentionUnet (class in models.attention.segmentation_model) ResidualAttentionUnetPlusPlus (class in models.attention.segmentation_model) ResidualMode (class in utils.types) ResidualTwoPlusOneDataModule (class in scripts.attention_unet) ResidualTwoPlusOneDataset (class in dataset) (class in dataset.dataset) ResNetV2 (class in models.transunet) return_type (metrics.GeneralizedDiceScoreVariant attribute) RGB (utils.types.LoadingMode attribute)

S

samples (metrics.GeneralizedDiceScoreVariant attribute) (metrics.jaccard.BinaryMJaccardIndex attribute) (metrics.jaccard.MulticlassMJaccardIndex attribute) (metrics.jaccard.MultilabelMJaccardIndex attribute) (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMJaccardIndex attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMJaccardIndex attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) (metrics.precision_recall.MulticlassMF1Score attribute) (metrics.precision_recall.MulticlassMPrecision attribute) (metrics.precision_recall.MulticlassMRecall attribute) (metrics.precision_recall.MultilabelMF1Score attribute) (metrics.precision_recall.MultilabelMPrecision attribute) (metrics.precision_recall.MultilabelMRecall attribute) scheduler (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) scheduler_kwargs (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) score (metrics.GeneralizedDiceScoreVariant attribute) (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute) score_running (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) scripts module scripts.attention_unet module scripts.cine module

scripts.four_stream module scripts.lge module scripts.optuna module scripts.three_stream module scripts.tscsenet module scripts.two_plus_one module scripts.urr_attention_unet module seed_worker() (in module dataset.dataset) setup() (models.common.CommonModelMixin method) (scripts.attention_unet.ResidualTwoPlusOneDataModule method) (scripts.cine.CineBaselineDataModule method) (scripts.four_stream.FourStreamDataModule method) (scripts.lge.LGEBaselineDataModule method) (scripts.three_stream.ThreeStreamDataModule method) (scripts.two_plus_one.TwoPlusOneDataModule method) setup_metrics() (in module metrics) (in module metrics.logging) shared_metric_calculation() (in module metrics) (in module metrics.logging) shared_metric_logging_epoch_end() (in module metrics) (in module metrics.logging) show_r2_plots (models.common.CommonModelMixin attribute) single_attention_instance (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) span (metrics.infarct.InfarctResults attribute), [1] (metrics.InfarctResults attribute), [1] SpatialAttentionBlock (class in models.attention.model) SpatialTransformer (class in models.fusion.stn.model) SpatialTransformerType (class in models.fusion.stn.utils) step() (utils.utils.LightningGradualWarmupScheduler method) STN (class in models.fusion.stn.model) StructureLoss (class in metrics) (class in metrics.loss) SUBTRACT_NEXT_FRAME (utils.types.ResidualMode attribute)

T

Temporal3DConv (class in models.two_plus_one) TEMPORAL_3D (models.two_plus_one.TemporalConvolutionalType attribute) TemporalConvolutionalType (class in models.two_plus_one) TemporalDenoiseTransform (class in dataset.dataset) test_dataloader() (scripts.attention_unet.ResidualTwoPlusOneDataModule method) (scripts.cine.CineBaselineDataModule method) (scripts.four_stream.FourStreamDataModule method) (scripts.lge.LGEBaselineDataModule method) (scripts.three_stream.ThreeStreamDataModule method) (scripts.two_plus_one.TwoPlusOneDataModule method) test_step() (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method) ThreeStreamAttentionCLI (class in scripts.three_stream) ThreeStreamAttentionLightningModule (class in models.fusion.lightning_module) ThreeStreamAttentionUnet (class in models.fusion.segmentation_model) ThreeStreamDataModule (class in scripts.three_stream) ThreeStreamDataset (class in dataset) (class in dataset.dataset) ThreeStreamVisionModule (class in models.fusion.model) tn (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) to_tensor() (metrics.infarct.InfarctResults method) (metrics.InfarctResults method) total (metrics.hausdorff.HausdorffDistanceVariant attribute) (metrics.HausdorffDistanceVariant attribute) total_epochs (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.common.CommonModelMixin attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) tp (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute)

train_dataloader() (scripts.attention_unet.ResidualTwoPlusOneDataModule method) (scripts.cine.CineBaselineDataModule method) (scripts.four_stream.FourStreamDataModule method) (scripts.lge.LGEBaselineDataModule method) (scripts.three_stream.ThreeStreamDataModule method) (scripts.two_plus_one.TwoPlusOneDataModule method) train_idxs (dataset.dataset.DefaultDatasetProtocol attribute) training (metrics.GeneralizedDiceScoreVariant attribute) (metrics.HausdorffDistanceVariant attribute) (metrics.MulticlassMF1Score attribute) (metrics.MulticlassMJaccardIndex attribute) (metrics.MulticlassMPrecision attribute) (metrics.MulticlassMRecall attribute) (metrics.MultilabelMF1Score attribute) (metrics.MultilabelMJaccardIndex attribute) (metrics.MultilabelMPrecision attribute) (metrics.MultilabelMRecall attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) training_step() (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule method) (models.attention.urr.URRResidualAttentionLightningModule method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method) TRANS_UNET (utils.types.ModelType attribute) transform() (dataset.dataset.NormaliseImageFramesByHistogram method) (dataset.dataset.RemoveBlackLevelLiftByHistogram method) (dataset.dataset.RemoveBlackLevelLiftByMin method) (dataset.dataset.TemporalDenoiseTransform method) Transformer (class in models.transunet) transmurality (metrics.infarct.InfarctResults attribute), [1] (metrics.InfarctResults attribute), [1] TransUnet (class in models.transunet) TSCSECLI (class in scripts.tscsenet) TwoPlusOneCLI (class in scripts.two_plus_one) TwoPlusOneDataModule (class in scripts.two_plus_one) TwoPlusOneDataset (class in dataset) (class in dataset.dataset) TwoPlusOneUnet (class in models.two_plus_one) TwoPlusOneUnetLightning (class in models.two_plus_one) TwoStreamUnet (class in models.two_stream) TwoStreamUnetLightning (class in models.two_stream)

U

uncertainty_mode (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) UncertaintyMode (class in models.attention.urr.utils) UNET (utils.types.ModelType attribute) UNET_PLUS_PLUS (utils.types.ModelType attribute) UnetDecoderURR (class in models.attention.urr.segmentation_model) UnetPlusPlusDecoderURR (class in models.attention.urr.segmentation_model) update() (metrics.dice.GeneralizedDiceScoreVariant method) (metrics.GeneralizedDiceScoreVariant method) (metrics.hausdorff.HausdorffDistanceVariant method) (metrics.HausdorffDistanceVariant method) (metrics.InfarctArea method) (metrics.InfarctAreaRatio method) (metrics.InfarctSpan method) (metrics.InfarctTransmuralities method) (metrics.jaccard.BinaryMJaccardIndex method) (metrics.jaccard.MulticlassMJaccardIndex method) (metrics.jaccard.MultilabelMJaccardIndex method) (metrics.MulticlassMF1Score method) (metrics.MulticlassMJaccardIndex method) (metrics.MulticlassMPrecision method) (metrics.MulticlassMRecall method) (metrics.MultilabelMF1Score method) (metrics.MultilabelMJaccardIndex method) (metrics.MultilabelMPrecision method) (metrics.MultilabelMRecall method) (metrics.precision_recall.MulticlassMF1Score method) (metrics.precision_recall.MulticlassMPrecision method) (metrics.precision_recall.MulticlassMRecall method) (metrics.precision_recall.MultilabelMF1Score method) (metrics.precision_recall.MultilabelMPrecision method) (metrics.precision_recall.MultilabelMRecall method)

UR (models.attention.urr.utils.UncertaintyMode attribute) URR (models.attention.urr.utils.UncertaintyMode attribute) urr_source (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) URRDecoder (class in models.attention.urr.segmentation_model) URRResidualAttentionLightningModule (class in models.attention.urr) (class in models.attention.urr.lightning_module) URRResidualAttentionUnet (class in models.attention.urr) (class in models.attention.urr.segmentation_model) URRResidualAttentionUnetPlusPlus (class in models.attention.urr) (class in models.attention.urr.segmentation_model) URRSource (class in models.attention.urr.utils) use_stn (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute) utils module utils.global_progress_bar module utils.logging module utils.prediction_writer module utils.types module utils.utils module

V

val_dataloader() (scripts.attention_unet.ResidualTwoPlusOneDataModule method) (scripts.cine.CineBaselineDataModule method) (scripts.four_stream.FourStreamDataModule method) (scripts.lge.LGEBaselineDataModule method) (scripts.three_stream.ThreeStreamDataModule method) (scripts.two_plus_one.TwoPlusOneDataModule method) valid_idxs (dataset.dataset.DefaultDatasetProtocol attribute)

validation_step() (models.attention.lightning_module.ResidualAttentionLightningModule method) (models.attention.ResidualAttentionLightningModule method) (models.default_unet.LightningUnetWrapper method) (models.fusion.lightning_module.FourStreamAttentionLightningModule method) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule method) (models.two_plus_one.TwoPlusOneUnetLightning method) (models.two_stream.TwoStreamUnetLightning method) viz() (metrics.infarct.InfarctVisualisation method)

W

weighted_avg_metric (metrics.dice.GeneralizedDiceScoreVariant attribute) (metrics.GeneralizedDiceScoreVariant attribute) WeightedDiceLoss (class in metrics) (class in metrics.loss) weights_from_ckpt_path (models.attention.lightning_module.ResidualAttentionLightningModule attribute) (models.attention.ResidualAttentionLightningModule attribute) (models.attention.urr.lightning_module.URRResidualAttentionLightningModule attribute) (models.attention.urr.URRResidualAttentionLightningModule attribute) (models.fusion.lightning_module.FourStreamAttentionLightningModule attribute) (models.fusion.lightning_module.ThreeStreamAttentionLightningModule attribute)

write_on_epoch_end() (metrics.InfarctPredictionWriter method) (utils.prediction_writer.MaskImageWriter method)