Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W A ae (tractolearn.config.experiment.LearningTask attribute) (tractolearn.config.experiment.LossFunctionTypes attribute) ae_contrastive_lecun_classes (tractolearn.config.experiment.LearningTask attribute) (tractolearn.config.experiment.LossFunctionTypes attribute) ae_triplet_classes (tractolearn.config.experiment.LearningTask attribute) (tractolearn.config.experiment.LossFunctionTypes attribute) ae_triplet_hierarchical_classes (tractolearn.config.experiment.LearningTask attribute) (tractolearn.config.experiment.LossFunctionTypes attribute) analyze() (tractolearn.filtering.streamline_space_filtering.StreamlineLocalOrientationAnalyzer method) ARBITRARY_STREAMLINES_FNAMES (tractolearn.config.experiment.ExperimentKeys attribute) argparse() (tractolearn.tractoio.dataset_fetch.Dataset static method) ATLAS_PATH (tractolearn.config.experiment.ThresholdTestKeys attribute) avg (tractolearn.models.model_performance_history.LossHistory property) B balanced_accuracy_label (tractolearn.filtering.LatentSpaceKeys attribute) batch_filtering() (in module scripts.ae_bundle_streamlines) BATCH_SIZE (tractolearn.config.experiment.ExperimentKeys attribute) best_checkpoint (tractolearn.learning.trainer_manager.Trainer property) best_model_fname (tractolearn.learning.trainer_manager.Trainer attribute) build_model() (tractolearn.learning.trainer_manager.Trainer method) BUNDLE_DICTIONARIES (tractolearn.anatomy.BundleSettings attribute) BUNDLE_KEYS (tractolearn.config.experiment.ExperimentKeys attribute) BUNDLE_LABEL_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) BundlesAdditionalLabels (class in tractolearn.anatomy.bundles_additional_labels) BundleSettings (class in tractolearn.anatomy) C check_hash() (in module tractolearn.tractoio.dataset_fetch) colorbar_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) compute_alignment() (tractolearn.filtering.streamline_space_filtering.StreamlineLocalOrientationAnalyzer static method) compute_angle() (in module tractolearn.tractomath.utils) compute_distance_on_latent() (tractolearn.filtering.latent_space_distance_informer.LatentSpaceDistanceInformer method) compute_distances() (tractolearn.filtering.latent_space_distance_informer.LatentSpaceDistanceInformer method) compute_filtering_roc_curve() (in module tractolearn.filtering.latent_space_featuring) compute_isocenter() (in module tractolearn.transformation.volume_utils) compute_local_orientation_alignment2() (in module tractolearn.filtering.streamline_space_filtering) compute_maximum_accuracy_roc_threshold_index() (in module tractolearn.filtering.latent_space_featuring) compute_optimal_roc_difference_index() (in module tractolearn.filtering.latent_space_featuring) compute_optimal_roc_intersection_index() (in module tractolearn.filtering.latent_space_featuring) compute_streamline_local_orientation() (in module tractolearn.filtering.streamline_space_filtering) compute_streamline_to_peaks_angles() (in module tractolearn.filtering.streamline_space_filtering) compute_volume() (in module tractolearn.transformation.volume_utils) confusion_matrix_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) contrastive (tractolearn.config.experiment.DatasetTypes attribute) CONTRASTIVE_AUTOENCODER_WEIGHTS (tractolearn.tractoio.dataset_fetch.Dataset attribute) contrastive_lecun_classes (tractolearn.config.experiment.LearningTask attribute) (tractolearn.config.experiment.LossFunctionTypes attribute) ContrastiveDataset (class in tractolearn.learning.dataset) copyfileobj_withprogress() (in module tractolearn.tractoio.dataset_fetch) CORTICAL_GAP (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) CSF (tractolearn.anatomy.Tissue attribute) cut_streamlines_outside_mask() (in module tractolearn.filtering.streamline_space_filtering) D DATA_IN_MEMORY (tractolearn.config.experiment.ExperimentKeys attribute) DataManager (class in tractolearn.learning.data_manager) Dataset (class in tractolearn.tractoio.dataset_fetch) DATASET_NAME (tractolearn.config.experiment.ExperimentKeys attribute) DATASET_TYPE (tractolearn.config.experiment.ExperimentKeys attribute) DatasetError DatasetTypes (class in tractolearn.config.experiment) decode() (tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch.IncrFeatStridedConvFCUpsampReflectPadAE method) DEVICE (tractolearn.config.experiment.ThresholdTestKeys attribute) DISTANCE_FUNCTION (tractolearn.config.experiment.ExperimentKeys attribute) E encode() (tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch.IncrFeatStridedConvFCUpsampReflectPadAE method) encode_data() (in module tractolearn.models.autoencoding_utils) end_epoch() (tractolearn.models.model_performance_history.LossHistory method) EPOCHS (tractolearn.config.experiment.ExperimentKeys attribute) EXCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES (tractolearn.config.experiment.ExperimentKeys attribute) experiment (tractolearn.learning.trainer_manager.Trainer property) ExperimentFormatter (class in tractolearn.config.experiment) ExperimentKeys (class in tractolearn.config.experiment) F FA (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) fetch_data() (in module tractolearn.tractoio.dataset_fetch) FetcherError filter_grid_roi() (in module tractolearn.filtering.streamline_space_filtering) filter_streamlines_only() (in module tractolearn.filtering.latent_space_featuring) filtering_stats_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) find_tractogram_filtering_threshold_v2() (in module tractolearn.filtering.latent_space_featuring) flip_random_streamlines() (in module tractolearn.transformation.streamline_transformation) flip_streamlines() (in module tractolearn.transformation.streamline_transformation) fname_extension_sep (tractolearn.logger.LoggerKeys attribute) forward() (tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch.IncrFeatStridedConvFCUpsampReflectPadAE method) forward_ae() (in module tractolearn.models.forward) forward_ae_contrastive() (in module tractolearn.models.forward) forward_contrastive() (in module tractolearn.models.forward) G generate_points() (in module tractolearn.generative.generate_points) generate_uuid() (in module tractolearn.utils.utils) GENERATIVE_LOA_CONE_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) GENERATIVE_SEED_STRML_RATIO_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) GENERATIVE_STRML_MAX_COUNT_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) GENERATIVE_STRML_RQ_COUNT_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) GENERATIVE_WM_TISSUE_CRITERION_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) generic_streamline_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) generic_streamline_class_name (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) generic_streamline_data_fname_label (tractolearn.logger.LoggerKeys attribute) get_batch_iterator() (tractolearn.learning.trainer_manager.Trainer method) get_closest_peaks_from_angles() (in module tractolearn.filtering.streamline_space_filtering) get_compliant_indices() (tractolearn.filtering.streamline_space_filtering.TractographyChecker method) get_dataset_long_name_from_dataset_name() (in module tractolearn.filtering.latent_space_featuring) get_model() (in module tractolearn.models.model_pool) get_peak_count() (in module tractolearn.transformation.peaks_utils) get_random_streamline_from_class() (tractolearn.learning.dataset.StreamlineClassificationDataset method) get_random_streamline_from_class_with_merge() (tractolearn.learning.dataset.StreamlineClassificationDatasetTree method) get_random_streamline_from_class_without_merge() (tractolearn.learning.dataset.StreamlineClassificationDatasetTree method) GM (tractolearn.anatomy.Tissue attribute) GM_OCCUPANCY (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) H hdf5_invalid_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) HDF5_PATH (tractolearn.config.experiment.ExperimentKeys attribute) hdf5dataset (tractolearn.config.experiment.DatasetTypes attribute) hierarchical (tractolearn.config.experiment.DatasetTypes attribute) HierarchicalDataset (class in tractolearn.learning.dataset) I implaus_streamlines_tractogram_latent_distances_cbar_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) implausible_streamlines_latent_distances_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) INCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES (tractolearn.config.experiment.ExperimentKeys attribute) IncrFeatStridedConvFCUpsampReflectPadAE (class in tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch) interpolate_peak_dirs_at_streamline_locations() (in module tractolearn.filtering.streamline_space_filtering) interpolate_volume_at_coordinates() (in module tractolearn.transformation.volume_utils) interpolated_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) interpolated_class_name (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) interpolated_plot_fname_label (tractolearn.logger.LoggerKeys attribute) INV_DIAGONAL_INTERSECT (tractolearn.filtering.latent_space_featuring.ROCSalientPoint attribute) INVALID_BUNDLE_FILE (tractolearn.config.experiment.ThresholdTestKeys attribute) INVALID_BUNDLE_FILE_TEST (tractolearn.config.experiment.ThresholdTestKeys attribute) invalid_connection_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) invalid_connection_class_name (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) is_feature_plausible() (in module tractolearn.filtering.streamline_space_filtering) is_normalized() (in module tractolearn.tractomath.utils) J json_extension (tractolearn.logger.LoggerKeys attribute) L LATENT_DIMS (tractolearn.config.experiment.ThresholdTestKeys attribute) latent_distance_plot_fname_label (tractolearn.logger.LoggerKeys attribute) latent_plot_fname_label (tractolearn.logger.LoggerKeys attribute) LATENT_SPACE_DIMS (tractolearn.config.experiment.ExperimentKeys attribute) latent_space_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) latent_space_histogram_cont_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) latent_space_histogram_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) latent_space_roc_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) latent_space_stats_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) latent_space_stats_raincloud_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) LatentSpaceDistanceInformer (class in tractolearn.filtering.latent_space_distance_informer) LatentSpaceKeys (class in tractolearn.filtering) LearningTask (class in tractolearn.config.experiment) LENGTH (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) load_bundles_dict() (in module tractolearn.tractoio.utils) load_checkpoint() (tractolearn.learning.trainer_manager.Trainer method) load_data2() (in module tractolearn.tractoio.utils) load_process_streamlines2() (in module tractolearn.tractoio.utils) load_ref_anat_image() (in module tractolearn.tractoio.utils) load_streamline_learning_data() (in module tractolearn.tractoio.utils) load_streamlines() (in module tractolearn.tractoio.utils) LOCAL_ORIENTATION_ANGLE (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) LOG_INTERVAL (tractolearn.config.experiment.ExperimentKeys attribute) logger_file_basename (tractolearn.logger.LoggerKeys attribute) LoggerKeys (class in tractolearn.logger) loss_contrastive_lecun_classes() (in module tractolearn.utils.losses) LOSS_FN (tractolearn.config.experiment.ExperimentKeys attribute) loss_function_ae() (in module tractolearn.utils.losses) loss_function_vae() (in module tractolearn.utils.losses) loss_plot_file_basename (tractolearn.logger.LoggerKeys attribute) loss_triplet_classes() (in module tractolearn.utils.losses) loss_triplet_hierarchical_classes() (in module tractolearn.utils.losses) LossFunctionTypes (class in tractolearn.config.experiment) LossHistory (class in tractolearn.models.model_performance_history) lowest_loss (tractolearn.learning.trainer_manager.Trainer property) M main() (in module scripts.ae_bundle_streamlines) (in module scripts.ae_find_thresholds) (in module scripts.ae_train) (in module scripts.fetch_data) make_forward() (in module tractolearn.models.forward) make_run_dir() (in module tractolearn.config.experiment) (in module tractolearn.utils.utils) MAX_ACCURACY (tractolearn.filtering.latent_space_featuring.ROCSalientPoint attribute) MAX_IMPLAUSIBLE (tractolearn.config.experiment.ThresholdTestKeys attribute) MAX_PLAUSIBLE (tractolearn.config.experiment.ThresholdTestKeys attribute) MEAN_CURVATURE (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) MNI2009CNONLINSYMM_ANAT (tractolearn.tractoio.dataset_fetch.Dataset attribute) MODEL (tractolearn.config.experiment.ThresholdTestKeys attribute) model (tractolearn.learning.trainer_manager.Trainer property) MODEL_NAME (tractolearn.config.experiment.ExperimentKeys attribute) model_name (tractolearn.learning.trainer_manager.Trainer property) MODEL_TYPE (tractolearn.config.experiment.ThresholdTestKeys attribute) module scripts scripts.ae_bundle_streamlines scripts.ae_find_thresholds scripts.ae_train scripts.fetch_data tractolearn tractolearn.analysis tractolearn.anatomy tractolearn.anatomy.bundles_additional_labels tractolearn.clustering tractolearn.config tractolearn.config.experiment tractolearn.filtering tractolearn.filtering.latent_space_distance_informer tractolearn.filtering.latent_space_featuring tractolearn.filtering.streamline_space_filtering tractolearn.generative tractolearn.generative.generate_points tractolearn.learning tractolearn.learning.data_manager tractolearn.learning.dataset tractolearn.learning.trainer_manager tractolearn.logger tractolearn.models tractolearn.models.autoencoding_utils tractolearn.models.forward tractolearn.models.model_performance_history tractolearn.models.model_pool tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch tractolearn.tractoio tractolearn.tractoio.dataset_fetch tractolearn.tractoio.utils tractolearn.tractomath tractolearn.tractomath.utils tractolearn.transformation tractolearn.transformation.peaks_utils tractolearn.transformation.streamline_transformation tractolearn.transformation.volume_utils tractolearn.utils tractolearn.utils.layer_utils tractolearn.utils.logging_setup tractolearn.utils.losses tractolearn.utils.processing_utils tractolearn.utils.timer tractolearn.utils.utils N nearest_neighbor_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) nearest_neighbor_class_name (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) nearest_neighbor_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) NO_THRESHOLD (tractolearn.config.experiment.ThresholdTestKeys attribute) NORMALIZE (tractolearn.config.experiment.ExperimentKeys attribute) normalize (tractolearn.learning.trainer_manager.Trainer property) NUM_POINTS (tractolearn.config.experiment.ExperimentKeys attribute) num_points (tractolearn.learning.dataset.ContrastiveDataset property) (tractolearn.learning.dataset.HierarchicalDataset property) NUM_WORKERS (tractolearn.config.experiment.ExperimentKeys attribute) O OnTheFlyDataset (class in tractolearn.learning.dataset) OUT_PATH (tractolearn.config.experiment.ExperimentKeys attribute) OUTPUT (tractolearn.config.experiment.ThresholdTestKeys attribute) P path_str() (in module tractolearn.config.experiment) PKL_PATH (tractolearn.config.experiment.ExperimentKeys attribute) plaus_streamlines_tractogram_latent_distances_cbar_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) plausible_streamlines_latent_distances_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) plot_extension (tractolearn.logger.LoggerKeys attribute) plot_filtering_threshold_features() (in module tractolearn.filtering.latent_space_featuring) plot_horizontal_lines() (in module tractolearn.filtering.latent_space_featuring) plot_latent_space() (in module tractolearn.filtering.latent_space_featuring) plot_latent_space_distance_features() (in module tractolearn.filtering.latent_space_featuring) plot_latent_space_histogram() (in module tractolearn.filtering.latent_space_featuring) plot_latent_space_stats() (in module tractolearn.filtering.latent_space_featuring) plot_results() (tractolearn.learning.trainer_manager.Trainer method) plot_roc() (in module tractolearn.filtering.latent_space_featuring) plot_vertical_lines() (in module tractolearn.filtering.latent_space_featuring) point_dims (tractolearn.learning.dataset.ContrastiveDataset property) (tractolearn.learning.dataset.HierarchicalDataset property) postprocess() (in module tractolearn.utils.processing_utils) predict() (tractolearn.utils.layer_utils.PredictWrapper method) PredictWrapper (class in tractolearn.utils.layer_utils) R RANDOM_FLIP (tractolearn.config.experiment.ExperimentKeys attribute) read_data_from_json_file() (in module tractolearn.tractoio.utils) read_data_from_pickle_file() (in module tractolearn.tractoio.utils) RECOBUNDLESX_ATLAS (tractolearn.tractoio.dataset_fetch.Dataset attribute) RECOBUNDLESX_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) record_experiment() (tractolearn.config.experiment.ExperimentFormatter method) REF_ANAT_FNAME (tractolearn.config.experiment.ExperimentKeys attribute) REFERENCE (tractolearn.config.experiment.ThresholdTestKeys attribute) reference_class (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) reference_class_name (tractolearn.anatomy.bundles_additional_labels.BundlesAdditionalLabels attribute) REGION (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) RejectionSampler (class in tractolearn.generative.generate_points) resample_streamlines() (in module tractolearn.transformation.streamline_transformation) reshape_peaks_for_computing() (in module tractolearn.transformation.peaks_utils) retrieve_dataset() (in module tractolearn.tractoio.dataset_fetch) rng (tractolearn.learning.dataset.ContrastiveDataset property) (tractolearn.learning.dataset.HierarchicalDataset property) roc_curve_computation() (in module tractolearn.filtering.latent_space_featuring) roc_data_file_basename (tractolearn.filtering.LatentSpaceKeys attribute) ROCSalientPoint (class in tractolearn.filtering.latent_space_featuring) S sample() (tractolearn.generative.generate_points.RejectionSampler method) save_checkpoint() (tractolearn.learning.trainer_manager.Trainer method) save_data_to_json_file() (in module tractolearn.tractoio.utils) save_data_to_pickle_file() (in module tractolearn.tractoio.utils) save_loss_history() (in module tractolearn.tractoio.utils) (tractolearn.learning.trainer_manager.Trainer method) save_streamlines() (in module tractolearn.tractoio.utils) scripts module scripts.ae_bundle_streamlines module scripts.ae_find_thresholds module scripts.ae_train module scripts.fetch_data module separate_pl_impl() (in module scripts.ae_find_thresholds) separate_pl_impl_latent() (in module scripts.ae_find_thresholds) set_seed() (tractolearn.learning.dataset.ContrastiveDataset method) (tractolearn.learning.dataset.HierarchicalDataset method) (tractolearn.learning.dataset.StreamlineClassificationDataset method) (tractolearn.learning.dataset.StreamlineClassificationDatasetTree method) set_threshold() (in module scripts.ae_find_thresholds) set_up() (in module tractolearn.utils.logging_setup) setup_data_loader() (tractolearn.learning.data_manager.DataManager method) setup_dataset() (tractolearn.learning.data_manager.DataManager method) setup_experiment() (tractolearn.config.experiment.ExperimentFormatter method) setup_task() (tractolearn.config.experiment.ExperimentFormatter method) sft_voxel_transform() (in module tractolearn.transformation.streamline_transformation) sort_streamline_per_bundle() (in module scripts.ae_find_thresholds) STREAMLINE_CLASSES (tractolearn.config.experiment.ThresholdTestKeys attribute) STREAMLINE_COUNT_SUBSAMPLE_FACTOR (tractolearn.config.experiment.ExperimentKeys attribute) STREAMLINE_LENGTH (tractolearn.config.experiment.ThresholdTestKeys attribute) StreamlineClassificationDataset (class in tractolearn.learning.dataset) StreamlineClassificationDatasetTree (class in tractolearn.learning.dataset) StreamlineFeatures (class in tractolearn.filtering.streamline_space_filtering) StreamlineLocalOrientationAnalyzer (class in tractolearn.filtering.streamline_space_filtering) StreamlineLocalOrientationChecker (class in tractolearn.filtering.streamline_space_filtering) SURFACE_INCIDENCE_ANGLE (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) SURFACE_INTERSECTION (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) SURFACE_PROJECTED_ANGLE (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) T TASK (tractolearn.config.experiment.ExperimentKeys attribute) test_data_batch_input_file_basename (tractolearn.logger.LoggerKeys attribute) test_data_fn_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_data_fname_label (tractolearn.logger.LoggerKeys attribute) test_data_fp_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_data_reconst_batch_file_basename (tractolearn.logger.LoggerKeys attribute) test_data_reconst_implaus_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_data_reconst_plaus_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_data_reconst_tractogram_fname_root (tractolearn.logger.LoggerKeys attribute) test_data_tn_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_data_tp_tractogram_fname_root (tractolearn.filtering.LatentSpaceKeys attribute) test_loader (tractolearn.learning.trainer_manager.Trainer property) test_loss_data_file_basename (tractolearn.logger.LoggerKeys attribute) test_loss_recorder (tractolearn.learning.trainer_manager.Trainer property) threshold_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) THRESHOLDS_FILE (tractolearn.config.experiment.ThresholdTestKeys attribute) ThresholdTestKeys (class in tractolearn.config.experiment) Timer (class in tractolearn.utils.timer) Tissue (class in tractolearn.anatomy) TO_SWAP (tractolearn.config.experiment.ExperimentKeys attribute) TOTAL_LOSS (tractolearn.logger.LoggerKeys attribute) TRACTOGRAM_DET_IMPLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_DET_PLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_FILTERING_DISTANCE_TEST_IMPLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_FILTERING_DISTANCE_TEST_PLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) tractogram_fname_label (tractolearn.filtering.LatentSpaceKeys attribute) TRACTOGRAM_GT_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_PROB_IMPLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_PROB_PLAUS_TRACK_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_TEST_IMPLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_TEST_PLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_TRAIN_IMPLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_TRAIN_PLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_VALID_IMPLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TRACTOGRAM_VALID_PLAUS_DATA_PATH (tractolearn.config.experiment.ExperimentKeys attribute) TractographyChecker (class in tractolearn.filtering.streamline_space_filtering) TractographyFeatureAnalyzer (class in tractolearn.filtering.streamline_space_filtering) TRACTOINFERNO_HCP_CONTRASTIVE_THR_CONFIG (tractolearn.tractoio.dataset_fetch.Dataset attribute) TRACTOINFERNO_HCP_REF_TRACTOGRAPHY (tractolearn.tractoio.dataset_fetch.Dataset attribute) tractolearn module tractolearn.analysis module tractolearn.anatomy module tractolearn.anatomy.bundles_additional_labels module tractolearn.clustering module tractolearn.config module tractolearn.config.experiment module tractolearn.filtering module tractolearn.filtering.latent_space_distance_informer module tractolearn.filtering.latent_space_featuring module tractolearn.filtering.streamline_space_filtering module tractolearn.generative module tractolearn.generative.generate_points module tractolearn.learning module tractolearn.learning.data_manager module tractolearn.learning.dataset module tractolearn.learning.trainer_manager module tractolearn.logger module tractolearn.models module tractolearn.models.autoencoding_utils module tractolearn.models.forward module tractolearn.models.model_performance_history module tractolearn.models.model_pool module tractolearn.models.track_ae_cnn1d_incr_feat_strided_conv_fc_upsamp_reflect_pad_pytorch module tractolearn.tractoio module tractolearn.tractoio.dataset_fetch module tractolearn.tractoio.utils module tractolearn.tractomath module tractolearn.tractomath.utils module tractolearn.transformation module tractolearn.transformation.peaks_utils module tractolearn.transformation.streamline_transformation module tractolearn.transformation.volume_utils module tractolearn.utils module tractolearn.utils.layer_utils module tractolearn.utils.logging_setup module tractolearn.utils.losses module tractolearn.utils.processing_utils module tractolearn.utils.timer module tractolearn.utils.utils module train() (tractolearn.learning.trainer_manager.Trainer method) train_loader (tractolearn.learning.trainer_manager.Trainer property) train_loss_data_file_basename (tractolearn.logger.LoggerKeys attribute) train_loss_recorder (tractolearn.learning.trainer_manager.Trainer property) Trainer (class in tractolearn.learning.trainer_manager) triplet (tractolearn.config.experiment.DatasetTypes attribute) triplet_margin_with_distance_loss_hierarchical() (in module tractolearn.utils.losses) TripletDataset (class in tractolearn.learning.dataset) trk_extension (tractolearn.logger.LoggerKeys attribute) TRK_PATH (tractolearn.config.experiment.ExperimentKeys attribute) U underscore (tractolearn.logger.LoggerKeys attribute) unit_vector() (in module tractolearn.tractomath.utils) update() (tractolearn.models.model_performance_history.LossHistory method) V valid() (tractolearn.learning.trainer_manager.Trainer method) VALID_BUNDLE_PATH (tractolearn.config.experiment.ThresholdTestKeys attribute) VALID_BUNDLE_PATH_TEST (tractolearn.config.experiment.ThresholdTestKeys attribute) valid_data_fname_label (tractolearn.logger.LoggerKeys attribute) valid_loader (tractolearn.learning.trainer_manager.Trainer property) valid_loss_data_file_basename (tractolearn.logger.LoggerKeys attribute) valid_loss_recorder (tractolearn.learning.trainer_manager.Trainer property) verify_conditions() (tractolearn.filtering.streamline_space_filtering.StreamlineLocalOrientationChecker method) VIZ (tractolearn.config.experiment.ExperimentKeys attribute) (tractolearn.config.experiment.ThresholdTestKeys attribute) W WEIGHTS (tractolearn.config.experiment.ExperimentKeys attribute) whole_filtering() (in module scripts.ae_bundle_streamlines) WINDING (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) WM (tractolearn.anatomy.Tissue attribute) WM_MEMBERSHIP (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) WM_OCCUPANCY (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) WM_VOXEL_OCCUPANCY_RATIO (tractolearn.filtering.streamline_space_filtering.StreamlineFeatures attribute) write_bundles() (in module tractolearn.tractoio.utils)