Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __getitem__() (InnerEye.ML.dataset.cropping_dataset.CroppingDataset method) A Accuracy05 (class in InnerEye.ML.lightning_metrics) ACCURACY_AT_OPTIMAL_THRESHOLD (InnerEye.Common.metrics_constants.MetricType attribute) ACCURACY_AT_THRESHOLD_05 (InnerEye.Common.metrics_constants.MetricType attribute) AccuracyAtOptimalThreshold (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) AccuracyAtThreshold05 (InnerEye.Common.metrics_constants.LoggingColumns attribute) activation_map_layers (InnerEye.ML.config.SegmentationModelBase attribute) Adam (InnerEye.ML.deep_learning_config.OptimizerType attribute) adam_betas (InnerEye.ML.deep_learning_config.OptimizerParams attribute) add() (InnerEye.ML.utils.metrics_util.MetricsPerPatientWriter method) add_and_validate() (InnerEye.Common.generic_parsing.GenericConfig method) add_args() (InnerEye.Common.generic_parsing.GenericConfig class method) add_average_foreground_dice() (in module InnerEye.ML.metrics) add_diagnostics() (InnerEye.ML.metrics_dict.MetricsDict method) add_differences_for_features (InnerEye.ML.scalar_config.ScalarModelBase attribute) add_label_stats_to_dataframe() (in module InnerEye.ML.utils.dataset_util) add_legend() (in module InnerEye.ML.plotting) add_metric() (InnerEye.ML.metrics_dict.MetricsDict method) add_predictions() (InnerEye.ML.metrics_dict.Hue method) (InnerEye.ML.metrics_dict.MetricsDict method) add_record() (InnerEye.ML.metrics_dict.DataframeLogger method) add_subfolder() (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig method) add_submodules_to_path() (in module InnerEye.Common.fixed_paths) AddGaussianNoise (class in InnerEye.ML.augmentations.image_transforms) additional_run_tags() (in module InnerEye.Azure.azure_runner) aggregate_and_save_execution_mode_metrics() (InnerEye.ML.metrics_dict.ScalarMetricsDict static method) aggregation_type (InnerEye.ML.scalar_config.ScalarModelBase attribute) AggregationType (class in InnerEye.ML.scalar_config) all_azure_dataset_ids() (InnerEye.ML.deep_learning_config.DatasetParams method) all_dataset_mountpoints() (InnerEye.ML.deep_learning_config.DatasetParams method) all_local_dataset_paths() (InnerEye.ML.deep_learning_config.DatasetParams method) allow_empty (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) allow_incomplete_labels (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.dataset.sample.PatientDatasetSource attribute) AMSGrad (InnerEye.ML.deep_learning_config.OptimizerType attribute) annotator (InnerEye.ML.surface_distance_heatmaps.Segmentation attribute) annotators (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) any_pairwise_larger() (in module InnerEye.Common.common_util) any_smaller_or_equal_than() (in module InnerEye.Common.common_util) application_id (InnerEye.Azure.azure_config.AzureConfig attribute) apply() (InnerEye.ML.utils.transforms.Compose3D static method) apply_mask_to_posteriors() (in module InnerEye.ML.utils.image_util) apply_overrides() (InnerEye.Common.generic_parsing.GenericConfig method) apply_sequence_model_loss() (in module InnerEye.ML.utils.sequence_utils) apply_slice_exclusion_rules() (in module InnerEye.ML.utils.image_util) apply_summed_probability_rules() (in module InnerEye.ML.utils.image_util) architecture (InnerEye.ML.config.SegmentationModelBase attribute) AREA_UNDER_PR_CURVE (InnerEye.Common.metrics_constants.MetricType attribute) AREA_UNDER_ROC_CURVE (InnerEye.Common.metrics_constants.MetricType attribute) AreaUnderPRCurve (InnerEye.Common.metrics_constants.LoggingColumns attribute) AreaUnderPrecisionRecallCurve (class in InnerEye.ML.lightning_metrics) AreaUnderRocCurve (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) args (InnerEye.Azure.azure_config.ParserResult attribute) as_data_loader() (InnerEye.ML.dataset.full_image_dataset.GeneralDataset method) autosave_every_n_val_epochs (InnerEye.ML.deep_learning_config.TrainerParams attribute) Average (InnerEye.ML.config.EnsembleAggregationType attribute) (InnerEye.ML.scalar_config.AggregationType attribute) (InnerEye.ML.scalar_config.EnsembleAggregationType attribute) average() (InnerEye.Common.resource_monitor.GpuUtilization method) (InnerEye.ML.metrics_dict.MetricsDict method) average_metric_values() (in module InnerEye.ML.metrics_dict) AveragePooling (class in InnerEye.ML.models.layers.pooling_layers) AverageWithoutNan (class in InnerEye.ML.lightning_metrics) avoid_process_spawn_in_data_loaders (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) AXIAL (InnerEye.ML.utils.surface_distance_utils.Plane attribute) azure_dataset_id (InnerEye.ML.deep_learning_config.DatasetParams attribute) AzureConfig (class in InnerEye.Azure.azure_config) azureml (InnerEye.Azure.azure_config.AzureConfig attribute) azureml_datastore (InnerEye.Azure.azure_config.AzureConfig attribute) B BaseSegmentationModel (class in InnerEye.ML.models.architectures.base_model) Basic (InnerEye.ML.config.ModelArchitectureConfig attribute) BasicLayer (class in InnerEye.ML.models.layers.basic) BasicModel2Epochs (class in InnerEye.ML.configs.segmentation.BasicModel2Epochs) BasicModel2Epochs1Channel (class in InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel) BasicModel2EpochsMoreData (class in InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData) BasicModelForEnsembleTest (class in InnerEye.ML.configs.segmentation.BasicModel2Epochs) batch_size (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) bias (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) binaries_from_multi_label_array() (in module InnerEye.ML.utils.image_util) binary_classification_accuracy() (in module InnerEye.ML.utils.metrics_util) (InnerEye.ML.metrics_dict.ScalarMetricsDict method) BinaryCrossEntropyWithLogits (class in InnerEye.ML.lightning_metrics) (InnerEye.ML.scalar_config.ScalarLoss attribute) BinaryCrossEntropyWithLogitsLoss (class in InnerEye.ML.utils.supervised_criterion) BiTResNetV2 (class in InnerEye.ML.models.architectures.classification.bit) BitsAllocated (InnerEye.ML.utils.io_util.DicomTags attribute) BitsStored (InnerEye.ML.utils.io_util.DicomTags attribute) branch (InnerEye.Azure.azure_config.GitInformation attribute) build_branch (InnerEye.Azure.azure_config.AzureConfig attribute) build_net() (in module InnerEye.ML.utils.model_util) build_number (InnerEye.Azure.azure_config.AzureConfig attribute) build_source_author (InnerEye.Azure.azure_config.AzureConfig attribute) build_source_id (InnerEye.Azure.azure_config.AzureConfig attribute) build_source_message (InnerEye.Azure.azure_config.AzureConfig attribute) build_source_repository (InnerEye.Azure.azure_config.AzureConfig attribute) build_user (InnerEye.Azure.azure_config.AzureConfig attribute) build_user_email (InnerEye.Azure.azure_config.AzureConfig attribute) C calculate_metrics_per_class() (in module InnerEye.ML.metrics) calculate_surface_distances() (in module InnerEye.ML.utils.surface_distance_utils) categorical_columns (InnerEye.ML.scalar_config.ScalarModelBase attribute) categorical_feature_encoder (InnerEye.ML.scalar_config.ScalarModelBase attribute) categorical_non_image_features (InnerEye.ML.dataset.scalar_sample.ScalarItemBase attribute) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource attribute) CategoricalToOneHotEncoder (class in InnerEye.ML.utils.dataset_util) center_crop_size (InnerEye.ML.scalar_config.ScalarModelBase attribute) center_indices (InnerEye.ML.dataset.sample.CroppedSample attribute) center_size (InnerEye.ML.config.SegmentationModelBase property) change_working_directory() (in module InnerEye.Common.common_util) channel_column (InnerEye.ML.scalar_config.ScalarModelBase attribute) channel_files (InnerEye.ML.dataset.scalar_sample.ScalarDataSource attribute) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource attribute) check_array_range() (in module InnerEye.ML.utils.image_util) check_exclusive (InnerEye.ML.config.SegmentationModelBase attribute) check_if_posterior_array() (in module InnerEye.ML.utils.image_util) check_is_any_of() (in module InnerEye.Common.common_util) check_properties_are_not_none() (in module InnerEye.Common.common_util) check_size_matches() (in module InnerEye.ML.utils.ml_util) CheckPatchSamplingConfig (class in InnerEye.ML.visualizers.patch_sampling) checkpoint_folder (InnerEye.ML.deep_learning_config.OutputParams property) checkpoint_paths (InnerEye.ML.model_inference_config.ModelInferenceConfig attribute) checkpoints_roots (InnerEye.ML.utils.run_recovery.RunRecovery attribute) CheXpert (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) class_and_index_with_background() (InnerEye.ML.config.SegmentationModelBase method) class_names (InnerEye.ML.scalar_config.ScalarModelBase attribute) class_weight_power (InnerEye.ML.config.MixtureLossComponent attribute) class_weights (InnerEye.ML.config.SegmentationModelBase attribute) Classification (InnerEye.ML.deep_learning_config.ModelCategory attribute) CLASSIFICATION_LABEL (InnerEye.ML.utils.image_util.ImageDataType attribute) clone_with_overrides() (InnerEye.ML.dataset.sample.SampleBase method) cluster (InnerEye.Azure.azure_config.AzureConfig attribute) col_type_converters (InnerEye.ML.config.SegmentationModelBase attribute) collate_with_metadata() (in module InnerEye.ML.dataset.full_image_dataset) colours (InnerEye.ML.config.SegmentationModelBase attribute) commit_author (InnerEye.Azure.azure_config.GitInformation attribute) commit_id (InnerEye.Azure.azure_config.GitInformation attribute) commit_message (InnerEye.Azure.azure_config.GitInformation attribute) comparison_blob_storage_paths (InnerEye.ML.config.SegmentationModelBase attribute) ComplexModel (class in InnerEye.ML.models.architectures.complex) Compose3D (class in InnerEye.ML.utils.transforms) compute() (InnerEye.ML.lightning_metrics.AccuracyAtOptimalThreshold method) (InnerEye.ML.lightning_metrics.AreaUnderPrecisionRecallCurve method) (InnerEye.ML.lightning_metrics.AreaUnderRocCurve method) (InnerEye.ML.lightning_metrics.AverageWithoutNan method) (InnerEye.ML.lightning_metrics.BinaryCrossEntropyWithLogits method) (InnerEye.ML.lightning_metrics.FalseNegativeRateOptimalThreshold method) (InnerEye.ML.lightning_metrics.FalsePositiveRateOptimalThreshold method) (InnerEye.ML.lightning_metrics.OptimalThreshold method) (InnerEye.ML.lightning_metrics.ScalarMetricsBase method) compute_all() (InnerEye.ML.lightning_metrics.MetricForMultipleStructures method) compute_and_log_metrics() (InnerEye.ML.scalar_config.ScalarModelBase method) compute_dice_across_patches() (in module InnerEye.ML.metrics) compute_grad_cam (InnerEye.ML.deep_learning_config.DeepLearningConfig property) compute_masked_statistics() (InnerEye.ML.utils.features_util.FeatureStatistics static method) compute_mean_teacher_model (InnerEye.ML.deep_learning_config.DeepLearningConfig property) compute_scalar_metrics() (in module InnerEye.ML.metrics) compute_tensor_memory_megabytes() (InnerEye.ML.visualizers.model_summary.ModelSummary static method) compute_uncertainty_map_from_posteriors() (in module InnerEye.ML.utils.image_util) conda_dependencies_files (InnerEye.Azure.azure_config.SourceConfig attribute) convert_channels_to_file_paths() (in module InnerEye.ML.dataset.full_image_dataset) convert_input_and_label() (in module InnerEye.ML.utils.metrics_util) CORONAL (InnerEye.ML.utils.surface_distance_utils.Plane attribute) correct (InnerEye.ML.lightning_metrics.Accuracy05 attribute) Cosine (InnerEye.ML.deep_learning_config.LRSchedulerType attribute) count (InnerEye.Common.resource_monitor.GpuUtilization attribute) CovidDataset (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) create() (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig static method) (InnerEye.ML.metrics_dict.SequenceMetricsDict static method) create_and_set_torch_datasets() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) create_argparser() (InnerEye.Common.generic_parsing.GenericConfig class method) create_data_loaders() (InnerEye.ML.model_config_base.ModelConfigBase method) create_dataset_configs() (in module InnerEye.Azure.azure_runner) create_dicom_series() (in module InnerEye.ML.utils.io_util) create_encoder() (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) create_experiment_name() (in module InnerEye.Azure.azure_runner) create_file_or_folder_path() (InnerEye.Common.output_directories.OutputFolderForTests method) create_filesystem() (InnerEye.ML.deep_learning_config.OutputParams method) create_from_dataframe() (InnerEye.ML.utils.dataset_util.CategoricalToOneHotEncoder static method) create_from_matching_params() (in module InnerEye.Common.generic_parsing) create_metric_computers() (InnerEye.ML.scalar_config.ScalarModelBase method) create_mlp() (in module InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) create_model() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.configs.regression.DummyRegression.DummyRegression method) (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) create_model_config_from_name() (InnerEye.ML.utils.config_loader.ModelConfigLoader method) create_model_with_temperature_scaling() (in module InnerEye.ML.utils.model_util) create_non_image_and_image_aggregator() (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) create_optimizer() (in module InnerEye.ML.utils.model_util) create_parser() (in module InnerEye.ML.normalize_and_visualize_dataset) create_possibly_padded_sample_for_cropping() (InnerEye.ML.dataset.cropping_dataset.CroppingDataset static method) create_random_cropped_sample() (InnerEye.ML.dataset.cropping_dataset.CroppingDataset static method) create_runner_parser() (in module InnerEye.Azure.azure_runner) create_scalar_loss_function() (in module InnerEye.ML.utils.model_util) create_scatterplots() (in module InnerEye.ML.visualizers.metrics_scatterplot) create_segmentation_loss_component() (in module InnerEye.ML.utils.model_util) create_segmentation_loss_function() (in module InnerEye.ML.utils.model_util) create_status_string() (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) create_torch_datasets() (InnerEye.ML.scalar_config.ScalarModelBase method) create_transforms_from_config() (in module InnerEye.ML.augmentations.transform_pipeline) create_unique_timestamp_id() (in module InnerEye.ML.common) crop_size (InnerEye.ML.config.SegmentationModelBase attribute) CroppedSample (class in InnerEye.ML.dataset.sample) CroppingDataset (class in InnerEye.ML.dataset.cropping_dataset) CropSizeConstraints (class in InnerEye.ML.models.architectures.base_model) CROSS_ENTROPY (InnerEye.Common.metrics_constants.MetricType attribute) cross_validation_split_index (InnerEye.ML.deep_learning_config.WorkflowParams attribute) CrossEntropy (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.ML.config.SegmentationLoss attribute) CrossEntropyLoss (class in InnerEye.ML.models.losses.cross_entropy) CrossValidationSplitIndex (InnerEye.Common.metrics_constants.LoggingColumns attribute) CTRange (class in InnerEye.ML.utils.transforms) CtWindow (InnerEye.ML.config.PhotometricNormalizationMethod attribute) CustomClassification (InnerEye.ML.scalar_config.ScalarLoss attribute) CustomRegression (InnerEye.ML.scalar_config.ScalarLoss attribute) D data_item (InnerEye.ML.utils.model_util.ScalarModelInputsAndLabels attribute) DATAFRAME_COLUMNS (InnerEye.ML.metrics_dict.MetricsDict attribute) DataframeLogger (class in InnerEye.ML.metrics_dict) dataset (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) dataset_csv (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) dataset_data_frame (InnerEye.ML.deep_learning_config.DeepLearningConfig property) dataset_expected_spacing_xyz (InnerEye.ML.config.SegmentationModelBase attribute) dataset_mountpoint (InnerEye.ML.deep_learning_config.DatasetParams attribute) dataset_stats_hook (InnerEye.ML.scalar_config.ScalarModelBase attribute) DatasetExample (class in InnerEye.ML.utils.dataset_util) DatasetParams (class in InnerEye.ML.deep_learning_config) DatasetSplits (class in InnerEye.ML.utils.split_dataset) DataSourceReader (class in InnerEye.ML.dataset.scalar_dataset) DataSplit (InnerEye.Common.metrics_constants.LoggingColumns attribute) DATE (InnerEye.ML.utils.hdf5_util.HDF5Field attribute) debug_mode (InnerEye.ML.config.SegmentationModelBase attribute) DeepLearningConfig (class in InnerEye.ML.deep_learning_config) DeepLearningFileSystemConfig (class in InnerEye.ML.deep_learning_config) DEFAULT (InnerEye.Common.common_util.ModelProcessing attribute) DEFAULT_HUE_KEY (InnerEye.ML.metrics_dict.MetricsDict attribute) delete_hue() (InnerEye.ML.metrics_dict.MetricsDict method) delete_metric() (InnerEye.ML.metrics_dict.MetricsDict method) detect_anomaly (InnerEye.ML.deep_learning_config.TrainerParams attribute) device (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) DeviceAwareModule (class in InnerEye.ML.utils.device_aware_module) diagnostics (InnerEye.ML.metrics_dict.ScalarMetricsDict attribute) (InnerEye.ML.metrics_dict.SequenceMetricsDict attribute) Dice (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) DICE (InnerEye.Common.metrics_constants.MetricType attribute) dice_score (InnerEye.ML.surface_distance_heatmaps.Segmentation attribute) DiceNumeric (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) Dicom (InnerEye.ML.utils.io_util.DicomFileType attribute) DicomFileType (class in InnerEye.ML.utils.io_util) DicomTags (class in InnerEye.ML.utils.io_util) difference() (InnerEye.ML.scalar_config.LabelTransformation static method) dilation (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) dir_for_subject() (in module InnerEye.ML.utils.surface_distance_utils) direction (InnerEye.ML.utils.image_util.ImageHeader attribute) disable_extra_postprocessing (InnerEye.ML.config.SegmentationModelBase attribute) disable_logging_to_file() (in module InnerEye.Common.common_util) docker_shm_size (InnerEye.Azure.azure_config.AzureConfig attribute) download_run_output_file() (in module InnerEye.Azure.azure_util) download_run_outputs_by_prefix() (in module InnerEye.Azure.azure_util) drop_last (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) drop_last_batch_in_training (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) drop_rows_missing_important_values() (in module InnerEye.ML.utils.csv_util) DummyRegression (class in InnerEye.ML.configs.regression.DummyRegression) E ece_num_bins (InnerEye.ML.deep_learning_config.TemperatureScalingConfig attribute) ECELoss (class in InnerEye.ML.models.losses.ece) Edge (InnerEye.ML.config.PaddingMode attribute) ElasticTransform (class in InnerEye.ML.augmentations.image_transforms) empty_string_to_none() (in module InnerEye.Common.common_util) encode() (InnerEye.ML.common.OneHotEncoderBase method) (InnerEye.ML.utils.dataset_util.CategoricalToOneHotEncoder method) encode_and_aggregate() (in module InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) (InnerEye.ML.models.architectures.classification.segmentation_encoder.MultiSegmentationEncoder method) ensemble_aggregation_type (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.scalar_config.ScalarModelBase attribute) ENSEMBLE_CREATION (InnerEye.Common.common_util.ModelProcessing attribute) ensemble_inference_on_test_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) ensemble_inference_on_train_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) ensemble_inference_on_val_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) EnsembleAggregationType (class in InnerEye.ML.config) (class in InnerEye.ML.scalar_config) entry_script (InnerEye.Azure.azure_config.SourceConfig attribute) enumerate() (InnerEye.Common.resource_monitor.GpuUtilization method) enumerate_single_values() (InnerEye.ML.metrics_dict.Hue method) (InnerEye.ML.metrics_dict.MetricsDict method) enumerate_single_values_groupwise() (InnerEye.ML.metrics_dict.MetricsDict method) environment_variables (InnerEye.Azure.azure_config.SourceConfig attribute) Epoch (InnerEye.Common.metrics_constants.LoggingColumns attribute) epoch (InnerEye.ML.utils.dataset_util.DatasetExample attribute) eps (InnerEye.ML.models.losses.soft_dice.SoftDiceLoss attribute) equally_weighted_classes() (in module InnerEye.ML.config) example_images_folder (InnerEye.ML.config.SegmentationModelBase property) execution_mode (InnerEye.ML.metrics.InferenceMetricsForSegmentation attribute) (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) ExpandChannels (class in InnerEye.ML.augmentations.image_transforms) expected_column_values (InnerEye.ML.scalar_config.ScalarModelBase attribute) experiment_name (InnerEye.Azure.azure_config.AzureConfig attribute) EXPLAINED_VAR (InnerEye.Common.metrics_constants.MetricType attribute) ExplainedVariance (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) Exponential (InnerEye.ML.deep_learning_config.LRSchedulerType attribute) external_class (InnerEye.ML.config.SummedProbabilityRule attribute) extra_azure_dataset_ids (InnerEye.ML.deep_learning_config.DatasetParams attribute) extra_code_directory (InnerEye.Azure.azure_config.AzureConfig attribute) extra_dataset_mountpoints (InnerEye.ML.deep_learning_config.DatasetParams attribute) extra_local_dataset_paths (InnerEye.ML.deep_learning_config.DatasetParams attribute) extract_activation_maps() (in module InnerEye.ML.visualizers.activation_maps) extract_border() (in module InnerEye.ML.utils.surface_distance_utils) extract_label_classification() (in module InnerEye.ML.dataset.scalar_dataset) extract_largest_foreground_connected_component() (in module InnerEye.ML.utils.image_util) extract_outliers() (in module InnerEye.ML.utils.csv_util) F FALSE_NEGATIVE_RATE_AT_OPTIMAL_THRESHOLD (InnerEye.Common.metrics_constants.MetricType attribute) FALSE_POSITIVE_RATE_AT_OPTIMAL_THRESHOLD (InnerEye.Common.metrics_constants.MetricType attribute) FalseNegativeRateAtOptimalThreshold (InnerEye.Common.metrics_constants.LoggingColumns attribute) FalseNegativeRateOptimalThreshold (class in InnerEye.ML.lightning_metrics) FalsePositiveRateAtOptimalThreshold (InnerEye.Common.metrics_constants.LoggingColumns attribute) FalsePositiveRateOptimalThreshold (class in InnerEye.ML.lightning_metrics) feature_channels (InnerEye.ML.config.SegmentationModelBase attribute) features_valid() (InnerEye.ML.dataset.scalar_sample.ScalarItemBase method) FeatureStatistics (class in InnerEye.ML.utils.features_util) fetch_child_runs() (in module InnerEye.Azure.azure_util) fetch_run() (in module InnerEye.Azure.azure_util) (InnerEye.Azure.azure_config.AzureConfig method) fetch_runs() (in module InnerEye.Azure.azure_util) file_system_config (InnerEye.ML.deep_learning_config.OutputParams attribute) files_by_stem() (in module InnerEye.ML.dataset.scalar_dataset) files_valid() (InnerEye.ML.dataset.scalar_sample.ScalarDataSource method) fill_holes (InnerEye.ML.config.SegmentationModelBase attribute) filter_dataframe() (InnerEye.ML.scalar_config.ScalarModelBase method) filter_valid_classification_data_sources_items() (in module InnerEye.ML.dataset.scalar_dataset) filter_valid_data_sources_items() (InnerEye.ML.dataset.scalar_dataset.ScalarDataset method) (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) find_intersection_array_indices() (in module InnerEye.ML.utils.image_util) first_class (InnerEye.ML.config.SummedProbabilityRule attribute) flush() (InnerEye.ML.metrics_dict.DataframeLogger method) Focal (InnerEye.ML.config.SegmentationLoss attribute) focal_loss_gamma (InnerEye.ML.config.SegmentationModelBase attribute) fork (InnerEye.ML.deep_learning_config.MultiprocessingStartMethod attribute) forkserver (InnerEye.ML.deep_learning_config.MultiprocessingStartMethod attribute) format_metric() (in module InnerEye.ML.utils.metrics_util) forward() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) (InnerEye.ML.models.architectures.classification.bit.BiTResNetV2 method) (InnerEye.ML.models.architectures.classification.bit.ResNetV2Block method) (InnerEye.ML.models.architectures.classification.bit.ResNetV2Layer method) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageAndNonImageFeaturesAggregator method) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoderWithMlp method) (InnerEye.ML.models.architectures.classification.segmentation_encoder.MultiSegmentationEncoder method) (InnerEye.ML.models.architectures.classification.segmentation_encoder.SegmentationEncoder method) (InnerEye.ML.models.architectures.complex.ComplexModel method) (InnerEye.ML.models.architectures.mlp.MLP method) (InnerEye.ML.models.architectures.mlp.MLP.HiddenLayer method) (InnerEye.ML.models.architectures.unet_3d.UNet3D method) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetDecodeBlock method) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetEncodeBlock method) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetEncodeBlockSynthesis method) (InnerEye.ML.models.blocks.residual.ResidualBlock method) (InnerEye.ML.models.layers.basic.BasicLayer method) (InnerEye.ML.models.layers.identity.Identity method) (InnerEye.ML.models.layers.pooling_layers.AveragePooling method) (InnerEye.ML.models.layers.pooling_layers.Gated3dPoolingLayer method) (InnerEye.ML.models.layers.pooling_layers.MaxPooling method) (InnerEye.ML.models.layers.pooling_layers.MixPooling method) (InnerEye.ML.models.layers.pooling_layers.ZAdaptive3dAvgLayer method) (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d method) (InnerEye.ML.models.losses.ece.ECELoss method) (InnerEye.ML.utils.supervised_criterion.SupervisedLearningCriterion method) (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature method) (InnerEye.ML.visualizers.model_hooks.HookBasedFeatureExtractor method) forward_hook_fn() (InnerEye.ML.visualizers.model_hooks.HookBasedFeatureExtractor method) forward_minibatch() (InnerEye.ML.models.losses.cross_entropy.CrossEntropyLoss method) (InnerEye.ML.models.losses.mixture.MixtureLoss method) (InnerEye.ML.models.losses.soft_dice.SoftDiceLoss method) (InnerEye.ML.utils.supervised_criterion.BinaryCrossEntropyWithLogitsLoss method) (InnerEye.ML.utils.supervised_criterion.SupervisedLearningCriterion method) forward_preserve_state() (in module InnerEye.ML.visualizers.model_summary) FrameOfReferenceUID (InnerEye.ML.utils.io_util.DicomTags attribute) from_data_sources() (InnerEye.ML.utils.features_util.FeatureStatistics static method) from_dataframe() (InnerEye.ML.dataset.sample.PatientMetadata static method) from_dict() (InnerEye.ML.dataset.sample.SampleBase class method) (InnerEye.ML.model_inference_config.ModelInferenceConfig class method) from_file() (InnerEye.ML.utils.hdf5_util.HDF5Object class method) from_gpu() (InnerEye.Common.resource_monitor.GpuUtilization static method) from_groups() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) from_institutions() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) from_json() (InnerEye.ML.model_inference_config.ModelInferenceConfig class method) from_proportions() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) from_subject_ids() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) from_yaml() (InnerEye.Azure.azure_config.AzureConfig static method) full_ml_test_data_path() (in module InnerEye.Common.fixed_paths_for_tests) FullImageDataset (class in InnerEye.ML.dataset.full_image_dataset) G Gated3dPoolingLayer (class in InnerEye.ML.models.layers.pooling_layers) GatedPooling (InnerEye.ML.scalar_config.AggregationType attribute) gaussian_smooth_posteriors() (in module InnerEye.ML.utils.image_util) GbmBase (class in InnerEye.ML.configs.segmentation.GbmBase) GeneralDataset (class in InnerEye.ML.dataset.full_image_dataset) GeneralSampleMetadata (class in InnerEye.ML.dataset.sample) generate_and_print_model_summary() (in module InnerEye.ML.utils.model_util) generate_custom_report() (InnerEye.ML.model_config_base.ModelConfigBase method) generate_model_summary() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) generate_random_colours_list() (in module InnerEye.ML.utils.model_metadata_util) generate_report (InnerEye.ML.deep_learning_config.WorkflowParams attribute) generate_summary() (InnerEye.ML.visualizers.model_summary.ModelSummary method) GenericConfig (class in InnerEye.Common.generic_parsing) get_accuracy_at05() (InnerEye.ML.metrics_dict.MetricsDict method) get_all_child_layers() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) (InnerEye.ML.models.architectures.complex.ComplexModel method) (InnerEye.ML.models.architectures.unet_2d.UNet2D method) (InnerEye.ML.models.architectures.unet_3d.UNet3D method) get_all_environment_files() (in module InnerEye.Azure.azure_util) get_all_image_filepaths() (InnerEye.ML.dataset.scalar_sample.ScalarDataSource method) get_all_non_imaging_features() (InnerEye.ML.dataset.scalar_sample.ScalarItem method) get_annotations_and_majority_vote() (in module InnerEye.ML.utils.surface_distance_utils) get_best_checkpoint_path() (in module InnerEye.ML.common) get_best_checkpoint_paths() (InnerEye.ML.utils.run_recovery.RunRecovery method) get_best_epoch_results_path() (in module InnerEye.Common.common_util) get_center_crop() (in module InnerEye.ML.utils.image_util) get_center_size() (in module InnerEye.ML.config) get_class_counts() (InnerEye.ML.dataset.scalar_dataset.ScalarDataset method) get_class_weights() (in module InnerEye.ML.utils.image_util) get_column_name_for_logging() (in module InnerEye.ML.metrics_dict) get_comparison_baseline_paths() (in module InnerEye.Azure.azure_util) get_configs() (in module InnerEye.ML.normalize_and_visualize_dataset) get_cropped_axes() (in module InnerEye.ML.utils.plotting_util) get_cropped_image_sample_transforms() (InnerEye.ML.config.SegmentationModelBase method) get_cross_entropy() (InnerEye.ML.metrics_dict.MetricsDict method) get_cross_validation_dataset_splits() (InnerEye.ML.model_config_base.ModelConfigBase method) get_cross_validation_hyperdrive_config() (InnerEye.ML.model_config_base.ModelConfigBase method) get_cross_validation_hyperdrive_sampler() (InnerEye.ML.model_config_base.ModelConfigBase method) get_cross_validation_split_index() (in module InnerEye.Azure.azure_util) get_current_learning_rates() (in module InnerEye.ML.utils.lr_scheduler) get_dataset_splits() (InnerEye.ML.model_config_base.ModelConfigBase method) get_default_search_module() (InnerEye.ML.utils.config_loader.ModelConfigLoader static method) get_devices() (InnerEye.ML.utils.device_aware_module.DeviceAwareModule method) get_df_from_ids() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) get_dict() (InnerEye.ML.dataset.sample.SampleBase method) get_effective_random_seed() (InnerEye.ML.deep_learning_config.WorkflowParams method) get_environment_yaml_file() (in module InnerEye.Common.fixed_paths) get_feature_length() (InnerEye.ML.common.OneHotEncoderBase method) (InnerEye.ML.utils.dataset_util.CategoricalToOneHotEncoder method) get_first_child_run() (in module InnerEye.ML.utils.surface_distance_utils) get_focal_loss_pixel_weights() (InnerEye.ML.models.losses.cross_entropy.CrossEntropyLoss method) get_full_image_filepath() (InnerEye.ML.dataset.scalar_sample.ScalarDataSource static method) get_full_image_sample_transforms() (InnerEye.ML.config.SegmentationModelBase method) get_git_information() (InnerEye.Azure.azure_config.AzureConfig method) get_git_tags() (in module InnerEye.Azure.azure_runner) get_gpu_tensor_if_possible() (InnerEye.ML.utils.transforms.Transform3D method) get_hue_name_from_target_index() (InnerEye.ML.metrics_dict.SequenceMetricsDict static method) get_hue_names() (InnerEye.ML.metrics_dict.MetricsDict method) get_hyperdrive_config() (InnerEye.ML.model_config_base.ModelConfigBase method) get_image_transform() (InnerEye.ML.scalar_config.ScalarModelBase method) get_input_tensors() (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) (InnerEye.ML.models.architectures.classification.segmentation_encoder.MultiSegmentationEncoder method) (InnerEye.ML.models.architectures.mlp.MLP method) (InnerEye.ML.utils.device_aware_module.DeviceAwareModule method) (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature method) get_items_from_string() (in module InnerEye.Common.common_util) get_k_fold_cross_validation_splits() (InnerEye.ML.utils.split_dataset.DatasetSplits method) get_label_overlap_stats() (in module InnerEye.ML.utils.metrics_util) get_label_transform() (InnerEye.ML.configs.regression.DummyRegression.DummyRegression method) (InnerEye.ML.scalar_config.ScalarModelBase method) get_label_volume() (in module InnerEye.ML.utils.metrics_util) get_labels() (InnerEye.ML.metrics_dict.Hue method) (InnerEye.ML.metrics_dict.MetricsDict method) get_labels_for_imbalanced_sampler() (InnerEye.ML.dataset.scalar_dataset.ScalarDataset method) (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) get_largest_z_slice() (in module InnerEye.ML.utils.image_util) get_last_encoder_layer_names() (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder method) (InnerEye.ML.utils.device_aware_module.DeviceAwareModule method) (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature method) get_last_lr() (InnerEye.ML.utils.lr_scheduler.SchedulerWithWarmUp method) get_log_level_string() (in module InnerEye.Common.common_util) get_loss_function() (InnerEye.ML.scalar_config.ScalarModelBase method) get_lr() (InnerEye.ML.utils.lr_scheduler.LinearWarmUp method) (InnerEye.ML.utils.lr_scheduler.PolynomialLR method) get_majority_vote() (in module InnerEye.ML.utils.surface_distance_utils) get_masked_model_outputs_and_labels() (in module InnerEye.ML.utils.sequence_utils) get_mean_absolute_error() (InnerEye.ML.metrics_dict.MetricsDict method) get_mean_squared_error() (InnerEye.ML.metrics_dict.MetricsDict method) get_metric_name_with_hue_prefix() (in module InnerEye.ML.metrics_dict) get_metrics_at_optimal_cutoff() (InnerEye.ML.metrics_dict.MetricsDict method) get_metrics_log_key() (InnerEye.ML.metrics.InferenceMetricsForSegmentation method) get_metrics_path() (in module InnerEye.ML.utils.surface_distance_utils) get_model_train_test_dataset_splits() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.configs.regression.DummyRegression.DummyRegression method) (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModel2Epochs method) (InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData.BasicModel2EpochsMoreData method) (InnerEye.ML.configs.segmentation.GbmBase.GbmBase method) (InnerEye.ML.configs.segmentation.HeadAndNeckBase.HeadAndNeckBase method) (InnerEye.ML.configs.segmentation.HelloWorld.HelloWorld method) (InnerEye.ML.configs.segmentation.Hippocampus.Hippocampus method) (InnerEye.ML.configs.segmentation.Lung.Lung method) (InnerEye.ML.configs.segmentation.ProstateBase.ProstateBase method) (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) get_non_image_feature_channels_dict() (InnerEye.ML.scalar_config.ScalarModelBase method) get_non_image_features_dict() (in module InnerEye.ML.scalar_config) get_number_of_voxels_per_class() (in module InnerEye.ML.utils.metrics_util) get_number_trainable_parameters() (InnerEye.ML.utils.device_aware_module.DeviceAwareModule method) get_optimal_idx() (InnerEye.ML.metrics_dict.MetricsDict class method) get_output_shape() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) get_output_size() (InnerEye.ML.config.SegmentationModelBase method) get_overridable_parameters() (InnerEye.Common.generic_parsing.GenericConfig class method) get_padding_from_kernel_size() (in module InnerEye.ML.utils.layer_util) get_parameter_search_hyperdrive_config() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.configs.segmentation.HelloWorld.HelloWorld method) (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) get_path_to_best_checkpoint() (InnerEye.ML.deep_learning_config.OutputParams method) get_path_to_checkpoint() (InnerEye.ML.deep_learning_config.OutputParams method) get_positive_class_weights() (InnerEye.ML.utils.supervised_criterion.BinaryCrossEntropyWithLogitsLoss method) get_post_loss_logits_normalization_function() (InnerEye.ML.scalar_config.ScalarModelBase method) get_pr_auc() (InnerEye.ML.metrics_dict.MetricsDict method) get_predictions() (InnerEye.ML.metrics_dict.Hue method) (InnerEye.ML.metrics_dict.MetricsDict method) get_predictions_and_labels_per_subject() (InnerEye.ML.metrics_dict.Hue method) (InnerEye.ML.metrics_dict.MetricsDict method) get_r2_score() (InnerEye.ML.metrics_dict.MetricsDict method) get_range_for_window_level() (in module InnerEye.ML.utils.transforms) get_recovery_checkpoint_paths() (InnerEye.ML.utils.run_recovery.RunRecovery method) get_roc_auc() (InnerEye.ML.metrics_dict.MetricsDict method) get_run_context_or_default() (in module InnerEye.Azure.azure_util) get_run_output_dir() (in module InnerEye.ML.utils.surface_distance_utils) get_samples_at_index() (InnerEye.ML.dataset.full_image_dataset.FullImageDataset method) get_scalar_item_transform() (InnerEye.ML.scalar_config.ScalarModelBase method) get_scalar_model_inputs_and_labels() (in module InnerEye.ML.utils.model_util) get_scaling_transform() (InnerEye.ML.scalar_config.LabelTransformation static method) get_scheduler() (InnerEye.ML.utils.lr_scheduler.SchedulerWithWarmUp method) get_secret_from_environment() (InnerEye.Azure.secrets_handling.SecretsHandling method) get_secrets_from_environment_or_file() (InnerEye.Azure.secrets_handling.SecretsHandling method) get_segmentation_transform() (InnerEye.ML.scalar_config.ScalarModelBase method) get_service_principal_auth() (InnerEye.Azure.azure_config.AzureConfig method) get_single_metric() (InnerEye.ML.metrics_dict.MetricsDict method) get_status() (InnerEye.ML.dataset.scalar_dataset.ScalarDataset method) get_subject_prefix() (in module InnerEye.ML.utils.surface_distance_utils) get_subject_ranges_for_splits() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) get_supported_dataset_column_names() (InnerEye.ML.common.OneHotEncoderBase method) (InnerEye.ML.utils.dataset_util.CategoricalToOneHotEncoder method) get_target_index_from_hue_name() (InnerEye.ML.metrics_dict.SequenceMetricsDict static method) get_torch_dataset_for_inference() (InnerEye.ML.model_config_base.ModelConfigBase method) get_total_number_of_categorical_non_imaging_features() (InnerEye.ML.scalar_config.ScalarModelBase method) get_total_number_of_non_imaging_features() (InnerEye.ML.scalar_config.ScalarModelBase method) get_total_number_of_numerical_non_imaging_features() (InnerEye.ML.scalar_config.ScalarModelBase method) get_total_number_of_training_epochs() (InnerEye.ML.deep_learning_config.DeepLearningConfig method) get_total_number_of_training_samples() (InnerEye.ML.scalar_config.ScalarModelBase method) get_total_number_of_validation_epochs() (InnerEye.ML.deep_learning_config.DeepLearningConfig method) get_train_epochs() (InnerEye.ML.deep_learning_config.DeepLearningConfig method) get_training_class_counts() (InnerEye.ML.scalar_config.ScalarModelBase method) get_unit_image_header() (in module InnerEye.ML.utils.image_util) get_upsampling_kernel_size() (in module InnerEye.ML.utils.layer_util) get_val_dice_names() (in module InnerEye.ML.plotting) get_view_dim_and_origin() (in module InnerEye.ML.utils.plotting_util) get_weights() (InnerEye.ML.dataset.full_image_dataset.ImbalancedSampler method) get_workspace() (InnerEye.Azure.azure_config.AzureConfig method) get_worst_performing_outliers() (in module InnerEye.ML.utils.csv_util) GitInformation (class in InnerEye.Azure.azure_config) GpuUtilization (class in InnerEye.Common.resource_monitor) ground_truth_channels (InnerEye.ML.dataset.sample.PatientDatasetSource attribute) ground_truth_dir (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) ground_truth_ids (InnerEye.ML.config.SegmentationModelBase attribute) ground_truth_ids_display_names (InnerEye.ML.config.SegmentationModelBase attribute) group_column (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) groups (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) gt_channel (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) H has_prediction_entries (InnerEye.ML.metrics_dict.Hue property) has_prediction_entries() (InnerEye.ML.metrics_dict.MetricsDict method) has_predictions (InnerEye.ML.lightning_metrics.Accuracy05 property) (InnerEye.ML.lightning_metrics.ExplainedVariance property) (InnerEye.ML.lightning_metrics.MeanAbsoluteError property) (InnerEye.ML.lightning_metrics.MeanSquaredError property) (InnerEye.ML.lightning_metrics.ScalarMetricsBase property) HAUSDORFF_mm (InnerEye.Common.metrics_constants.MetricType attribute) HausdorffDistanceMM (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) HDF5 (InnerEye.ML.utils.io_util.HDF5FileType attribute) HDF5_COMPRESSED_GZ (InnerEye.ML.utils.io_util.HDF5FileType attribute) HDF5_COMPRESSED_SZ (InnerEye.ML.utils.io_util.HDF5FileType attribute) HDF5_EXPLICIT (InnerEye.ML.utils.io_util.HDF5FileType attribute) HDF5Field (class in InnerEye.ML.utils.hdf5_util) HDF5FileType (class in InnerEye.ML.utils.io_util) HDF5ImageDataType (class in InnerEye.ML.utils.hdf5_util) HDF5Object (class in InnerEye.ML.utils.hdf5_util) HeadAndNeckBase (class in InnerEye.ML.configs.segmentation.HeadAndNeckBase) HeadAndNeckPaper (class in InnerEye.ML.configs.segmentation.HeadAndNeckPaper) header (InnerEye.ML.utils.dataset_util.DatasetExample attribute) (InnerEye.ML.utils.io_util.ImageWithHeader attribute) HelloWorld (class in InnerEye.ML.configs.segmentation.HelloWorld) HIGH (InnerEye.ML.utils.csv_util.OutlierType attribute) HighBit (InnerEye.ML.utils.io_util.DicomTags attribute) higher_class (InnerEye.ML.config.SliceExclusionRule attribute) higher_dominates (InnerEye.ML.config.SliceExclusionRule attribute) Hippocampus (class in InnerEye.ML.configs.segmentation.Hippocampus) HookBasedFeatureExtractor (class in InnerEye.ML.visualizers.model_hooks) Hue (class in InnerEye.ML.metrics_dict) (InnerEye.Common.metrics_constants.LoggingColumns attribute) hues (InnerEye.ML.metrics_dict.ScalarMetricsDict attribute) (InnerEye.ML.metrics_dict.SequenceMetricsDict attribute) hyperdrive (InnerEye.Azure.azure_config.AzureConfig attribute) hyperdrive_config_func (InnerEye.Azure.azure_config.SourceConfig attribute) I id (InnerEye.Common.resource_monitor.GpuUtilization attribute) (InnerEye.ML.dataset.sample.GeneralSampleMetadata attribute) (InnerEye.ML.dataset.scalar_sample.ScalarItemBase property) Identity (class in InnerEye.ML.models.layers.identity) identity() (InnerEye.ML.scalar_config.LabelTransformation static method) ignore_mask (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) image (InnerEye.ML.dataset.sample.Sample attribute) Image (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImagingFeatureType attribute) image (InnerEye.ML.utils.dataset_util.DatasetExample attribute) IMAGE (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) (InnerEye.ML.utils.image_util.ImageDataType attribute) image (InnerEye.ML.utils.io_util.ImageWithHeader attribute) image_channel (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) image_channels (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.dataset.sample.PatientDatasetSource attribute) (InnerEye.ML.scalar_config.ScalarModelBase attribute) image_file_column (InnerEye.ML.scalar_config.ScalarModelBase attribute) image_header (InnerEye.ML.dataset.sample.PatientMetadata attribute) image_size (InnerEye.ML.scalar_config.ScalarModelBase attribute) image_spacing (InnerEye.ML.dataset.sample.Sample property) ImageAndNonImageFeaturesAggregator (class in InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) ImageAndSegmentation (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImagingFeatureType attribute) ImageAndSegmentations (class in InnerEye.ML.utils.io_util) ImageDataType (class in InnerEye.ML.utils.image_util) ImageEncoder (class in InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) ImageEncoderWithMlp (class in InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) ImageHeader (class in InnerEye.ML.utils.image_util) ImagePositionPatient (InnerEye.ML.utils.io_util.DicomTags attribute) images (InnerEye.ML.dataset.scalar_sample.ScalarItem attribute) (InnerEye.ML.utils.io_util.ImageAndSegmentations attribute) ImageTransformationPipeline (class in InnerEye.ML.augmentations.transform_pipeline) ImageType (InnerEye.ML.utils.io_util.DicomTags attribute) ImageWithHeader (class in InnerEye.ML.utils.io_util) ImagingFeatureType (class in InnerEye.ML.models.architectures.classification.image_encoder_with_mlp) ImbalancedSampler (class in InnerEye.ML.dataset.full_image_dataset) inference_batch_size (InnerEye.ML.config.SegmentationModelBase attribute) inference_on_test_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) inference_on_train_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) inference_on_val_set (InnerEye.ML.deep_learning_config.WorkflowParams attribute) inference_stride_size (InnerEye.ML.config.SegmentationModelBase property) InferenceMetrics (class in InnerEye.ML.metrics) InferenceMetricsForClassification (class in InnerEye.ML.metrics) InferenceMetricsForSegmentation (class in InnerEye.ML.metrics) inferred_max_dice() (in module InnerEye.ML.visualizers.metrics_scatterplot) init_weights() (in module InnerEye.ML.utils.model_util) initialise_layer_weights() (in module InnerEye.ML.utils.layer_util) initialise_surface_distance_dictionary() (in module InnerEye.ML.utils.surface_distance_utils) initialize_instance_variables() (in module InnerEye.Common.common_util) InnerEye.Azure.azure_config module InnerEye.Azure.azure_runner module InnerEye.Azure.azure_util module InnerEye.Azure.parser_util module InnerEye.Azure.secrets_handling module InnerEye.Common.common_util module InnerEye.Common.fixed_paths module InnerEye.Common.fixed_paths_for_tests module InnerEye.Common.generic_parsing module InnerEye.Common.metrics_constants module InnerEye.Common.output_directories module InnerEye.Common.resource_monitor module InnerEye.Common.spawn_subprocess module InnerEye.ML.augmentations.augmentation_for_segmentation_utils module InnerEye.ML.augmentations.image_transforms module InnerEye.ML.augmentations.transform_pipeline module InnerEye.ML.common module InnerEye.ML.config module InnerEye.ML.configs.regression.DummyRegression module InnerEye.ML.configs.segmentation.BasicModel2Epochs module InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel module InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData module InnerEye.ML.configs.segmentation.GbmBase module InnerEye.ML.configs.segmentation.HeadAndNeckBase module InnerEye.ML.configs.segmentation.HeadAndNeckPaper module InnerEye.ML.configs.segmentation.HelloWorld module InnerEye.ML.configs.segmentation.Hippocampus module InnerEye.ML.configs.segmentation.Lung module InnerEye.ML.configs.segmentation.ProstateBase module InnerEye.ML.configs.segmentation.ProstatePaper module InnerEye.ML.dataset.cropping_dataset module InnerEye.ML.dataset.full_image_dataset module InnerEye.ML.dataset.sample module InnerEye.ML.dataset.scalar_dataset module InnerEye.ML.dataset.scalar_sample module InnerEye.ML.deep_learning_config module InnerEye.ML.lightning_metrics module InnerEye.ML.metrics module InnerEye.ML.metrics_dict module InnerEye.ML.model_config_base module InnerEye.ML.model_inference_config module InnerEye.ML.models.architectures.base_model module InnerEye.ML.models.architectures.classification.bit module InnerEye.ML.models.architectures.classification.image_encoder_with_mlp module InnerEye.ML.models.architectures.classification.segmentation_encoder module InnerEye.ML.models.architectures.complex module InnerEye.ML.models.architectures.mlp module InnerEye.ML.models.architectures.unet_2d module InnerEye.ML.models.architectures.unet_3d module InnerEye.ML.models.blocks.residual module InnerEye.ML.models.layers.basic module InnerEye.ML.models.layers.identity module InnerEye.ML.models.layers.pooling_layers module InnerEye.ML.models.layers.weight_standardization module InnerEye.ML.models.losses.cross_entropy module InnerEye.ML.models.losses.ece module InnerEye.ML.models.losses.mixture module InnerEye.ML.models.losses.soft_dice module InnerEye.ML.normalize_and_visualize_dataset module InnerEye.ML.photometric_normalization module InnerEye.ML.plotting module InnerEye.ML.scalar_config module InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets module InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets module InnerEye.ML.SSL.datamodules_and_datasets.dataset_cls_utils module InnerEye.ML.surface_distance_heatmaps module InnerEye.ML.utils.config_loader module InnerEye.ML.utils.csv_util module InnerEye.ML.utils.dataset_util module InnerEye.ML.utils.device_aware_module module InnerEye.ML.utils.features_util module InnerEye.ML.utils.hdf5_util module InnerEye.ML.utils.image_util module InnerEye.ML.utils.io_util module InnerEye.ML.utils.layer_util module InnerEye.ML.utils.lr_scheduler module InnerEye.ML.utils.metrics_util module InnerEye.ML.utils.ml_util module InnerEye.ML.utils.model_metadata_util module InnerEye.ML.utils.model_util module InnerEye.ML.utils.plotting_util module InnerEye.ML.utils.run_recovery module InnerEye.ML.utils.sequence_utils module InnerEye.ML.utils.split_dataset module InnerEye.ML.utils.supervised_criterion module InnerEye.ML.utils.surface_distance_utils module InnerEye.ML.utils.temperature_scaling module InnerEye.ML.utils.transforms module InnerEye.ML.visualizers.activation_maps module InnerEye.ML.visualizers.metrics_scatterplot module InnerEye.ML.visualizers.model_hooks module InnerEye.ML.visualizers.model_summary module InnerEye.ML.visualizers.patch_sampling module InnerEye.ML.visualizers.regression_visualization module InnerEye.ML.visualizers.reliability_curve module InnerEyeCIFAR10 (class in InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets) InnerEyeCIFAR100 (class in InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets) InnerEyeCXRDatasetBase (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) InnerEyeCXRDatasetWithReturnIndex (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) InnerEyeDataClassBaseWithReturnIndex (class in InnerEye.ML.SSL.datamodules_and_datasets.dataset_cls_utils) input_range (InnerEye.ML.utils.transforms.LinearTransform attribute) input_shape (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) InstanceNumber (InnerEye.ML.utils.io_util.DicomTags attribute) Institution (InnerEye.Common.metrics_constants.LoggingColumns attribute) institution (InnerEye.ML.dataset.sample.PatientMetadata attribute) interpreter (InnerEye.ML.config.SegmentationModelBase attribute) IntTuple (class in InnerEye.Common.generic_parsing) IOV (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceRunType attribute) is_binary_array() (in module InnerEye.ML.utils.image_util) is_classification_loss() (InnerEye.ML.scalar_config.ScalarLoss method) is_classification_model (InnerEye.ML.scalar_config.ScalarModelBase property) is_cross_validation_child_run() (in module InnerEye.Azure.azure_util) is_dicom_file_path() (in module InnerEye.ML.utils.io_util) is_dirty (InnerEye.Azure.azure_config.GitInformation attribute) is_ensemble_run() (in module InnerEye.Azure.azure_util) is_gpu_available() (in module InnerEye.ML.utils.ml_util) is_gpu_tensor() (in module InnerEye.Common.common_util) is_hdf5_file_path() (in module InnerEye.ML.utils.io_util) is_inference_required() (InnerEye.ML.deep_learning_config.WorkflowParams method) is_linux() (in module InnerEye.Common.common_util) is_long_path() (in module InnerEye.Common.common_util) is_missing_ground_truth() (in module InnerEye.ML.utils.metrics_util) is_model_on_gpu() (InnerEye.ML.utils.device_aware_module.DeviceAwareModule method) is_nifti_file_path() (in module InnerEye.ML.utils.io_util) is_non_imaging_model (InnerEye.ML.scalar_config.ScalarModelBase property) is_numpy_file_path() (in module InnerEye.ML.utils.io_util) is_offline_run (InnerEye.ML.deep_learning_config.WorkflowParams property) is_offline_run_context() (in module InnerEye.Azure.azure_util) is_parent_run() (in module InnerEye.Azure.azure_util) is_plotting_enabled (InnerEye.ML.config.SegmentationModelBase attribute) is_png() (in module InnerEye.ML.utils.io_util) is_private_field_name() (in module InnerEye.Common.common_util) is_regression_loss() (InnerEye.ML.scalar_config.ScalarLoss method) is_regression_model (InnerEye.ML.scalar_config.ScalarModelBase property) is_running_on_azure_agent() (in module InnerEye.Azure.azure_util) is_scalar (InnerEye.ML.deep_learning_config.ModelCategory property) is_scalar_model (InnerEye.ML.deep_learning_config.DeepLearningConfig property) is_segmentation_model (InnerEye.ML.deep_learning_config.DeepLearningConfig property) is_tensor_nan() (in module InnerEye.ML.utils.ml_util) is_tensor_nan_or_inf() (in module InnerEye.ML.utils.ml_util) is_test_from_execution_mode() (in module InnerEye.ML.utils.ml_util) is_val_dice() (in module InnerEye.ML.plotting) is_valid() (InnerEye.ML.dataset.scalar_sample.ScalarDataSource method) (InnerEye.ML.dataset.scalar_sample.ScalarItemBase method) is_valid_item_index() (in module InnerEye.ML.dataset.scalar_dataset) is_windows() (in module InnerEye.Common.common_util) items (InnerEye.ML.dataset.scalar_dataset.ScalarDataset attribute) (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase attribute) K kernel_size (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) known_settings_from_yaml (InnerEye.Azure.azure_config.ParserResult attribute) L l_rate (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_exponential_gamma (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_multi_step_gamma (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_multi_step_milestones (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_polynomial_gamma (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_scheduler (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_step_gamma (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_step_step_size (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_warmup (InnerEye.ML.deep_learning_config.OptimizerParams attribute) l_rate_warmup_epochs (InnerEye.ML.deep_learning_config.OptimizerParams attribute) Label (InnerEye.Common.metrics_constants.LoggingColumns attribute) label (InnerEye.ML.dataset.scalar_sample.ScalarItemBase attribute) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource attribute) label_channels (InnerEye.ML.scalar_config.ScalarModelBase attribute) label_smoothing_eps (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) label_value_column (InnerEye.ML.scalar_config.ScalarModelBase attribute) labels (InnerEye.ML.dataset.sample.Sample attribute) (InnerEye.ML.metrics_dict.Hue attribute) (InnerEye.ML.metrics_dict.PredictionEntry attribute) (InnerEye.ML.utils.dataset_util.DatasetExample attribute) (InnerEye.ML.utils.model_util.ScalarModelInputsAndLabels attribute) (InnerEye.ML.utils.sequence_utils.MaskedModelOutputAndLabelSequences attribute) labels_center_crop (InnerEye.ML.dataset.sample.CroppedSample attribute) labels_valid() (InnerEye.ML.dataset.scalar_sample.ScalarItemBase method) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource method) LabelTransformation (class in InnerEye.ML.scalar_config) largest_connected_component_foreground_classes (InnerEye.ML.config.SegmentationModelBase property) largest_connected_components() (in module InnerEye.ML.utils.image_util) last_encoder_layer (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoderWithMlp attribute) LayerSummary (class in InnerEye.ML.visualizers.model_summary) LEARNING_RATE (InnerEye.Common.metrics_constants.MetricType attribute) LearningRate (InnerEye.Common.metrics_constants.LoggingColumns attribute) level (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.utils.transforms.CTRange attribute) Linear (InnerEye.ML.deep_learning_config.LRWarmUpType attribute) LinearRamp (InnerEye.ML.config.PaddingMode attribute) LinearTransform (class in InnerEye.ML.utils.transforms) LinearWarmUp (class in InnerEye.ML.utils.lr_scheduler) ListOrDictParam (class in InnerEye.Common.generic_parsing) load (InnerEye.Common.resource_monitor.GpuUtilization attribute) load_all_data_sources() (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) load_checkpoint() (in module InnerEye.ML.deep_learning_config) load_checkpoint_and_modify() (InnerEye.ML.deep_learning_config.DeepLearningConfig method) load_csv() (in module InnerEye.ML.utils.csv_util) load_data_sources() (InnerEye.ML.dataset.scalar_dataset.DataSourceReader method) load_data_sources_as_per_config() (InnerEye.ML.dataset.scalar_dataset.DataSourceReader static method) load_dataset_sources() (in module InnerEye.ML.dataset.full_image_dataset) load_datasources_for_subject() (InnerEye.ML.dataset.scalar_dataset.DataSourceReader method) load_dicom_image() (in module InnerEye.ML.utils.io_util) load_dicom_series() (in module InnerEye.ML.utils.io_util) load_dicom_series_and_save() (in module InnerEye.ML.utils.io_util) load_execution_mode_metrics_from_df() (InnerEye.ML.metrics_dict.ScalarMetricsDict static method) load_ground_truth_from_run() (in module InnerEye.ML.utils.surface_distance_utils) load_hdf5_dataset_from_file() (in module InnerEye.ML.utils.io_util) load_hdf5_file() (in module InnerEye.ML.utils.io_util) load_image() (in module InnerEye.ML.utils.io_util) load_image_in_known_formats() (in module InnerEye.ML.utils.io_util) load_images() (InnerEye.ML.dataset.scalar_sample.ScalarDataSource method) load_images_and_stack() (in module InnerEye.ML.utils.io_util) load_images_from_dataset_source() (in module InnerEye.ML.utils.io_util) load_item() (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) load_labels_from_dataset_source() (in module InnerEye.ML.utils.io_util) load_nifti_image() (in module InnerEye.ML.utils.io_util) load_numpy_image() (in module InnerEye.ML.utils.io_util) load_predictions() (in module InnerEye.ML.surface_distance_heatmaps) load_segmentation (InnerEye.ML.scalar_config.ScalarModelBase attribute) load_single_data_source() (in module InnerEye.ML.dataset.scalar_dataset) load_state_dict() (InnerEye.ML.utils.lr_scheduler.SchedulerWithWarmUp method) local_dataset (InnerEye.ML.deep_learning_config.DatasetParams attribute) (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) local_weights_path (InnerEye.ML.deep_learning_config.WorkflowParams attribute) log_level (InnerEye.Azure.azure_config.AzureConfig attribute) log_metrics() (InnerEye.ML.metrics.InferenceMetricsForSegmentation method) log_summaries_to_files (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) log_to_parent_run (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) log_to_tensorboard() (InnerEye.Common.resource_monitor.ResourceMonitor method) logging_only_to_file() (in module InnerEye.Common.common_util) logging_section() (in module InnerEye.Common.common_util) logging_to_file() (in module InnerEye.Common.common_util) logging_to_stdout() (in module InnerEye.Common.common_util) LoggingColumns (class in InnerEye.Common.metrics_constants) logs_folder (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) (InnerEye.ML.deep_learning_config.OutputParams property) Loss (InnerEye.Common.metrics_constants.LoggingColumns attribute) LOSS (InnerEye.Common.metrics_constants.MetricType attribute) loss_class_weight_power (InnerEye.ML.config.SegmentationModelBase attribute) loss_type (InnerEye.ML.config.MixtureLossComponent attribute) (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.scalar_config.ScalarModelBase attribute) LOW (InnerEye.ML.utils.csv_util.OutlierType attribute) lower_class (InnerEye.ML.config.SliceExclusionRule attribute) lr (InnerEye.ML.deep_learning_config.TemperatureScalingConfig attribute) LRSchedulerType (class in InnerEye.ML.deep_learning_config) LRWarmUpType (class in InnerEye.ML.deep_learning_config) Lung (class in InnerEye.ML.configs.segmentation.Lung) M main() (in module InnerEye.ML.normalize_and_visualize_dataset) (in module InnerEye.ML.surface_distance_heatmaps) (in module InnerEye.ML.visualizers.metrics_scatterplot) make_sub_dir() (InnerEye.Common.output_directories.OutputFolderForTests method) manufacturer (InnerEye.ML.config.SegmentationModelBase attribute) map_packed_sequence_data() (in module InnerEye.ML.utils.sequence_utils) mark_outliers() (in module InnerEye.ML.utils.csv_util) mask (InnerEye.ML.dataset.sample.Sample attribute) MASK (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) (InnerEye.ML.utils.image_util.ImageDataType attribute) mask_center_crop (InnerEye.ML.dataset.sample.CroppedSample attribute) mask_channel (InnerEye.ML.dataset.sample.PatientDatasetSource attribute) mask_id (InnerEye.ML.config.SegmentationModelBase attribute) MaskedModelOutputAndLabelSequences (class in InnerEye.ML.utils.sequence_utils) max() (InnerEye.Common.resource_monitor.GpuUtilization method) max_batch_grad_cam (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) max_dice (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) max_iter (InnerEye.ML.deep_learning_config.TemperatureScalingConfig attribute) max_num_gpus (InnerEye.ML.deep_learning_config.TrainerParams attribute) max_run_duration (InnerEye.Azure.azure_config.AzureConfig attribute) Maximum (InnerEye.ML.config.PaddingMode attribute) MaxPooling (class in InnerEye.ML.models.layers.pooling_layers) (InnerEye.ML.scalar_config.AggregationType attribute) Mean (InnerEye.ML.config.PaddingMode attribute) mean (InnerEye.ML.utils.features_util.FeatureStatistics attribute) MEAN_ABSOLUTE_ERROR (InnerEye.Common.metrics_constants.MetricType attribute) mean_absolute_error() (in module InnerEye.ML.utils.metrics_util) MEAN_SQUARED_ERROR (InnerEye.Common.metrics_constants.MetricType attribute) mean_squared_error() (in module InnerEye.ML.utils.metrics_util) MEAN_SURFACE_DIST_mm (InnerEye.Common.metrics_constants.MetricType attribute) mean_teacher_alpha (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) MeanAbsoluteError (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) MeanDistanceMM (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) MeanSquaredError (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.ML.scalar_config.ScalarLoss attribute) Median (InnerEye.ML.config.PaddingMode attribute) MedicalImageFileType (class in InnerEye.ML.utils.io_util) mem_allocated_gb (InnerEye.Common.resource_monitor.GpuUtilization attribute) mem_reserved_gb (InnerEye.Common.resource_monitor.GpuUtilization attribute) mem_util (InnerEye.Common.resource_monitor.GpuUtilization attribute) memory_in_gb() (in module InnerEye.Common.resource_monitor) merge_conda_files() (in module InnerEye.Common.common_util) merge_masks() (in module InnerEye.ML.utils.image_util) metadata (InnerEye.ML.dataset.sample.PatientDatasetSource attribute) (InnerEye.ML.dataset.sample.Sample attribute) (InnerEye.ML.dataset.scalar_sample.ScalarItemBase attribute) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource attribute) MetricForMultipleStructures (class in InnerEye.ML.lightning_metrics) metrics (InnerEye.ML.metrics.InferenceMetricsForClassification attribute) (InnerEye.ML.metrics.InferenceMetricsForSegmentation attribute) metrics_scatterplot() (in module InnerEye.ML.visualizers.metrics_scatterplot) metrics_scatterplot_from_dicts() (in module InnerEye.ML.visualizers.metrics_scatterplot) MetricsDict (class in InnerEye.ML.metrics_dict) MetricsFileColumns (class in InnerEye.Common.metrics_constants) MetricsPerPatientWriter (class in InnerEye.ML.utils.metrics_util) MetricsScatterplotConfig (class in InnerEye.ML.visualizers.metrics_scatterplot) MetricType (class in InnerEye.Common.metrics_constants) min_dice (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) min_l_rate (InnerEye.ML.deep_learning_config.OptimizerParams property) Minimum (InnerEye.ML.config.PaddingMode attribute) MixPooling (class in InnerEye.ML.models.layers.pooling_layers) (InnerEye.ML.scalar_config.AggregationType attribute) Mixture (InnerEye.ML.config.SegmentationLoss attribute) mixture_loss_components (InnerEye.ML.config.SegmentationModelBase attribute) MixtureLoss (class in InnerEye.ML.models.losses.mixture) MixtureLossComponent (class in InnerEye.ML.config) MLP (class in InnerEye.ML.models.architectures.mlp) MLP.HiddenLayer (class in InnerEye.ML.models.architectures.mlp) Modality (InnerEye.ML.utils.io_util.DicomTags attribute) model (InnerEye.Azure.azure_config.AzureConfig attribute) model_category (InnerEye.ML.deep_learning_config.DeepLearningConfig property) model_configs_namespace (InnerEye.ML.model_inference_config.ModelInferenceConfig attribute) (InnerEye.ML.utils.config_loader.ModelConfigLoader attribute) model_id (InnerEye.ML.deep_learning_config.WorkflowParams attribute) model_inputs (InnerEye.ML.utils.model_util.ScalarModelInputsAndLabels attribute) model_name (InnerEye.ML.deep_learning_config.OutputParams property) (InnerEye.ML.model_inference_config.ModelInferenceConfig attribute) (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) model_outputs (InnerEye.ML.utils.sequence_utils.MaskedModelOutputAndLabelSequences attribute) ModelArchitectureConfig (class in InnerEye.ML.config) ModelCategory (class in InnerEye.ML.deep_learning_config) ModelConfigBase (class in InnerEye.ML.model_config_base) ModelConfigBaseMeta (class in InnerEye.ML.model_config_base) ModelConfigLoader (class in InnerEye.ML.utils.config_loader) ModelExecutionMode (class in InnerEye.ML.common) (InnerEye.Common.metrics_constants.LoggingColumns attribute) ModelInferenceConfig (class in InnerEye.ML.model_inference_config) ModelOutput (InnerEye.Common.metrics_constants.LoggingColumns attribute) ModelProcessing (class in InnerEye.Common.common_util) ModelSummary (class in InnerEye.ML.visualizers.model_summary) ModelTransformsPerExecutionMode (class in InnerEye.ML.model_config_base) ModelWithTemperature (class in InnerEye.ML.utils.temperature_scaling) module InnerEye.Azure.azure_config InnerEye.Azure.azure_runner InnerEye.Azure.azure_util InnerEye.Azure.parser_util InnerEye.Azure.secrets_handling InnerEye.Common.common_util InnerEye.Common.fixed_paths InnerEye.Common.fixed_paths_for_tests InnerEye.Common.generic_parsing InnerEye.Common.metrics_constants InnerEye.Common.output_directories InnerEye.Common.resource_monitor InnerEye.Common.spawn_subprocess InnerEye.ML.augmentations.augmentation_for_segmentation_utils InnerEye.ML.augmentations.image_transforms InnerEye.ML.augmentations.transform_pipeline InnerEye.ML.common InnerEye.ML.config InnerEye.ML.configs.regression.DummyRegression InnerEye.ML.configs.segmentation.BasicModel2Epochs InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData InnerEye.ML.configs.segmentation.GbmBase InnerEye.ML.configs.segmentation.HeadAndNeckBase InnerEye.ML.configs.segmentation.HeadAndNeckPaper InnerEye.ML.configs.segmentation.HelloWorld InnerEye.ML.configs.segmentation.Hippocampus InnerEye.ML.configs.segmentation.Lung InnerEye.ML.configs.segmentation.ProstateBase InnerEye.ML.configs.segmentation.ProstatePaper InnerEye.ML.dataset.cropping_dataset InnerEye.ML.dataset.full_image_dataset InnerEye.ML.dataset.sample InnerEye.ML.dataset.scalar_dataset InnerEye.ML.dataset.scalar_sample InnerEye.ML.deep_learning_config InnerEye.ML.lightning_metrics InnerEye.ML.metrics InnerEye.ML.metrics_dict InnerEye.ML.model_config_base InnerEye.ML.model_inference_config InnerEye.ML.models.architectures.base_model InnerEye.ML.models.architectures.classification.bit InnerEye.ML.models.architectures.classification.image_encoder_with_mlp InnerEye.ML.models.architectures.classification.segmentation_encoder InnerEye.ML.models.architectures.complex InnerEye.ML.models.architectures.mlp InnerEye.ML.models.architectures.unet_2d InnerEye.ML.models.architectures.unet_3d InnerEye.ML.models.blocks.residual InnerEye.ML.models.layers.basic InnerEye.ML.models.layers.identity InnerEye.ML.models.layers.pooling_layers InnerEye.ML.models.layers.weight_standardization InnerEye.ML.models.losses.cross_entropy InnerEye.ML.models.losses.ece InnerEye.ML.models.losses.mixture InnerEye.ML.models.losses.soft_dice InnerEye.ML.normalize_and_visualize_dataset InnerEye.ML.photometric_normalization InnerEye.ML.plotting InnerEye.ML.scalar_config InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets InnerEye.ML.SSL.datamodules_and_datasets.dataset_cls_utils InnerEye.ML.surface_distance_heatmaps InnerEye.ML.utils.config_loader InnerEye.ML.utils.csv_util InnerEye.ML.utils.dataset_util InnerEye.ML.utils.device_aware_module InnerEye.ML.utils.features_util InnerEye.ML.utils.hdf5_util InnerEye.ML.utils.image_util InnerEye.ML.utils.io_util InnerEye.ML.utils.layer_util InnerEye.ML.utils.lr_scheduler InnerEye.ML.utils.metrics_util InnerEye.ML.utils.ml_util InnerEye.ML.utils.model_metadata_util InnerEye.ML.utils.model_util InnerEye.ML.utils.plotting_util InnerEye.ML.utils.run_recovery InnerEye.ML.utils.sequence_utils InnerEye.ML.utils.split_dataset InnerEye.ML.utils.supervised_criterion InnerEye.ML.utils.surface_distance_utils InnerEye.ML.utils.temperature_scaling InnerEye.ML.utils.transforms InnerEye.ML.visualizers.activation_maps InnerEye.ML.visualizers.metrics_scatterplot InnerEye.ML.visualizers.model_hooks InnerEye.ML.visualizers.model_summary InnerEye.ML.visualizers.patch_sampling InnerEye.ML.visualizers.regression_visualization InnerEye.ML.visualizers.reliability_curve momentum (InnerEye.ML.deep_learning_config.OptimizerParams attribute) monitor_gpu (InnerEye.ML.deep_learning_config.TrainerParams attribute) monitor_loading (InnerEye.ML.deep_learning_config.TrainerParams attribute) monitoring_interval_seconds (InnerEye.ML.deep_learning_config.WorkflowParams attribute) MONOCHROME1 (InnerEye.ML.utils.io_util.PhotometricInterpretation attribute) MONOCHROME2 (InnerEye.ML.utils.io_util.PhotometricInterpretation attribute) move_to_device() (InnerEye.ML.utils.model_util.ScalarModelInputsAndLabels method) mri_window() (in module InnerEye.ML.photometric_normalization) MriWindow (InnerEye.ML.config.PhotometricNormalizationMethod attribute) multi_label_array_to_binary() (in module InnerEye.ML.utils.image_util) multiprocessing_start_method (InnerEye.ML.deep_learning_config.WorkflowParams attribute) MultiprocessingStartMethod (class in InnerEye.ML.deep_learning_config) MultiSegmentationEncoder (class in InnerEye.ML.models.architectures.classification.segmentation_encoder) MultiStep (InnerEye.ML.deep_learning_config.LRSchedulerType attribute) N n_obs (InnerEye.ML.lightning_metrics.ExplainedVariance attribute) n_params (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) n_trainable_params (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) name (InnerEye.Azure.azure_config.AzureConfig attribute) (InnerEye.Common.generic_parsing.GenericConfig attribute) (InnerEye.Common.resource_monitor.GpuUtilization property) (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.configs.regression.DummyRegression.DummyRegression attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModel2Epochs attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModelForEnsembleTest attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel.BasicModel2Epochs1Channel attribute) (InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData.BasicModel2EpochsMoreData attribute) (InnerEye.ML.configs.segmentation.GbmBase.GbmBase attribute) (InnerEye.ML.configs.segmentation.HeadAndNeckBase.HeadAndNeckBase attribute) (InnerEye.ML.configs.segmentation.HeadAndNeckPaper.HeadAndNeckPaper attribute) (InnerEye.ML.configs.segmentation.HelloWorld.HelloWorld attribute) (InnerEye.ML.configs.segmentation.Hippocampus.Hippocampus attribute) (InnerEye.ML.configs.segmentation.Lung.Lung attribute) (InnerEye.ML.configs.segmentation.ProstateBase.ProstateBase attribute) (InnerEye.ML.configs.segmentation.ProstatePaper.ProstatePaper attribute) (InnerEye.ML.deep_learning_config.DatasetParams attribute) (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) (InnerEye.ML.deep_learning_config.OptimizerParams attribute) (InnerEye.ML.deep_learning_config.OutputParams attribute) (InnerEye.ML.deep_learning_config.TemperatureScalingConfig attribute) (InnerEye.ML.deep_learning_config.TrainerParams attribute) (InnerEye.ML.deep_learning_config.WorkflowParams attribute) (InnerEye.ML.metrics_dict.Hue attribute) (InnerEye.ML.model_config_base.ModelConfigBase attribute) (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) (InnerEye.ML.photometric_normalization.PhotometricNormalization attribute) (InnerEye.ML.photometric_normalization.WindowNormalizationForScalarItem attribute) (InnerEye.ML.scalar_config.ScalarModelBase attribute) (InnerEye.ML.utils.config_loader.ModelConfigLoader attribute) (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) (InnerEye.ML.utils.transforms.CTRange attribute) (InnerEye.ML.utils.transforms.LinearTransform attribute) (InnerEye.ML.utils.transforms.Transform3D attribute) (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) namespace_to_path() (in module InnerEye.Common.common_util) nanmean() (in module InnerEye.ML.lightning_metrics) NIFTI (InnerEye.ML.utils.io_util.MedicalImageFileType attribute) NIFTI_COMPRESSED_GZ (InnerEye.ML.utils.io_util.MedicalImageFileType attribute) NIHCXR (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) non_image_feature_channels (InnerEye.ML.scalar_config.ScalarModelBase attribute) NoPadding (InnerEye.ML.config.PaddingMode attribute) norm_method (InnerEye.ML.config.SegmentationModelBase attribute) normalize_trim() (in module InnerEye.ML.photometric_normalization) NormalizeAndVisualizeConfig (class in InnerEye.ML.normalize_and_visualize_dataset) NoWarmUp (InnerEye.ML.deep_learning_config.LRWarmUpType attribute) num_classes (InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets.InnerEyeCIFAR10 property) (InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets.InnerEyeCIFAR100 property) (InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets.CovidDataset property) (InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets.RSNAKaggleCXR property) (InnerEye.ML.SSL.datamodules_and_datasets.dataset_cls_utils.InnerEyeDataClassBaseWithReturnIndex property) num_dataload_workers (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) num_dataset_reader_workers (InnerEye.ML.scalar_config.ScalarModelBase attribute) num_downsampling_paths (InnerEye.ML.config.SegmentationModelBase attribute) num_entries() (InnerEye.ML.metrics_dict.MetricsDict method) num_epochs (InnerEye.ML.deep_learning_config.TrainerParams attribute) num_gpus_per_node() (InnerEye.ML.deep_learning_config.TrainerParams method) num_nodes (InnerEye.Azure.azure_config.AzureConfig attribute) num_workers (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) number_of_classes (InnerEye.ML.config.SegmentationModelBase property) number_of_cross_validation_splits (InnerEye.ML.deep_learning_config.WorkflowParams attribute) number_of_image_channels (InnerEye.ML.config.SegmentationModelBase property) number_of_subjects() (InnerEye.ML.utils.split_dataset.DatasetSplits method) number_samples (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) numerical_columns (InnerEye.ML.scalar_config.ScalarModelBase attribute) numerical_non_image_features (InnerEye.ML.dataset.scalar_sample.ScalarItemBase attribute) (InnerEye.ML.dataset.scalar_sample.SequenceDataSource attribute) NUMPY (InnerEye.ML.utils.io_util.NumpyFile attribute) NUMPY_COMPRESSED (InnerEye.ML.utils.io_util.NumpyFile attribute) numpy_random_state (InnerEye.ML.utils.ml_util.RandomStateSnapshot attribute) NumpyFile (class in InnerEye.ML.utils.io_util) NumTrainableParameters (InnerEye.Common.metrics_constants.LoggingColumns attribute) O one_hot_encoder (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase attribute) one_hot_to_class_indices() (in module InnerEye.ML.utils.image_util) OneHotEncoderBase (class in InnerEye.ML.common) only_first (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) only_register_model (InnerEye.Azure.azure_config.AzureConfig attribute) opt_eps (InnerEye.ML.deep_learning_config.OptimizerParams attribute) OPTIMAL_THRESHOLD (InnerEye.Common.metrics_constants.MetricType attribute) OptimalThreshold (class in InnerEye.ML.lightning_metrics) (InnerEye.Common.metrics_constants.LoggingColumns attribute) optimizer_type (InnerEye.ML.deep_learning_config.OptimizerParams attribute) OptimizerParams (class in InnerEye.ML.deep_learning_config) OptimizerType (class in InnerEye.ML.deep_learning_config) origin (InnerEye.ML.utils.image_util.ImageHeader attribute) out_channels (InnerEye.ML.models.architectures.classification.segmentation_encoder.SegmentationEncoder property) (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) outlier_range (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) OUTLIERS (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceRunType attribute) OutlierType (class in InnerEye.ML.utils.csv_util) output_folder (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) output_img_dir (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) output_memory_megabytes (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) output_padding (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) output_range (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.utils.transforms.CTRange attribute) (InnerEye.ML.utils.transforms.LinearTransform attribute) output_shape (InnerEye.ML.visualizers.model_summary.LayerSummary attribute) output_to (InnerEye.ML.deep_learning_config.OutputParams attribute) OutputFolderForTests (class in InnerEye.Common.output_directories) OutputParams (class in InnerEye.ML.deep_learning_config) outputs_folder (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) (InnerEye.ML.deep_learning_config.OutputParams property) overrides (InnerEye.Azure.azure_config.ParserResult attribute) P pad_images() (in module InnerEye.ML.utils.image_util) pad_images_for_inference() (in module InnerEye.ML.utils.image_util) padding (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) padding_mode (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) PaddingMode (class in InnerEye.ML.config) param (InnerEye.Azure.azure_config.AzureConfig attribute) (InnerEye.Common.generic_parsing.GenericConfig attribute) (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.configs.regression.DummyRegression.DummyRegression attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModel2Epochs attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModelForEnsembleTest attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel.BasicModel2Epochs1Channel attribute) (InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData.BasicModel2EpochsMoreData attribute) (InnerEye.ML.configs.segmentation.GbmBase.GbmBase attribute) (InnerEye.ML.configs.segmentation.HeadAndNeckBase.HeadAndNeckBase attribute) (InnerEye.ML.configs.segmentation.HeadAndNeckPaper.HeadAndNeckPaper attribute) (InnerEye.ML.configs.segmentation.HelloWorld.HelloWorld attribute) (InnerEye.ML.configs.segmentation.Hippocampus.Hippocampus attribute) (InnerEye.ML.configs.segmentation.Lung.Lung attribute) (InnerEye.ML.configs.segmentation.ProstateBase.ProstateBase attribute) (InnerEye.ML.configs.segmentation.ProstatePaper.ProstatePaper attribute) (InnerEye.ML.deep_learning_config.DatasetParams attribute) (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) (InnerEye.ML.deep_learning_config.OptimizerParams attribute) (InnerEye.ML.deep_learning_config.OutputParams attribute) (InnerEye.ML.deep_learning_config.TemperatureScalingConfig attribute) (InnerEye.ML.deep_learning_config.TrainerParams attribute) (InnerEye.ML.deep_learning_config.WorkflowParams attribute) (InnerEye.ML.model_config_base.ModelConfigBase attribute) (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) (InnerEye.ML.photometric_normalization.PhotometricNormalization attribute) (InnerEye.ML.photometric_normalization.WindowNormalizationForScalarItem attribute) (InnerEye.ML.scalar_config.ScalarModelBase attribute) (InnerEye.ML.utils.config_loader.ModelConfigLoader attribute) (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) (InnerEye.ML.utils.transforms.CTRange attribute) (InnerEye.ML.utils.transforms.LinearTransform attribute) (InnerEye.ML.utils.transforms.Transform3D attribute) (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) (InnerEye.ML.visualizers.patch_sampling.CheckPatchSamplingConfig attribute) parse_acquisition_date() (InnerEye.ML.utils.hdf5_util.HDF5Object static method) parse_args() (InnerEye.Common.generic_parsing.GenericConfig class method) parse_args_and_add_yaml_variables() (in module InnerEye.Azure.azure_runner) parse_arguments() (in module InnerEye.Azure.azure_runner) parse_restriction_pattern() (InnerEye.ML.utils.split_dataset.DatasetSplits static method) ParserResult (class in InnerEye.Azure.azure_config) partition_model() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) (InnerEye.ML.models.architectures.unet_3d.UNet3D method) PATCH_CENTER (InnerEye.Common.metrics_constants.MetricType attribute) path_to_namespace() (in module InnerEye.Common.common_util) PathOrPathList (class in InnerEye.Common.generic_parsing) Patient (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) patient_id (InnerEye.ML.dataset.sample.PatientMetadata attribute) (InnerEye.ML.dataset.sample.Sample property) (InnerEye.ML.utils.dataset_util.DatasetExample attribute) PATIENT_ID (InnerEye.ML.utils.hdf5_util.HDF5Field attribute) PatientDatasetSource (class in InnerEye.ML.dataset.sample) PatientMetadata (class in InnerEye.ML.dataset.sample) PatientPosition (InnerEye.ML.utils.io_util.DicomTags attribute) perform_cross_validation (InnerEye.ML.deep_learning_config.WorkflowParams property) PhotometricInterpretation (class in InnerEye.ML.utils.io_util) (InnerEye.ML.utils.io_util.DicomTags attribute) PhotometricNormalization (class in InnerEye.ML.photometric_normalization) PhotometricNormalizationMethod (class in InnerEye.ML.config) pin_memory (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) pip_extra_index_url (InnerEye.Azure.azure_config.AzureConfig attribute) PixelRepresentation (InnerEye.ML.utils.io_util.DicomTags attribute) pl_check_val_every_n_epoch (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_deterministic (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_find_unused_parameters (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_limit_train_batches (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_limit_val_batches (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_num_sanity_val_steps (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_profiler (InnerEye.ML.deep_learning_config.TrainerParams attribute) pl_progress_bar_refresh_rate (InnerEye.ML.deep_learning_config.TrainerParams attribute) Plane (class in InnerEye.ML.utils.surface_distance_utils) plane (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) plot_before_after_statistics() (in module InnerEye.ML.plotting) plot_contours_for_all_classes() (in module InnerEye.ML.plotting) plot_image_and_label_contour() (in module InnerEye.ML.plotting) plot_loss_per_epoch() (in module InnerEye.ML.plotting) plot_normalization_result() (in module InnerEye.ML.plotting) plot_reliability_curve() (in module InnerEye.ML.visualizers.reliability_curve) plot_val_dice_per_epoch() (in module InnerEye.ML.plotting) plot_variation_error_prediction() (in module InnerEye.ML.visualizers.regression_visualization) Polynomial (InnerEye.ML.deep_learning_config.LRSchedulerType attribute) PolynomialLR (class in InnerEye.ML.utils.lr_scheduler) posterior_smoothing_mm (InnerEye.ML.config.SegmentationModelBase attribute) posteriors_to_segmentation() (in module InnerEye.ML.utils.image_util) pre_process_dataset_dataframe() (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) prediction (InnerEye.ML.utils.dataset_util.DatasetExample attribute) PredictionEntry (class in InnerEye.ML.metrics_dict) predictions (InnerEye.ML.metrics_dict.Hue attribute) (InnerEye.ML.metrics_dict.PredictionEntry attribute) prefetch_factor (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) prefixes (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) pretraining_run_checkpoints (InnerEye.ML.configs.segmentation.BasicModel2Epochs.BasicModelForEnsembleTest attribute) (InnerEye.ML.configs.segmentation.BasicModel2Epochs1Channel.BasicModel2Epochs1Channel attribute) (InnerEye.ML.configs.segmentation.BasicModel2EpochsMoreData.BasicModel2EpochsMoreData attribute) (InnerEye.ML.configs.segmentation.HeadAndNeckPaper.HeadAndNeckPaper attribute) (InnerEye.ML.configs.segmentation.ProstatePaper.ProstatePaper attribute) pretraining_run_recovery_id (InnerEye.ML.deep_learning_config.WorkflowParams attribute) print_exception() (in module InnerEye.Common.common_util) project_root (InnerEye.Azure.azure_config.AzureConfig attribute) (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) PROPORTION_FOREGROUND_VOXELS (InnerEye.Common.metrics_constants.MetricType attribute) props (InnerEye.ML.dataset.sample.GeneralSampleMetadata attribute) (InnerEye.ML.dataset.scalar_sample.ScalarItemBase property) ProstateBase (class in InnerEye.ML.configs.segmentation.ProstateBase) ProstatePaper (class in InnerEye.ML.configs.segmentation.ProstatePaper) pytest_mark (InnerEye.Azure.azure_config.AzureConfig attribute) Q QUANTITY (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) R r2_score() (in module InnerEye.ML.utils.metrics_util) random_colour() (in module InnerEye.ML.utils.model_metadata_util) random_crop() (in module InnerEye.ML.augmentations.augmentation_for_segmentation_utils) random_seed (InnerEye.ML.deep_learning_config.WorkflowParams attribute) random_select_patch_center() (in module InnerEye.ML.augmentations.augmentation_for_segmentation_utils) random_state (InnerEye.ML.utils.ml_util.RandomStateSnapshot attribute) RandomGamma (class in InnerEye.ML.augmentations.image_transforms) RandomStateSnapshot (class in InnerEye.ML.utils.ml_util) read_aggregate_metrics() (InnerEye.Common.resource_monitor.ResourceMonitor method) read_all_settings() (in module InnerEye.Azure.secrets_handling) read_dataset_if_needed() (InnerEye.ML.model_config_base.ModelConfigBase method) read_dataset_into_dataframe_and_pre_process() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.model_config_base.ModelConfigBase method) (InnerEye.ML.scalar_config.ScalarModelBase method) read_image_as_array_with_header() (in module InnerEye.ML.utils.io_util) read_model_inference_config() (in module InnerEye.ML.model_inference_config) read_secrets_from_file() (InnerEye.Azure.secrets_handling.SecretsHandling method) read_settings_and_merge() (in module InnerEye.Azure.secrets_handling) read_settings_yaml_file() (in module InnerEye.Azure.secrets_handling) reason_not_overridable() (InnerEye.Common.generic_parsing.GenericConfig static method) Reflect (InnerEye.ML.config.PaddingMode attribute) Regression (InnerEye.ML.deep_learning_config.ModelCategory attribute) regression_test_csv_tolerance (InnerEye.ML.deep_learning_config.WorkflowParams attribute) regression_test_folder (InnerEye.ML.deep_learning_config.WorkflowParams attribute) remove_and_create_folder() (in module InnerEye.Common.output_directories) remove_file_or_directory() (in module InnerEye.Common.common_util) RepeatDataLoader (class in InnerEye.ML.dataset.full_image_dataset) report_on_overrides() (InnerEye.Common.generic_parsing.GenericConfig method) repository (InnerEye.Azure.azure_config.GitInformation attribute) repository_parent_directory() (in module InnerEye.Common.fixed_paths) repository_root_directory() (in module InnerEye.Common.fixed_paths) RescaleIntercept (InnerEye.ML.utils.io_util.DicomTags attribute) RescaleSlope (InnerEye.ML.utils.io_util.DicomTags attribute) reset() (InnerEye.ML.lightning_metrics.MetricForMultipleStructures method) ResidualBlock (class in InnerEye.ML.models.blocks.residual) resize_and_save() (in module InnerEye.ML.plotting) ResNetV2Block (class in InnerEye.ML.models.architectures.classification.bit) ResNetV2Layer (class in InnerEye.ML.models.architectures.classification.bit) resource_group (InnerEye.Azure.azure_config.AzureConfig attribute) ResourceMonitor (class in InnerEye.Common.resource_monitor) restore_random_state() (InnerEye.ML.utils.ml_util.RandomStateSnapshot method) restrict_crop_size_to_image() (InnerEye.ML.models.architectures.base_model.CropSizeConstraints method) restrict_subjects (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) restrict_subjects() (InnerEye.ML.utils.split_dataset.DatasetSplits method) result_folder (InnerEye.ML.normalize_and_visualize_dataset.NormalizeAndVisualizeConfig attribute) reverse_tuple_float3() (in module InnerEye.ML.utils.io_util) rms_alpha (InnerEye.ML.deep_learning_config.OptimizerParams attribute) RMSprop (InnerEye.ML.deep_learning_config.OptimizerType attribute) robust_mean_std() (in module InnerEye.ML.photometric_normalization) roi_interpreted_types (InnerEye.ML.config.SegmentationModelBase attribute) root_dir (InnerEye.Common.output_directories.OutputFolderForTests attribute) root_folder (InnerEye.Azure.azure_config.SourceConfig attribute) row_labels (InnerEye.ML.metrics_dict.ScalarMetricsDict attribute) (InnerEye.ML.metrics_dict.SequenceMetricsDict attribute) RSNAKaggleCXR (class in InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets) run() (InnerEye.Common.resource_monitor.ResourceMonitor method) run_duration_string_to_seconds() (in module InnerEye.Azure.azure_runner) run_folder (InnerEye.ML.deep_learning_config.DeepLearningFileSystemConfig attribute) run_mode (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) run_recovery_id (InnerEye.Azure.azure_config.AzureConfig attribute) (InnerEye.ML.utils.surface_distance_utils.SurfaceDistanceConfig attribute) RunRecovery (class in InnerEye.ML.utils.run_recovery) S SAGITTAL (InnerEye.ML.utils.surface_distance_utils.Plane attribute) Sample (class in InnerEye.ML.dataset.sample) SampleBase (class in InnerEye.ML.dataset.sample) sampler (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) satisfies_prefixes() (in module InnerEye.ML.visualizers.metrics_scatterplot) save_aggregates_to_csv() (InnerEye.ML.utils.metrics_util.MetricsPerPatientWriter method) save_lines_to_file() (in module InnerEye.ML.utils.io_util) ScalarDataset (class in InnerEye.ML.dataset.scalar_dataset) ScalarDatasetBase (class in InnerEye.ML.dataset.scalar_dataset) ScalarDataSource (class in InnerEye.ML.dataset.scalar_sample) ScalarItem (class in InnerEye.ML.dataset.scalar_sample) ScalarItemAugmentation (class in InnerEye.ML.dataset.scalar_dataset) ScalarItemBase (class in InnerEye.ML.dataset.scalar_sample) ScalarLoss (class in InnerEye.ML.scalar_config) ScalarMetricsBase (class in InnerEye.ML.lightning_metrics) ScalarMetricsDict (class in InnerEye.ML.metrics_dict) ScalarModelBase (class in InnerEye.ML.scalar_config) ScalarModelInputsAndLabels (class in InnerEye.ML.utils.model_util) scan_with_transparent_overlay() (in module InnerEye.ML.plotting) SchedulerWithWarmUp (class in InnerEye.ML.utils.lr_scheduler) schema() (InnerEye.ML.model_inference_config.ModelInferenceConfig class method) script_params (InnerEye.Azure.azure_config.SourceConfig attribute) second_class (InnerEye.ML.config.SummedProbabilityRule attribute) SecretsHandling (class in InnerEye.Azure.secrets_handling) Segmentation (class in InnerEye.ML.surface_distance_heatmaps) (InnerEye.ML.deep_learning_config.ModelCategory attribute) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImagingFeatureType attribute) SEGMENTATION (InnerEye.ML.utils.hdf5_util.HDF5Field attribute) (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) (InnerEye.ML.utils.image_util.ImageDataType attribute) segmentation_and_groundtruth_plot() (in module InnerEye.ML.plotting) segmentation_path (InnerEye.ML.surface_distance_heatmaps.Segmentation attribute) segmentation_to_one_hot() (in module InnerEye.ML.utils.image_util) SegmentationEncoder (class in InnerEye.ML.models.architectures.classification.segmentation_encoder) SegmentationLoss (class in InnerEye.ML.config) SegmentationModelBase (class in InnerEye.ML.config) segmentations (InnerEye.ML.dataset.scalar_sample.ScalarItem attribute) (InnerEye.ML.utils.io_util.ImageAndSegmentations attribute) sequence_position (InnerEye.ML.dataset.sample.GeneralSampleMetadata attribute) SequenceDataSource (class in InnerEye.ML.dataset.scalar_sample) SequenceLength (InnerEye.Common.metrics_constants.LoggingColumns attribute) SequenceMetricsDict (class in InnerEye.ML.metrics_dict) sequences_to_padded_tensor() (in module InnerEye.ML.utils.sequence_utils) Series (InnerEye.Common.metrics_constants.LoggingColumns attribute) series (InnerEye.ML.dataset.sample.PatientMetadata attribute) SeriesInstanceUID (InnerEye.ML.utils.io_util.DicomTags attribute) set_derived_model_properties() (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.model_config_base.ModelConfigBase method) set_environment_variables_for_multi_node() (in module InnerEye.Azure.azure_runner) set_hook() (InnerEye.Common.generic_parsing.PathOrPathList method) (InnerEye.Common.generic_parsing.StringOrStringList method) set_model_to_eval_mode() (in module InnerEye.ML.utils.layer_util) set_output_to() (InnerEye.ML.deep_learning_config.OutputParams method) set_random_seed() (in module InnerEye.ML.utils.ml_util) set_temperature() (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature method) SGD (InnerEye.ML.deep_learning_config.OptimizerType attribute) sharpen (InnerEye.ML.config.SegmentationModelBase attribute) should_generate_multilabel_report() (InnerEye.ML.scalar_config.ScalarModelBase method) show_patch_sampling (InnerEye.ML.config.SegmentationModelBase attribute) shuffle (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) simple_norm() (in module InnerEye.ML.photometric_normalization) SimpleNorm (InnerEye.ML.config.PhotometricNormalizationMethod attribute) skip_nan_when_averaging (InnerEye.ML.metrics_dict.ScalarMetricsDict attribute) (InnerEye.ML.metrics_dict.SequenceMetricsDict attribute) slice_exclusion_rules (InnerEye.ML.config.SegmentationModelBase attribute) SliceExclusionRule (class in InnerEye.ML.config) slicers_for_random_crop() (in module InnerEye.ML.augmentations.augmentation_for_segmentation_utils) snapshot_random_state() (InnerEye.ML.utils.ml_util.RandomStateSnapshot static method) SoftDice (InnerEye.ML.config.SegmentationLoss attribute) SoftDiceLoss (class in InnerEye.ML.models.losses.soft_dice) SourceConfig (class in InnerEye.Azure.azure_config) spacing (InnerEye.ML.utils.image_util.ImageHeader attribute) spawn (InnerEye.ML.deep_learning_config.MultiprocessingStartMethod attribute) spawn_and_monitor_subprocess() (in module InnerEye.Common.spawn_subprocess) split_recovery_id() (in module InnerEye.Azure.azure_util) standardize() (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d static method) (InnerEye.ML.utils.features_util.FeatureStatistics method) standardize_log_level() (in module InnerEye.Common.common_util) standardize_non_imaging_features() (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase method) state_dict() (InnerEye.ML.utils.lr_scheduler.SchedulerWithWarmUp method) status (InnerEye.ML.dataset.scalar_dataset.ScalarDatasetBase attribute) std (InnerEye.ML.utils.features_util.FeatureStatistics attribute) Step (InnerEye.ML.deep_learning_config.LRSchedulerType attribute) step() (InnerEye.ML.utils.lr_scheduler.SchedulerWithWarmUp method) step_up_directories() (in module InnerEye.Azure.azure_util) store_and_upload_example() (in module InnerEye.ML.utils.dataset_util) store_as_nifti() (in module InnerEye.ML.utils.io_util) store_as_scaled_ubyte_nifti() (in module InnerEye.ML.utils.io_util) store_as_ubyte_nifti() (in module InnerEye.ML.utils.io_util) store_binary_mask_as_nifti() (in module InnerEye.ML.utils.io_util) store_dataset_sample (InnerEye.ML.config.SegmentationModelBase attribute) store_epoch_metrics() (in module InnerEye.ML.metrics) store_image_as_short_nifti() (in module InnerEye.ML.utils.io_util) store_metrics_per_subject() (InnerEye.ML.metrics_dict.ScalarMetricsDict method) store_posteriors_as_nifti() (in module InnerEye.ML.utils.io_util) store_to_file() (InnerEye.Common.resource_monitor.ResourceMonitor method) stride (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) string_to_integer_list() (in module InnerEye.ML.utils.ml_util) string_to_path() (in module InnerEye.Common.common_util) StringOrStringList (class in InnerEye.Common.generic_parsing) strip_prefix() (in module InnerEye.Azure.azure_util) Structure (InnerEye.Common.metrics_constants.LoggingColumns attribute) (InnerEye.Common.metrics_constants.MetricsFileColumns attribute) structure_name (InnerEye.ML.surface_distance_heatmaps.Segmentation attribute) StudyID (InnerEye.ML.utils.io_util.DicomTags attribute) StudyInstanceUID (InnerEye.ML.utils.io_util.DicomTags attribute) subject_column (InnerEye.ML.scalar_config.ScalarModelBase attribute) (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) SUBJECT_COUNT (InnerEye.Common.metrics_constants.MetricType attribute) subject_id (InnerEye.ML.metrics_dict.PredictionEntry attribute) (InnerEye.ML.surface_distance_heatmaps.Segmentation attribute) subject_ids (InnerEye.ML.metrics_dict.Hue attribute) (InnerEye.ML.utils.model_util.ScalarModelInputsAndLabels attribute) (InnerEye.ML.utils.sequence_utils.MaskedModelOutputAndLabelSequences attribute) subject_ids() (InnerEye.ML.metrics_dict.MetricsDict method) SubjectCount (InnerEye.Common.metrics_constants.LoggingColumns attribute) subscription_id (InnerEye.Azure.azure_config.AzureConfig attribute) sum_abs_error (InnerEye.ML.lightning_metrics.MeanAbsoluteError attribute) sum_error (InnerEye.ML.lightning_metrics.ExplainedVariance attribute) sum_squared_error (InnerEye.ML.lightning_metrics.ExplainedVariance attribute) (InnerEye.ML.lightning_metrics.MeanSquaredError attribute) sum_squared_target (InnerEye.ML.lightning_metrics.ExplainedVariance attribute) sum_target (InnerEye.ML.lightning_metrics.ExplainedVariance attribute) summarizer (InnerEye.ML.models.architectures.complex.ComplexModel attribute) (InnerEye.ML.models.architectures.unet_2d.UNet2D attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D attribute) summary (InnerEye.ML.models.architectures.complex.ComplexModel attribute) (InnerEye.ML.models.architectures.unet_2d.UNet2D attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D attribute) summary_crop_size (InnerEye.ML.models.architectures.complex.ComplexModel attribute) (InnerEye.ML.models.architectures.unet_2d.UNet2D attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D attribute) summary_for_segmentation_models() (in module InnerEye.ML.utils.model_util) summed_probability_rules (InnerEye.ML.config.SegmentationModelBase attribute) SummedProbabilityRule (class in InnerEye.ML.config) SupervisedLearningCriterion (class in InnerEye.ML.utils.supervised_criterion) surface_distance() (in module InnerEye.ML.metrics) surface_distance_ground_truth_plot() (in module InnerEye.ML.plotting) SurfaceDistanceConfig (class in InnerEye.ML.utils.surface_distance_utils) SurfaceDistanceRunType (class in InnerEye.ML.utils.surface_distance_utils) Symmetric (InnerEye.ML.config.PaddingMode attribute) T tabulate_dataframe() (in module InnerEye.ML.utils.io_util) tag (InnerEye.Azure.azure_config.AzureConfig attribute) tag_values_all_distinct() (in module InnerEye.Azure.azure_util) Tags (InnerEye.Common.metrics_constants.LoggingColumns attribute) tags_str (InnerEye.ML.dataset.sample.PatientMetadata attribute) tail (InnerEye.ML.config.SegmentationModelBase attribute) target_names (InnerEye.ML.scalar_config.ScalarModelBase attribute) temperature_scale() (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature method) TemperatureScalingConfig (class in InnerEye.ML.deep_learning_config) tenant_id (InnerEye.Azure.azure_config.AzureConfig attribute) tensorboard (InnerEye.Azure.azure_config.AzureConfig attribute) TEST (InnerEye.ML.common.ModelExecutionMode attribute) test (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) test_crop_size (InnerEye.ML.config.SegmentationModelBase attribute) tests_root_directory() (in module InnerEye.Common.fixed_paths_for_tests) THICKNESS (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) timeout (InnerEye.ML.dataset.full_image_dataset.RepeatDataLoader attribute) to_azure_friendly_container_path() (in module InnerEye.Azure.azure_util) to_azure_friendly_string() (in module InnerEye.Azure.azure_util) to_csv() (InnerEye.ML.utils.metrics_util.MetricsPerPatientWriter method) to_data_frame() (InnerEye.ML.metrics_dict.MetricsDict method) (InnerEye.ML.utils.metrics_util.MetricsPerPatientWriter method) to_device() (InnerEye.ML.dataset.scalar_sample.ScalarItem method) to_dict() (in module InnerEye.ML.visualizers.metrics_scatterplot) (InnerEye.ML.model_inference_config.ModelInferenceConfig method) to_json() (InnerEye.ML.model_inference_config.ModelInferenceConfig method) to_string() (InnerEye.ML.metrics_dict.MetricsDict method) torch_cuda_random_state (InnerEye.ML.utils.ml_util.RandomStateSnapshot attribute) torch_random_state (InnerEye.ML.utils.ml_util.RandomStateSnapshot attribute) total (InnerEye.ML.lightning_metrics.Accuracy05 attribute) (InnerEye.ML.lightning_metrics.MeanAbsoluteError attribute) (InnerEye.ML.lightning_metrics.MeanSquaredError attribute) TrackedMetrics (class in InnerEye.Common.metrics_constants) train (InnerEye.Azure.azure_config.AzureConfig attribute) TRAIN (InnerEye.ML.common.ModelExecutionMode attribute) train (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) train_batch_size (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) TrainerParams (class in InnerEye.ML.deep_learning_config) training (InnerEye.ML.lightning_metrics.MetricForMultipleStructures attribute) (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel attribute) (InnerEye.ML.models.architectures.classification.bit.BiTResNetV2 attribute) (InnerEye.ML.models.architectures.classification.bit.ResNetV2Block attribute) (InnerEye.ML.models.architectures.classification.bit.ResNetV2Layer attribute) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageAndNonImageFeaturesAggregator attribute) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoder attribute) (InnerEye.ML.models.architectures.classification.image_encoder_with_mlp.ImageEncoderWithMlp attribute) (InnerEye.ML.models.architectures.classification.segmentation_encoder.MultiSegmentationEncoder attribute) (InnerEye.ML.models.architectures.classification.segmentation_encoder.SegmentationEncoder attribute) (InnerEye.ML.models.architectures.complex.ComplexModel attribute) (InnerEye.ML.models.architectures.mlp.MLP attribute) (InnerEye.ML.models.architectures.mlp.MLP.HiddenLayer attribute) (InnerEye.ML.models.architectures.unet_2d.UNet2D attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetDecodeBlock attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetEncodeBlock attribute) (InnerEye.ML.models.architectures.unet_3d.UNet3D.UNetEncodeBlockSynthesis attribute) (InnerEye.ML.models.blocks.residual.ResidualBlock attribute) (InnerEye.ML.models.layers.basic.BasicLayer attribute) (InnerEye.ML.models.layers.identity.Identity attribute) (InnerEye.ML.models.layers.pooling_layers.AveragePooling attribute) (InnerEye.ML.models.layers.pooling_layers.Gated3dPoolingLayer attribute) (InnerEye.ML.models.layers.pooling_layers.MaxPooling attribute) (InnerEye.ML.models.layers.pooling_layers.MixPooling attribute) (InnerEye.ML.models.layers.pooling_layers.ZAdaptive3dAvgLayer attribute) (InnerEye.ML.models.losses.cross_entropy.CrossEntropyLoss attribute) (InnerEye.ML.models.losses.ece.ECELoss attribute) (InnerEye.ML.models.losses.mixture.MixtureLoss attribute) (InnerEye.ML.models.losses.soft_dice.SoftDiceLoss attribute) (InnerEye.ML.utils.device_aware_module.DeviceAwareModule attribute) (InnerEye.ML.utils.supervised_criterion.BinaryCrossEntropyWithLogitsLoss attribute) (InnerEye.ML.utils.supervised_criterion.SupervisedLearningCriterion attribute) (InnerEye.ML.utils.temperature_scaling.ModelWithTemperature attribute) (InnerEye.ML.visualizers.model_hooks.HookBasedFeatureExtractor attribute) transform() (InnerEye.ML.photometric_normalization.PhotometricNormalization method) (InnerEye.ML.utils.transforms.CTRange static method) (InnerEye.ML.utils.transforms.LinearTransform static method) Transform3D (class in InnerEye.ML.utils.transforms) transform_image() (InnerEye.ML.augmentations.transform_pipeline.ImageTransformationPipeline method) transposed (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) traverse_dirs_when_loading (InnerEye.ML.scalar_config.ScalarModelBase attribute) trim_percentiles (InnerEye.ML.config.SegmentationModelBase attribute) TrimmedNorm (InnerEye.ML.config.PhotometricNormalizationMethod attribute) U Unchanged (InnerEye.ML.config.PhotometricNormalizationMethod attribute) UNet2D (class in InnerEye.ML.models.architectures.unet_2d) (InnerEye.ML.config.ModelArchitectureConfig attribute) UNet3D (class in InnerEye.ML.models.architectures.unet_3d) (InnerEye.ML.config.ModelArchitectureConfig attribute) UNet3D.UNetDecodeBlock (class in InnerEye.ML.models.architectures.unet_3d) UNet3D.UNetEncodeBlock (class in InnerEye.ML.models.architectures.unet_3d) UNet3D.UNetEncodeBlockSynthesis (class in InnerEye.ML.models.architectures.unet_3d) unique_subjects() (InnerEye.ML.utils.split_dataset.DatasetSplits method) unknown (InnerEye.Azure.azure_config.ParserResult attribute) unknown_settings_from_yaml (InnerEye.Azure.azure_config.ParserResult attribute) update() (InnerEye.ML.lightning_metrics.AverageWithoutNan method) (InnerEye.ML.lightning_metrics.MetricForMultipleStructures method) (InnerEye.ML.lightning_metrics.ScalarMetricsBase method) update_metrics() (InnerEye.Common.resource_monitor.ResourceMonitor method) upload_timeout_seconds (InnerEye.Azure.azure_config.SourceConfig attribute) use_dataset_mount (InnerEye.Azure.azure_config.AzureConfig attribute) use_gpu (InnerEye.ML.deep_learning_config.TrainerParams property) (InnerEye.ML.utils.transforms.Transform3D attribute) use_imbalanced_sampler_for_training (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) use_mixed_precision (InnerEye.ML.deep_learning_config.TrainerParams attribute) use_model_parallel (InnerEye.ML.deep_learning_config.DeepLearningConfig attribute) V VAL (InnerEye.ML.common.ModelExecutionMode attribute) val (InnerEye.ML.utils.split_dataset.DatasetSplits attribute) Val_Loss (InnerEye.Common.metrics_constants.TrackedMetrics attribute) validate() (InnerEye.Azure.azure_config.AzureConfig method) (InnerEye.Common.generic_parsing.GenericConfig method) (InnerEye.ML.config.SegmentationModelBase method) (InnerEye.ML.config.SliceExclusionRule method) (InnerEye.ML.config.SummedProbabilityRule method) (InnerEye.ML.deep_learning_config.DatasetParams method) (InnerEye.ML.deep_learning_config.DeepLearningConfig method) (InnerEye.ML.deep_learning_config.OptimizerParams method) (InnerEye.ML.deep_learning_config.WorkflowParams method) (InnerEye.ML.models.architectures.base_model.CropSizeConstraints method) (InnerEye.ML.scalar_config.ScalarModelBase method) validate_class_weights() (InnerEye.ML.config.SegmentationModelBase static method) validate_crop_size() (InnerEye.ML.models.architectures.base_model.BaseSegmentationModel method) validate_dataset_paths() (in module InnerEye.ML.utils.ml_util) validate_inference_stride_size() (InnerEye.ML.config.SegmentationModelBase static method) value_to_string() (in module InnerEye.Azure.parser_util) values (InnerEye.ML.metrics_dict.Hue attribute) values() (InnerEye.ML.metrics_dict.MetricsDict method) VESSELS (InnerEye.ML.utils.hdf5_util.HDF5ImageDataType attribute) vis_activation_map() (in module InnerEye.ML.visualizers.activation_maps) visualization_folder (InnerEye.ML.deep_learning_config.OutputParams property) visualize_2d_activation_map() (in module InnerEye.ML.visualizers.activation_maps) visualize_3d_activation_map() (in module InnerEye.ML.visualizers.activation_maps) visualize_random_crops() (in module InnerEye.ML.visualizers.patch_sampling) visualize_random_crops_for_dataset() (in module InnerEye.ML.visualizers.patch_sampling) VOLUME (InnerEye.ML.utils.hdf5_util.HDF5Field attribute) VOXEL_COUNT (InnerEye.Common.metrics_constants.MetricType attribute) W wait_for_completion (InnerEye.Azure.azure_config.AzureConfig attribute) warmup_multiplier() (InnerEye.ML.utils.lr_scheduler.LinearWarmUp method) weight (InnerEye.ML.config.MixtureLossComponent attribute) (InnerEye.ML.models.layers.weight_standardization.WeightStandardizedConv2d attribute) weight_decay (InnerEye.ML.deep_learning_config.OptimizerParams attribute) WeightedCrossEntropyWithLogits (InnerEye.ML.scalar_config.ScalarLoss attribute) weights_url (InnerEye.ML.deep_learning_config.WorkflowParams attribute) WeightStandardizedConv2d (class in InnerEye.ML.models.layers.weight_standardization) window (InnerEye.ML.config.SegmentationModelBase attribute) (InnerEye.ML.utils.transforms.CTRange attribute) WindowNormalizationForScalarItem (class in InnerEye.ML.photometric_normalization) WorkflowParams (class in InnerEye.ML.deep_learning_config) workspace_name (InnerEye.Azure.azure_config.AzureConfig attribute) Wrap (InnerEye.ML.config.PaddingMode attribute) write_dataset_files() (InnerEye.ML.model_config_base.ModelConfigBase method) write_to_scatterplot_directory() (in module InnerEye.ML.visualizers.metrics_scatterplot) X x_name (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) x_path (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) Y y_name (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) y_path (InnerEye.ML.visualizers.metrics_scatterplot.MetricsScatterplotConfig attribute) Z ZAdaptive3dAvg (InnerEye.ML.scalar_config.AggregationType attribute) ZAdaptive3dAvgLayer (class in InnerEye.ML.models.layers.pooling_layers) Zero (InnerEye.ML.config.PaddingMode attribute) zip_random_dicom_series() (in module InnerEye.ML.utils.io_util)