tractolearn package#
Subpackages#
- tractolearn.analysis package
- tractolearn.anatomy package
- Submodules
- tractolearn.anatomy.bundles_additional_labels module
BundlesAdditionalLabels
BundlesAdditionalLabels.generic_streamline_class
BundlesAdditionalLabels.generic_streamline_class_name
BundlesAdditionalLabels.hdf5_invalid_class
BundlesAdditionalLabels.interpolated_class
BundlesAdditionalLabels.interpolated_class_name
BundlesAdditionalLabels.invalid_connection_class
BundlesAdditionalLabels.invalid_connection_class_name
BundlesAdditionalLabels.nearest_neighbor_class
BundlesAdditionalLabels.nearest_neighbor_class_name
BundlesAdditionalLabels.reference_class
BundlesAdditionalLabels.reference_class_name
- Module contents
- tractolearn.clustering package
- tractolearn.config package
- Submodules
- tractolearn.config.experiment module
DatasetTypes
ExperimentFormatter
ExperimentKeys
ExperimentKeys.ARBITRARY_STREAMLINES_FNAMES
ExperimentKeys.BATCH_SIZE
ExperimentKeys.BUNDLE_KEYS
ExperimentKeys.DATASET_NAME
ExperimentKeys.DATASET_TYPE
ExperimentKeys.DATA_IN_MEMORY
ExperimentKeys.DISTANCE_FUNCTION
ExperimentKeys.EPOCHS
ExperimentKeys.EXCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES
ExperimentKeys.HDF5_PATH
ExperimentKeys.INCLUDE_LABELS_TRACTOGRAM_FILE_ROOTNAMES
ExperimentKeys.LATENT_SPACE_DIMS
ExperimentKeys.LOG_INTERVAL
ExperimentKeys.LOSS_FN
ExperimentKeys.MODEL_NAME
ExperimentKeys.NORMALIZE
ExperimentKeys.NUM_POINTS
ExperimentKeys.NUM_WORKERS
ExperimentKeys.OUT_PATH
ExperimentKeys.PKL_PATH
ExperimentKeys.RANDOM_FLIP
ExperimentKeys.REF_ANAT_FNAME
ExperimentKeys.STREAMLINE_COUNT_SUBSAMPLE_FACTOR
ExperimentKeys.TASK
ExperimentKeys.TO_SWAP
ExperimentKeys.TRACTOGRAM_DET_IMPLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_DET_PLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_FILTERING_DISTANCE_TEST_IMPLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_FILTERING_DISTANCE_TEST_PLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_GT_DATA_PATH
ExperimentKeys.TRACTOGRAM_PROB_IMPLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_PROB_PLAUS_TRACK_DATA_PATH
ExperimentKeys.TRACTOGRAM_TEST_IMPLAUS_DATA_PATH
ExperimentKeys.TRACTOGRAM_TEST_PLAUS_DATA_PATH
ExperimentKeys.TRACTOGRAM_TRAIN_IMPLAUS_DATA_PATH
ExperimentKeys.TRACTOGRAM_TRAIN_PLAUS_DATA_PATH
ExperimentKeys.TRACTOGRAM_VALID_IMPLAUS_DATA_PATH
ExperimentKeys.TRACTOGRAM_VALID_PLAUS_DATA_PATH
ExperimentKeys.TRK_PATH
ExperimentKeys.VIZ
ExperimentKeys.WEIGHTS
LearningTask
LossFunctionTypes
ThresholdTestKeys
ThresholdTestKeys.ATLAS_PATH
ThresholdTestKeys.DEVICE
ThresholdTestKeys.INVALID_BUNDLE_FILE
ThresholdTestKeys.INVALID_BUNDLE_FILE_TEST
ThresholdTestKeys.LATENT_DIMS
ThresholdTestKeys.MAX_IMPLAUSIBLE
ThresholdTestKeys.MAX_PLAUSIBLE
ThresholdTestKeys.MODEL
ThresholdTestKeys.MODEL_TYPE
ThresholdTestKeys.NO_THRESHOLD
ThresholdTestKeys.OUTPUT
ThresholdTestKeys.REFERENCE
ThresholdTestKeys.STREAMLINE_CLASSES
ThresholdTestKeys.STREAMLINE_LENGTH
ThresholdTestKeys.THRESHOLDS_FILE
ThresholdTestKeys.VALID_BUNDLE_PATH
ThresholdTestKeys.VALID_BUNDLE_PATH_TEST
ThresholdTestKeys.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
ROCSalientPoint
compute_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
StreamlineFeatures
StreamlineFeatures.CORTICAL_GAP
StreamlineFeatures.FA
StreamlineFeatures.GM_OCCUPANCY
StreamlineFeatures.LENGTH
StreamlineFeatures.LOCAL_ORIENTATION_ANGLE
StreamlineFeatures.MEAN_CURVATURE
StreamlineFeatures.REGION
StreamlineFeatures.SURFACE_INCIDENCE_ANGLE
StreamlineFeatures.SURFACE_INTERSECTION
StreamlineFeatures.SURFACE_PROJECTED_ANGLE
StreamlineFeatures.WINDING
StreamlineFeatures.WM_MEMBERSHIP
StreamlineFeatures.WM_OCCUPANCY
StreamlineFeatures.WM_VOXEL_OCCUPANCY_RATIO
StreamlineLocalOrientationAnalyzer
StreamlineLocalOrientationChecker
TractographyChecker
TractographyFeatureAnalyzer
compute_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
LatentSpaceKeys
LatentSpaceKeys.balanced_accuracy_label
LatentSpaceKeys.colorbar_fname_label
LatentSpaceKeys.confusion_matrix_fname_root
LatentSpaceKeys.filtering_stats_file_basename
LatentSpaceKeys.implaus_streamlines_tractogram_latent_distances_cbar_file_basename
LatentSpaceKeys.implausible_streamlines_latent_distances_file_basename
LatentSpaceKeys.latent_space_fname_label
LatentSpaceKeys.latent_space_histogram_cont_fname_label
LatentSpaceKeys.latent_space_histogram_fname_label
LatentSpaceKeys.latent_space_roc_fname_label
LatentSpaceKeys.latent_space_stats_fname_label
LatentSpaceKeys.latent_space_stats_raincloud_fname_label
LatentSpaceKeys.nearest_neighbor_fname_label
LatentSpaceKeys.plaus_streamlines_tractogram_latent_distances_cbar_file_basename
LatentSpaceKeys.plausible_streamlines_latent_distances_file_basename
LatentSpaceKeys.roc_data_file_basename
LatentSpaceKeys.test_data_fn_tractogram_fname_root
LatentSpaceKeys.test_data_fp_tractogram_fname_root
LatentSpaceKeys.test_data_reconst_implaus_tractogram_fname_root
LatentSpaceKeys.test_data_reconst_plaus_tractogram_fname_root
LatentSpaceKeys.test_data_tn_tractogram_fname_root
LatentSpaceKeys.test_data_tp_tractogram_fname_root
LatentSpaceKeys.threshold_fname_label
LatentSpaceKeys.tractogram_fname_label
- tractolearn.generative package
- tractolearn.learning package
- Submodules
- tractolearn.learning.data_manager module
- tractolearn.learning.dataset module
- tractolearn.learning.trainer_manager module
Trainer
Trainer.best_checkpoint
Trainer.best_model_fname
Trainer.build_model()
Trainer.experiment
Trainer.get_batch_iterator()
Trainer.load_checkpoint()
Trainer.lowest_loss
Trainer.model
Trainer.model_name
Trainer.normalize
Trainer.plot_results()
Trainer.save_checkpoint()
Trainer.save_loss_history()
Trainer.test_loader
Trainer.test_loss_recorder
Trainer.train()
Trainer.train_loader
Trainer.train_loss_recorder
Trainer.valid()
Trainer.valid_loader
Trainer.valid_loss_recorder
- Module contents
- tractolearn.models package
- tractolearn.tractoio package
- Subpackages
- Submodules
- tractolearn.tractoio.dataset_fetch module
Dataset
Dataset.BUNDLE_LABEL_CONFIG
Dataset.CONTRASTIVE_AUTOENCODER_WEIGHTS
Dataset.GENERATIVE_LOA_CONE_CONFIG
Dataset.GENERATIVE_SEED_STRML_RATIO_CONFIG
Dataset.GENERATIVE_STRML_MAX_COUNT_CONFIG
Dataset.GENERATIVE_STRML_RQ_COUNT_CONFIG
Dataset.GENERATIVE_WM_TISSUE_CRITERION_CONFIG
Dataset.MNI2009CNONLINSYMM_ANAT
Dataset.RECOBUNDLESX_ATLAS
Dataset.RECOBUNDLESX_CONFIG
Dataset.TRACTOINFERNO_HCP_CONTRASTIVE_THR_CONFIG
Dataset.TRACTOINFERNO_HCP_REF_TRACTOGRAPHY
Dataset.argparse()
DatasetError
FetcherError
check_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:
Enum
An 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'#