tractolearn package#
Subpackages#
- tractolearn.analysis package
- tractolearn.anatomy package
- Submodules
- tractolearn.anatomy.bundles_additional_labels module
BundlesAdditionalLabelsBundlesAdditionalLabels.generic_streamline_classBundlesAdditionalLabels.generic_streamline_class_nameBundlesAdditionalLabels.hdf5_invalid_classBundlesAdditionalLabels.interpolated_classBundlesAdditionalLabels.interpolated_class_nameBundlesAdditionalLabels.invalid_connection_classBundlesAdditionalLabels.invalid_connection_class_nameBundlesAdditionalLabels.nearest_neighbor_classBundlesAdditionalLabels.nearest_neighbor_class_nameBundlesAdditionalLabels.reference_classBundlesAdditionalLabels.reference_class_name
- Module contents
- tractolearn.clustering package
- tractolearn.config package
- Submodules
- tractolearn.config.experiment module
DatasetTypesExperimentFormatterExperimentKeysExperimentKeys.ARBITRARY_STREAMLINES_FNAMESExperimentKeys.BATCH_SIZEExperimentKeys.BUNDLE_KEYSExperimentKeys.DATASET_NAMEExperimentKeys.DATASET_TYPEExperimentKeys.DATA_IN_MEMORYExperimentKeys.DISTANCE_FUNCTIONExperimentKeys.EPOCHSExperimentKeys.EXCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMESExperimentKeys.HDF5_PATHExperimentKeys.INCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMESExperimentKeys.LATENT_SPACE_DIMSExperimentKeys.LOG_INTERVALExperimentKeys.LOSS_FNExperimentKeys.MODEL_NAMEExperimentKeys.NORMALIZEExperimentKeys.NUM_POINTSExperimentKeys.NUM_WORKERSExperimentKeys.OUT_PATHExperimentKeys.PKL_PATHExperimentKeys.RANDOM_FLIPExperimentKeys.REF_ANAT_FNAMEExperimentKeys.STREAMLINE_COUNT_SUBSAMPLE_FACTORExperimentKeys.TASKExperimentKeys.TO_SWAPExperimentKeys.TRACTOGRAM_DET_IMPLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_DET_PLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_FILTERING_DISTANCE_TEST_IMPLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_FILTERING_DISTANCE_TEST_PLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_GT_DATA_PATHExperimentKeys.TRACTOGRAM_PROB_IMPLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_PROB_PLAUS_TRACK_DATA_PATHExperimentKeys.TRACTOGRAM_TEST_IMPLAUS_DATA_PATHExperimentKeys.TRACTOGRAM_TEST_PLAUS_DATA_PATHExperimentKeys.TRACTOGRAM_TRAIN_IMPLAUS_DATA_PATHExperimentKeys.TRACTOGRAM_TRAIN_PLAUS_DATA_PATHExperimentKeys.TRACTOGRAM_VALID_IMPLAUS_DATA_PATHExperimentKeys.TRACTOGRAM_VALID_PLAUS_DATA_PATHExperimentKeys.TRK_PATHExperimentKeys.VIZExperimentKeys.WEIGHTS
LearningTaskLossFunctionTypesThresholdTestKeysThresholdTestKeys.ATLAS_PATHThresholdTestKeys.DEVICEThresholdTestKeys.INVALID_BUNDLE_FILEThresholdTestKeys.INVALID_BUNDLE_FILE_TESTThresholdTestKeys.LATENT_DIMSThresholdTestKeys.MAX_IMPLAUSIBLEThresholdTestKeys.MAX_PLAUSIBLEThresholdTestKeys.MODELThresholdTestKeys.MODEL_TYPEThresholdTestKeys.NO_THRESHOLDThresholdTestKeys.OUTPUTThresholdTestKeys.REFERENCEThresholdTestKeys.STREAMLINE_CLASSESThresholdTestKeys.STREAMLINE_LENGTHThresholdTestKeys.THRESHOLDS_FILEThresholdTestKeys.VALID_BUNDLE_PATHThresholdTestKeys.VALID_BUNDLE_PATH_TESTThresholdTestKeys.VIZ
make_run_dir()path_str()
- Module contents
- tractolearn.filtering package
- Submodules
- tractolearn.filtering.latent_space_distance_informer module
- tractolearn.filtering.latent_space_featuring module
ROCSalientPointcompute_filtering_roc_curve()compute_maximum_accuracy_roc_threshold_index()compute_optimal_roc_difference_index()compute_optimal_roc_intersection_index()filter_streamlines_only()find_tractogram_filtering_threshold_v2()get_dataset_long_name_from_dataset_name()plot_filtering_threshold_features()plot_horizontal_lines()plot_latent_space()plot_latent_space_distance_features()plot_latent_space_histogram()plot_latent_space_stats()plot_roc()plot_vertical_lines()roc_curve_computation()
- tractolearn.filtering.streamline_space_filtering module
StreamlineFeaturesStreamlineFeatures.CORTICAL_GAPStreamlineFeatures.FAStreamlineFeatures.GM_OCCUPANCYStreamlineFeatures.LENGTHStreamlineFeatures.LOCAL_ORIENTATION_ANGLEStreamlineFeatures.MEAN_CURVATUREStreamlineFeatures.REGIONStreamlineFeatures.SURFACE_INCIDENCE_ANGLEStreamlineFeatures.SURFACE_INTERSECTIONStreamlineFeatures.SURFACE_PROJECTED_ANGLEStreamlineFeatures.WINDINGStreamlineFeatures.WM_MEMBERSHIPStreamlineFeatures.WM_OCCUPANCYStreamlineFeatures.WM_VOXEL_OCCUPANCY_RATIO
StreamlineLocalOrientationAnalyzerStreamlineLocalOrientationCheckerTractographyCheckerTractographyFeatureAnalyzercompute_local_orientation_alignment2()compute_streamline_local_orientation()compute_streamline_to_peaks_angles()cut_streamlines_outside_mask()filter_grid_roi()get_closest_peaks_from_angles()interpolate_peak_dirs_at_streamline_locations()is_feature_plausible()
- Module contents
LatentSpaceKeysLatentSpaceKeys.balanced_accuracy_labelLatentSpaceKeys.colorbar_fname_labelLatentSpaceKeys.confusion_matrix_fname_rootLatentSpaceKeys.filtering_stats_file_basenameLatentSpaceKeys.implaus_streamlines_tractogram_latent_distances_cbar_file_basenameLatentSpaceKeys.implausible_streamlines_latent_distances_file_basenameLatentSpaceKeys.latent_space_fname_labelLatentSpaceKeys.latent_space_histogram_cont_fname_labelLatentSpaceKeys.latent_space_histogram_fname_labelLatentSpaceKeys.latent_space_roc_fname_labelLatentSpaceKeys.latent_space_stats_fname_labelLatentSpaceKeys.latent_space_stats_raincloud_fname_labelLatentSpaceKeys.nearest_neighbor_fname_labelLatentSpaceKeys.plaus_streamlines_tractogram_latent_distances_cbar_file_basenameLatentSpaceKeys.plausible_streamlines_latent_distances_file_basenameLatentSpaceKeys.roc_data_file_basenameLatentSpaceKeys.test_data_fn_tractogram_fname_rootLatentSpaceKeys.test_data_fp_tractogram_fname_rootLatentSpaceKeys.test_data_reconst_implaus_tractogram_fname_rootLatentSpaceKeys.test_data_reconst_plaus_tractogram_fname_rootLatentSpaceKeys.test_data_tn_tractogram_fname_rootLatentSpaceKeys.test_data_tp_tractogram_fname_rootLatentSpaceKeys.threshold_fname_labelLatentSpaceKeys.tractogram_fname_label
- tractolearn.generative package
- tractolearn.learning package
- Submodules
- tractolearn.learning.data_manager module
- tractolearn.learning.dataset module
- tractolearn.learning.trainer_manager module
TrainerTrainer.best_checkpointTrainer.best_model_fnameTrainer.build_model()Trainer.experimentTrainer.get_batch_iterator()Trainer.load_checkpoint()Trainer.lowest_lossTrainer.modelTrainer.model_nameTrainer.normalizeTrainer.plot_results()Trainer.save_checkpoint()Trainer.save_loss_history()Trainer.test_loaderTrainer.test_loss_recorderTrainer.train()Trainer.train_loaderTrainer.train_loss_recorderTrainer.valid()Trainer.valid_loaderTrainer.valid_loss_recorder
- Module contents
- tractolearn.models package
- tractolearn.tractoio package
- Subpackages
- Submodules
- tractolearn.tractoio.dataset_fetch module
DatasetDataset.BUNDLE_LABEL_CONFIGDataset.CONTRASTIVE_AUTOENCODER_WEIGHTSDataset.GENERATIVE_LOA_CONE_CONFIGDataset.GENERATIVE_SEED_STRML_RATIO_CONFIGDataset.GENERATIVE_STRML_MAX_COUNT_CONFIGDataset.GENERATIVE_STRML_RQ_COUNT_CONFIGDataset.GENERATIVE_WM_TISSUE_CRITERION_CONFIGDataset.MNI2009CNONLINSYMM_ANATDataset.RECOBUNDLESX_ATLASDataset.RECOBUNDLESX_CONFIGDataset.TRACTOINFERNO_HCP_CONTRASTIVE_THR_CONFIGDataset.TRACTOINFERNO_HCP_REF_TRACTOGRAPHYDataset.argparse()
DatasetErrorFetcherErrorcheck_hash()copyfileobj_withprogress()fetch_data()retrieve_dataset()
- tractolearn.tractoio.utils module
- Module contents
- Subpackages
- tractolearn.tractomath package
- tractolearn.transformation package
- tractolearn.utils package
Submodules#
tractolearn.logger module#
- class tractolearn.logger.LoggerKeys(value)#
Bases:
EnumAn enumeration.
- TOTAL_LOSS = 'loss'#
- fname_extension_sep = '.'#
- generic_streamline_data_fname_label = 'generic_streamline'#
- interpolated_plot_fname_label = 'latent_interpolated'#
- json_extension = 'json'#
- latent_distance_plot_fname_label = 'latent_distance'#
- latent_plot_fname_label = 'latent'#
- logger_file_basename = 'logfile.log'#
- loss_plot_file_basename = 'loss.png'#
- plot_extension = 'png'#
- test_data_batch_input_file_basename = 'test_data_batch_input.png'#
- test_data_fname_label = 'test_data'#
- test_data_reconst_batch_file_basename = 'test_data_reconst_batch.png'#
- test_data_reconst_tractogram_fname_root = 'test_data_reconst'#
- test_loss_data_file_basename = 'test_loss.json'#
- train_loss_data_file_basename = 'train_loss.json'#
- trk_extension = 'trk'#
- underscore = '_'#
- valid_data_fname_label = 'valid_data'#
- valid_loss_data_file_basename = 'valid_loss.json'#