Index

A

add_verbosity_options_to_argparser() (in module PyMAIA.utils.log_utils)

C

convert_DICOM_folder_to_NIFTI_image() (in module PyMAIA.utils.volume_utils) convert_nifti_pred_to_dicom_seg() (in module PyMAIA.utils.file_utils) copy_data_from_dict_to_dataset_folder() (in module PyMAIA.utils.file_utils) copy_data_to_dataset_folder() (in module PyMAIA.utils.file_utils)

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

D

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

dcm2nii_mask() (in module PyMAIA.utils.volume_utils) dcm2nii_seg() (in module PyMAIA.utils.volume_utils)

G

generate_dataset_json() (in module PyMAIA.utils.file_utils) get_arg_parser() (in module PyMAIA_scripts.nndet_compute_metric_results) (in module PyMAIA_scripts.nndet_create_pipeline) (in module PyMAIA_scripts.nndet_extract_experiment_predictions) (in module PyMAIA_scripts.nndet_prepare_data_folder) (in module PyMAIA_scripts.nndet_run_preprocessing) (in module PyMAIA_scripts.nndet_run_training) (in module PyMAIA_scripts.nnunet_create_pipeline) (in module PyMAIA_scripts.nnunet_prepare_data_folder) (in module PyMAIA_scripts.nnunet_run_plan_and_preprocessing) (in module PyMAIA_scripts.nnunet_run_preprocessing) (in module PyMAIA_scripts.nnunet_run_training) (in module PyMAIA_scripts.PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset) (in module PyMAIA_scripts.PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG) (in module PyMAIA_scripts.PyMAIA_convert_semantic_to_instance_segmentation) (in module PyMAIA_scripts.PyMAIA_create_subset) (in module PyMAIA_scripts.PyMAIA_downsample_modality) (in module PyMAIA_scripts.PyMAIA_order_data_folder) (in module PyMAIA_scripts.PyMAIA_run_pipeline_from_file) (in module PyMAIA_scripts.script_template)

get_indices_of_iou() (in module PyMAIA_scripts.nndet_compute_metric_results) get_logger() (in module PyMAIA.utils.log_utils) get_unique_iou_thresholds() (in module PyMAIA_scripts.nndet_compute_metric_results)

I

iou_filter() (in module PyMAIA_scripts.nndet_compute_metric_results)

L

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

M

main() (in module PyMAIA_scripts.nndet_compute_metric_results) (in module PyMAIA_scripts.nndet_create_pipeline) (in module PyMAIA_scripts.nndet_extract_experiment_predictions) (in module PyMAIA_scripts.nndet_prepare_data_folder) (in module PyMAIA_scripts.nndet_run_preprocessing) (in module PyMAIA_scripts.nndet_run_training) (in module PyMAIA_scripts.nnunet_create_pipeline) (in module PyMAIA_scripts.nnunet_prepare_data_folder) (in module PyMAIA_scripts.nnunet_run_plan_and_preprocessing) (in module PyMAIA_scripts.nnunet_run_preprocessing) (in module PyMAIA_scripts.nnunet_run_training) (in module PyMAIA_scripts.PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset) (in module PyMAIA_scripts.PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG) (in module PyMAIA_scripts.PyMAIA_convert_semantic_to_instance_segmentation) (in module PyMAIA_scripts.PyMAIA_create_subset) (in module PyMAIA_scripts.PyMAIA_downsample_modality) (in module PyMAIA_scripts.PyMAIA_order_data_folder) (in module PyMAIA_scripts.PyMAIA_run_pipeline_from_file) (in module PyMAIA_scripts.script_template) module nndet_compute_metric_results nndet_create_pipeline nndet_extract_experiment_predictions nndet_prepare_data_folder nndet_run_preprocessing nndet_run_training nnunet_create_pipeline nnunet_prepare_data_folder nnunet_run_plan_and_preprocessing nnunet_run_preprocessing nnunet_run_training PyMAIA PyMAIA.monai PyMAIA.monai.apps PyMAIA.monai.apps.detection PyMAIA.monai.apps.detection.networks PyMAIA.utils PyMAIA.utils.file_utils PyMAIA.utils.log_utils PyMAIA.utils.seg_mask_utils PyMAIA.utils.volume_utils PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG PyMAIA_convert_semantic_to_instance_segmentation PyMAIA_create_subset PyMAIA_downsample_modality PyMAIA_order_data_folder PyMAIA_run_pipeline_from_file PyMAIA_scripts PyMAIA_scripts.nndet_compute_metric_results PyMAIA_scripts.nndet_create_pipeline PyMAIA_scripts.nndet_extract_experiment_predictions PyMAIA_scripts.nndet_prepare_data_folder PyMAIA_scripts.nndet_run_preprocessing PyMAIA_scripts.nndet_run_training PyMAIA_scripts.nnunet_create_pipeline PyMAIA_scripts.nnunet_prepare_data_folder PyMAIA_scripts.nnunet_run_plan_and_preprocessing PyMAIA_scripts.nnunet_run_preprocessing PyMAIA_scripts.nnunet_run_training PyMAIA_scripts.PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset PyMAIA_scripts.PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG PyMAIA_scripts.PyMAIA_convert_semantic_to_instance_segmentation PyMAIA_scripts.PyMAIA_create_subset PyMAIA_scripts.PyMAIA_downsample_modality PyMAIA_scripts.PyMAIA_order_data_folder PyMAIA_scripts.PyMAIA_run_pipeline_from_file PyMAIA_scripts.script_template

N

nndet_compute_metric_results module nndet_create_pipeline module nndet_extract_experiment_predictions module nndet_prepare_data_folder module nndet_run_preprocessing module nndet_run_training module

nnunet_create_pipeline module nnunet_prepare_data_folder module nnunet_run_plan_and_preprocessing module nnunet_run_preprocessing module nnunet_run_training module normalize_PET_to_SUV_BW() (in module PyMAIA.utils.volume_utils)

O

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

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

P

PyMAIA module PyMAIA.monai module PyMAIA.monai.apps module PyMAIA.monai.apps.detection module PyMAIA.monai.apps.detection.networks module PyMAIA.utils module PyMAIA.utils.file_utils module PyMAIA.utils.log_utils module PyMAIA.utils.seg_mask_utils module PyMAIA.utils.volume_utils module PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset module PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG module PyMAIA_convert_semantic_to_instance_segmentation module PyMAIA_create_subset module PyMAIA_downsample_modality module PyMAIA_order_data_folder module PyMAIA_run_pipeline_from_file module PyMAIA_scripts module PyMAIA_scripts.nndet_compute_metric_results module

PyMAIA_scripts.nndet_create_pipeline module PyMAIA_scripts.nndet_extract_experiment_predictions module PyMAIA_scripts.nndet_prepare_data_folder module PyMAIA_scripts.nndet_run_preprocessing module PyMAIA_scripts.nndet_run_training module PyMAIA_scripts.nnunet_create_pipeline module PyMAIA_scripts.nnunet_prepare_data_folder module PyMAIA_scripts.nnunet_run_plan_and_preprocessing module PyMAIA_scripts.nnunet_run_preprocessing module PyMAIA_scripts.nnunet_run_training module PyMAIA_scripts.PyMAIA_convert_DICOM_dataset_to_NIFTI_dataset module PyMAIA_scripts.PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG module PyMAIA_scripts.PyMAIA_convert_semantic_to_instance_segmentation module PyMAIA_scripts.PyMAIA_create_subset module PyMAIA_scripts.PyMAIA_downsample_modality module PyMAIA_scripts.PyMAIA_order_data_folder module PyMAIA_scripts.PyMAIA_run_pipeline_from_file module PyMAIA_scripts.script_template module

R

remove_empty_folder_recursive() (in module PyMAIA.utils.file_utils) resample_image() (in module PyMAIA.utils.volume_utils) run_data_and_folder_preparation_step() (in module PyMAIA_scripts.nndet_create_pipeline) (in module PyMAIA_scripts.nnunet_create_pipeline)

run_preprocessing_step() (in module PyMAIA_scripts.nndet_create_pipeline) (in module PyMAIA_scripts.nnunet_create_pipeline) run_training_step() (in module PyMAIA_scripts.nndet_create_pipeline) (in module PyMAIA_scripts.nnunet_create_pipeline)

S

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

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