Index

A

AbstractEvaluator (class in Hive.evaluation.abstract)

AbstractMetric (class in Hive.evaluation.abstract) add_verbosity_options_to_argparser() (in module Hive.utils.log_utils)

C

check_number_of_iou() (Hive.evaluation.abstract.DetectionMetric method) compute() (Hive.evaluation.abstract.AbstractMetric method) convert_DICOM_folder_to_NIFTI_image() (in module Hive.utils.volume_utils) convert_nifti_pred_to_dicom_seg() (in module Hive.utils.file_utils) copy_data_to_dataset_folder() (in module Hive.utils.file_utils)

copy_image_file() (in module Hive.utils.file_utils) copy_label_file() (in module Hive.utils.file_utils) copy_subject_folder_to_data_folder() (in module Hive.utils.file_utils) create_nndet_data_folder_tree() (in module Hive.utils.file_utils) create_nnunet_data_folder_tree() (in module Hive.utils.file_utils)

D

dcm2nii_CT() (in module Hive.utils.volume_utils)

dcm2nii_mask() (in module Hive.utils.volume_utils) DetectionMetric (class in Hive.evaluation.abstract)

F

finish_online_evaluation() (Hive.evaluation.abstract.AbstractEvaluator method)

G

generate_dataset_json() (in module Hive.utils.file_utils) get_arg_parser() (in module Hive_scripts.Hive_convert_DICOM_dataset_to_NIFTI_dataset) (in module Hive_scripts.Hive_convert_semantic_to_instance_segmentation) (in module Hive_scripts.Hive_create_subset) (in module Hive_scripts.Hive_extract_experiment_predictions) (in module Hive_scripts.Hive_order_data_folder) (in module Hive_scripts.Hive_run_pipeline_from_file) (in module Hive_scripts.nndet_create_pipeline) (in module Hive_scripts.nndet_prepare_data_folder) (in module Hive_scripts.nndet_run_preprocessing) (in module Hive_scripts.nndet_run_training) (in module Hive_scripts.script_template)

get_iou_thresholds() (Hive.evaluation.abstract.DetectionMetric method) get_logger() (in module Hive.utils.log_utils)

H

Hive module Hive.evaluation module Hive.evaluation.abstract module Hive.evaluation.detection module Hive.evaluation.detection.matching module Hive.utils module Hive.utils.file_utils module Hive.utils.log_utils module Hive.utils.seg_mask_utils module Hive.utils.volume_utils module Hive_convert_DICOM_dataset_to_NIFTI_dataset module Hive_convert_semantic_to_instance_segmentation module Hive_create_subset module Hive_extract_experiment_predictions module

Hive_order_data_folder module Hive_run_pipeline_from_file module Hive_scripts module Hive_scripts.Hive_convert_DICOM_dataset_to_NIFTI_dataset module Hive_scripts.Hive_convert_semantic_to_instance_segmentation module Hive_scripts.Hive_create_subset module Hive_scripts.Hive_extract_experiment_predictions module Hive_scripts.Hive_order_data_folder module Hive_scripts.Hive_run_pipeline_from_file module Hive_scripts.nndet_create_pipeline module Hive_scripts.nndet_prepare_data_folder module Hive_scripts.nndet_run_preprocessing module Hive_scripts.nndet_run_training module Hive_scripts.script_template module

L

log_lvl_from_verbosity_args() (in module Hive.utils.log_utils)

M

main() (in module Hive_scripts.Hive_convert_DICOM_dataset_to_NIFTI_dataset) (in module Hive_scripts.Hive_convert_semantic_to_instance_segmentation) (in module Hive_scripts.Hive_create_subset) (in module Hive_scripts.Hive_extract_experiment_predictions) (in module Hive_scripts.Hive_order_data_folder) (in module Hive_scripts.Hive_run_pipeline_from_file) (in module Hive_scripts.nndet_create_pipeline) (in module Hive_scripts.nndet_prepare_data_folder) (in module Hive_scripts.nndet_run_preprocessing) (in module Hive_scripts.nndet_run_training) (in module Hive_scripts.script_template) matching_batch() (in module Hive.evaluation.detection.matching) module Hive Hive.evaluation Hive.evaluation.abstract Hive.evaluation.detection Hive.evaluation.detection.matching Hive.utils Hive.utils.file_utils Hive.utils.log_utils Hive.utils.seg_mask_utils Hive.utils.volume_utils Hive_convert_DICOM_dataset_to_NIFTI_dataset Hive_convert_semantic_to_instance_segmentation Hive_create_subset Hive_extract_experiment_predictions Hive_order_data_folder Hive_run_pipeline_from_file Hive_scripts Hive_scripts.Hive_convert_DICOM_dataset_to_NIFTI_dataset Hive_scripts.Hive_convert_semantic_to_instance_segmentation Hive_scripts.Hive_create_subset Hive_scripts.Hive_extract_experiment_predictions Hive_scripts.Hive_order_data_folder Hive_scripts.Hive_run_pipeline_from_file Hive_scripts.nndet_create_pipeline Hive_scripts.nndet_prepare_data_folder Hive_scripts.nndet_run_preprocessing Hive_scripts.nndet_run_training Hive_scripts.script_template nndet_create_pipeline nndet_prepare_data_folder nndet_run_preprocessing nndet_run_training

N

nndet_create_pipeline module nndet_prepare_data_folder module

nndet_run_preprocessing module nndet_run_training module normalize_PET_to_SUV_BW() (in module Hive.utils.volume_utils)

O

order_data_folder_by_patient() (in module Hive.utils.file_utils)

order_data_in_single_folder() (in module Hive.utils.file_utils)

R

remove_empty_folder_recursive() (in module Hive.utils.file_utils) reset() (Hive.evaluation.abstract.AbstractEvaluator method) run_data_and_folder_preparation_step() (in module Hive_scripts.nndet_create_pipeline)

run_online_evaluation() (Hive.evaluation.abstract.AbstractEvaluator method) run_preprocessing_step() (in module Hive_scripts.nndet_create_pipeline) run_training_step() (in module Hive_scripts.nndet_create_pipeline)

S

save_config_json() (in module Hive.utils.file_utils) semantic_segmentation_to_instance() (in module Hive.utils.seg_mask_utils) setup_logging() (in module Hive.utils.log_utils)

split_dataset() (in module Hive.utils.file_utils) str2bool() (in module Hive.utils.log_utils) subfiles() (in module Hive.utils.file_utils) subfolders() (in module Hive.utils.file_utils)