Index

A

add_clean_arguments() (in module imperandi.ingest.clean) add_convert_arguments() (in module imperandi.process.convert) add_date() (in module imperandi.ingest.clean) add_parse_arguments() (in module imperandi.ingest.parse) add_phase_arguments() (in module imperandi.extract.phase)

add_radiomics_arguments() (in module imperandi.extract.radiomics) add_segment_arguments() (in module imperandi.process.segment) add_time() (in module imperandi.ingest.clean) apply_derived_columns() (in module imperandi.ingest.apply_hook_manifests) apply_id_standardization() (in module imperandi.ingest.apply_hook_manifests)

B

build_effective_tags() (in module imperandi.ingest.parse) build_global_readers() (in module imperandi.ingest.parse) build_output_column_map() (in module imperandi.process.segment) build_output_fetch_map() (in module imperandi.process.segment) build_parser() (in module imperandi.cli) (in module imperandi.extract.phase) (in module imperandi.extract.radiomics) (in module imperandi.ingest.clean) (in module imperandi.ingest.parse) (in module imperandi.process.convert) (in module imperandi.process.segment)

C

calculate_volume_length() (in module imperandi.ingest.clean) choose_ids() (in module imperandi.ingest.parse) clean_and_merge_masks() (in module imperandi.process.segment) clean_and_save_data() (in module imperandi.ingest.clean) clean_pixel_spacing() (in module imperandi.ingest.clean) clean_scan_size() (in module imperandi.ingest.clean) clip_hu_values() (in module imperandi.qc.viewer)

compute_acquisition_order() (in module imperandi.ingest.clean) compute_struct_elem() (in module imperandi.process.segment) compute_visit_order() (in module imperandi.ingest.clean) convert_dicom_to_nifti_parallel() (in module imperandi.process.convert) convert_list_str_to_list() (in module imperandi.process.convert) correct_volume_ids() (in module imperandi.ingest.clean) CTScanViewer (class in imperandi.qc.viewer)

D

default_output_dir() (in module imperandi.ingest.parse)

detect_archive_mode_by_subsample() (in module imperandi.ingest.parse) drop_irrelevant_dicom_tags() (in module imperandi.ingest.clean)

E

ensure_directory_exists() (in module imperandi.ingest.parse) extract_dicom_tags_recursive() (in module imperandi.ingest.parse)

extract_radiomics_organ_minus_tumor() (in module imperandi.extract.radiomics) extract_radiomics_safe() (in module imperandi.extract.radiomics)

F

filter_by_acquisition_plane() (in module imperandi.ingest.clean) filter_ct_modality() (in module imperandi.ingest.clean)

filter_image_type() (in module imperandi.ingest.clean) filter_volumes_by_size() (in module imperandi.ingest.clean)

G

generate_volume_id() (in module imperandi.ingest.clean) get_dicom_path_entries() (in module imperandi.ingest.parse)

get_dicom_paths() (in module imperandi.ingest.parse) group_volumes() (in module imperandi.ingest.clean)

I

imperandi module imperandi.cli module imperandi.extract.phase module imperandi.extract.radiomics module imperandi.ingest.apply_hook_manifests module imperandi.ingest.clean module

imperandi.ingest.parse module imperandi.process.convert module imperandi.process.segment module imperandi.qc.viewer module imperandi.qc.viewer_resample module infer_task_fetch_outputs() (in module imperandi.process.segment) infer_task_outputs() (in module imperandi.process.segment) init_widgets() (imperandi.qc.viewer.CTScanViewer method)

L

load_data() (imperandi.qc.viewer.CTScanViewer method) (in module imperandi.ingest.clean) load_nifti() (in module imperandi.process.segment) (in module imperandi.qc.viewer)

load_nifti_isotropic() (in module imperandi.qc.viewer_resample) load_oriented_nifti() (in module imperandi.qc.viewer_resample) load_segmentation_config() (in module imperandi.process.segment)

M

main() (in module imperandi) (in module imperandi.cli) (in module imperandi.extract.phase) (in module imperandi.extract.radiomics) (in module imperandi.ingest.parse) (in module imperandi.process.convert) (in module imperandi.process.segment) map_series_description() (in module imperandi.ingest.clean) mask_has_voxels() (in module imperandi.extract.radiomics) materialize_archive_dicom_paths() (in module imperandi.process.convert) module imperandi imperandi.cli imperandi.extract.phase imperandi.extract.radiomics imperandi.ingest.apply_hook_manifests imperandi.ingest.clean imperandi.ingest.parse imperandi.process.convert imperandi.process.segment imperandi.qc.viewer imperandi.qc.viewer_resample

N

normalize_clean_args() (in module imperandi.ingest.clean) normalize_convert_args() (in module imperandi.process.convert) normalize_parse_args() (in module imperandi.ingest.parse)

normalize_phase_args() (in module imperandi.extract.phase) normalize_radiomics_args() (in module imperandi.extract.radiomics) normalize_segment_args() (in module imperandi.process.segment)

O

on_center_on_lesion() (imperandi.qc.viewer.CTScanViewer method) on_date_change() (imperandi.qc.viewer.CTScanViewer method) on_key_press() (imperandi.qc.viewer.CTScanViewer method) on_next() (imperandi.qc.viewer.CTScanViewer method) on_next_date() (imperandi.qc.viewer.CTScanViewer method) on_next_patient() (imperandi.qc.viewer.CTScanViewer method) on_next_slice_manual() (imperandi.qc.viewer.CTScanViewer method) on_patient_change() (imperandi.qc.viewer.CTScanViewer method) on_phase_change() (imperandi.qc.viewer.CTScanViewer method)

on_plane_change() (imperandi.qc.viewer.CTScanViewer method) on_prev() (imperandi.qc.viewer.CTScanViewer method) on_prev_date() (imperandi.qc.viewer.CTScanViewer method) on_prev_patient() (imperandi.qc.viewer.CTScanViewer method) on_prev_slice() (imperandi.qc.viewer.CTScanViewer method) on_resolution_change() (imperandi.qc.viewer.CTScanViewer method) on_seg_visibility_change() (imperandi.qc.viewer.CTScanViewer method) on_slice_change() (imperandi.qc.viewer.CTScanViewer method) on_window_preset_change() (imperandi.qc.viewer.CTScanViewer method)

P

parse_arguments() (in module imperandi.extract.phase) (in module imperandi.extract.radiomics) (in module imperandi.ingest.clean) (in module imperandi.ingest.parse) (in module imperandi.process.convert)

prefetch_totalsegmentator_models() (in module imperandi.process.segment) process_single_volume() (in module imperandi.extract.phase) (in module imperandi.process.convert) (in module imperandi.process.segment) process_with_checkpoint() (in module imperandi.ingest.parse)

R

read_csv_with_valid_columns() (in module imperandi.ingest.clean) read_dicom_header() (in module imperandi.ingest.parse) read_dicom_header_archive_aware() (in module imperandi.ingest.parse) read_dicom_header_selected() (in module imperandi.ingest.parse) read_dicom_header_selected_archive_aware() (in module imperandi.ingest.parse) read_dicom_header_selected_standard() (in module imperandi.ingest.parse) read_dicom_header_standard() (in module imperandi.ingest.parse) read_dicom_header_with_force() (in module imperandi.ingest.parse) remove_mpr() (in module imperandi.ingest.clean)

remove_other_organs_description() (in module imperandi.ingest.clean) remove_pet_ct() (in module imperandi.ingest.clean) remove_scouts_localizers() (in module imperandi.ingest.clean) reorder_columns() (in module imperandi.ingest.clean) reorder_rows() (in module imperandi.ingest.clean) resample_to_isotropic() (in module imperandi.qc.viewer_resample) resolve_merge_outputs() (in module imperandi.process.segment) resolve_root_paths() (in module imperandi.ingest.parse) run() (imperandi.process.segment.TotalSegmentatorBackend method)

S

save_nifti() (in module imperandi.process.segment)

segment_volume() (in module imperandi.process.segment)

T

TotalSegmentatorBackend (class in imperandi.process.segment)

U

uniform_string() (in module imperandi.ingest.clean) update_display() (imperandi.qc.viewer.CTScanViewer method)

update_info_display() (imperandi.qc.viewer.CTScanViewer method) update_slice_slider() (imperandi.qc.viewer.CTScanViewer method)

V

validate_isotropic_resolution() (in module imperandi.qc.viewer_resample)

W

write_dicom_tags_snapshot() (in module imperandi.ingest.parse)