tractolearn.config package#
Submodules#
tractolearn.config.experiment module#
- class tractolearn.config.experiment.DatasetTypes#
Bases:
object- contrastive = 'contrastive'#
- hdf5dataset = 'hdf5dataset'#
- hierarchical = 'hierarchichal'#
- triplet = 'triplet'#
- class tractolearn.config.experiment.ExperimentFormatter(config: str, hdf5_path: str, bundle_keys_path: str, output_path: str, ref_anat_fname: str)#
Bases:
object- record_experiment(api_key: str)#
- setup_experiment()#
- setup_task()#
- class tractolearn.config.experiment.ExperimentKeys#
Bases:
object- ARBITRARY_STREAMLINES_FNAMES = 'arbitrary_streamlines_fnames'#
- BATCH_SIZE = 'batch_size'#
- BUNDLE_KEYS = 'bundle_keys'#
- DATASET_NAME = 'dataset_name'#
- DATASET_TYPE = 'dataset_type'#
- DATA_IN_MEMORY = 'data_in_memory'#
- DISTANCE_FUNCTION = 'distance_function'#
- EPOCHS = 'epochs'#
- EXCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES = 'exclude_labels_tractogram_file_rootnames'#
- HDF5_PATH = 'hdf5_path'#
- INCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES = 'include_labels_tractogram_file_rootnames'#
- LATENT_SPACE_DIMS = 'latent_space_dims'#
- LOG_INTERVAL = 'log_interval'#
- LOSS_FN = 'loss'#
- MODEL_NAME = 'model_name'#
- NORMALIZE = 'normalize'#
- NUM_POINTS = 'num_points'#
- NUM_WORKERS = 'num_workers'#
- OUT_PATH = 'out_path'#
- PKL_PATH = 'pickle_path'#
- RANDOM_FLIP = 'random_flip'#
- REF_ANAT_FNAME = 'ref_anat_fname'#
- STREAMLINE_COUNT_SUBSAMPLE_FACTOR = 'streamline_count_subsample_factor'#
- TASK = 'task'#
- TO_SWAP = 'to_swap'#
- TRACTOGRAM_DET_IMPLAUS_TRACK_DATA_PATH = 'tractogram_det_implaus_track_data_path'#
- TRACTOGRAM_DET_PLAUS_TRACK_DATA_PATH = 'tractogram_det_plaus_track_data_path'#
- TRACTOGRAM_FILTERING_DISTANCE_TEST_IMPLAUS_TRACK_DATA_PATH = 'tractogram_filtering_distance_test_implaus_track_data_path'#
- TRACTOGRAM_FILTERING_DISTANCE_TEST_PLAUS_TRACK_DATA_PATH = 'tractogram_filtering_distance_test_plaus_track_data_path'#
- TRACTOGRAM_GT_DATA_PATH = 'tractogram_gt_data_path'#
- TRACTOGRAM_PROB_IMPLAUS_TRACK_DATA_PATH = 'tractogram_prob_implaus_track_data_path'#
- TRACTOGRAM_PROB_PLAUS_TRACK_DATA_PATH = 'tractogram_prob_plaus_track_data_path'#
- TRACTOGRAM_TEST_IMPLAUS_DATA_PATH = 'tractogram_test_implausibles_data_path'#
- TRACTOGRAM_TEST_PLAUS_DATA_PATH = 'tractogram_test_plausibles_data_path'#
- TRACTOGRAM_TRAIN_IMPLAUS_DATA_PATH = 'tractogram_train_implausibles_data_path'#
- TRACTOGRAM_TRAIN_PLAUS_DATA_PATH = 'tractogram_train_plausibles_data_path'#
- TRACTOGRAM_VALID_IMPLAUS_DATA_PATH = 'tractogram_valid_implausibles_data_path'#
- TRACTOGRAM_VALID_PLAUS_DATA_PATH = 'tractogram_valid_plausibles_data_path'#
- TRK_PATH = 'trk_path'#
- VIZ = 'viz'#
- WEIGHTS = 'weights'#
- class tractolearn.config.experiment.LearningTask#
Bases:
object- ae = 'ae'#
- ae_contrastive_lecun_classes = 'ae_contrastive_lecun_classes'#
- ae_triplet_classes = 'ae_triplet_classes'#
- ae_triplet_hierarchical_classes = 'ae_triplet_hierarchical_classes'#
- contrastive_lecun_classes = 'contrastive_lecun_classes'#
- class tractolearn.config.experiment.LossFunctionTypes#
Bases:
object- ae = 'ae'#
- ae_contrastive_lecun_classes = 'ae_contrastive_lecun_classes'#
- ae_triplet_classes = 'ae_triplet_classes'#
- ae_triplet_hierarchical_classes = 'ae_triplet_hierarchical_classes'#
- contrastive_lecun_classes = 'contrastive_lecun_classes'#
- class tractolearn.config.experiment.ThresholdTestKeys#
Bases:
object- ATLAS_PATH = 'atlas_path'#
- DEVICE = 'device'#
- INVALID_BUNDLE_FILE = 'invalid_bundle_file'#
- INVALID_BUNDLE_FILE_TEST = 'invalid_bundle_file_test'#
- LATENT_DIMS = 'latent_dims'#
- MAX_IMPLAUSIBLE = 'max_implausible'#
- MAX_PLAUSIBLE = 'max_plausible'#
- MODEL = 'model'#
- MODEL_TYPE = 'model_type'#
- NO_THRESHOLD = 'no_threshold'#
- OUTPUT = 'output'#
- REFERENCE = 'reference'#
- STREAMLINE_CLASSES = 'streamline_classes'#
- STREAMLINE_LENGTH = 'streamline_length'#
- THRESHOLDS_FILE = 'thresholds_file'#
- VALID_BUNDLE_PATH = 'valid_bundle_path'#
- VALID_BUNDLE_PATH_TEST = 'valid_bundle_path_test'#
- VIZ = 'viz'#
- tractolearn.config.experiment.make_run_dir(out_path=None)#
Create a directory for this training run
- tractolearn.config.experiment.path_str(x)#