Index

A

activity_log_message() (xfworkerutil.XFWorkerJob method) ActivityLogLevel (class in xfworkerutil) additional_pixels_filenames (omni.Image property) after_last() (in module xfsortorder) aim_type (aimio.AimReader attribute) aim_version_3 (aimio.AimReader attribute) aimio module AimReader (class in aimio) AimWriter (class in aimio)

AlphaLUTHardcoded (class in lifsnapshot) append_field() (aimio.ProcessingLog method) append_min_max_data_values() (aimio.ProcessingLog method) append_min_max_data_values_from_pixels() (aimio.ProcessingLog method) append_parameter_name_and_units() (aimio.ProcessingLog method) append_parameter_seg() (aimio.ProcessingLog method) attributes (plyio.PlyMesh property) AuthorizationToken (class in network) AuthorizationToken.AuthorizationScope (class in network) axes (omni.Image property)

B

basic_authentication() (in module network) bearer_authentication() (in module network) before_first() (in module xfsortorder) between() (in module xfsortorder)

border_size (omni.InvalidPixels property) bounding_max (omnimesh.Mesh property) bounding_min (omnimesh.Mesh property) BulkChunk (class in lifsnapshot)

C

calibrated_to_raw() (omni.Calibration method) Calibration (class in omni) Calibrations (class in aimio) Camera (class in lifsnapshot) check_all_read() (aimio.AimReader method) (isqio.IsqReader method) check_status() (network.Connection method) checked_aim_image() (in module iplutil) Chunk (class in lifsnapshot) ChunkCheck (class in labspecio) ChunkCode (class in labspecio) ChunkType (class in labspecio) clear_error_message() (xfworkerutil.XFWorkerJob method) ClipPlane (class in lifsnapshot) ClipPlaneCollection (class in lifsnapshot) CLKernel (class in openclutil) close() (aimio.AimReader method) (aimio.AimWriter method) (network.Connection method) CodecInfo (class in ffmpegutil) color (omnimesh.MeshGroup property) ColorLUTHardcoded (class in lifsnapshot) common_prefix() (in module xfsortorder) configure_logging() (in module logutil) Connection (class in network) convert_ipl_syntax() (in module iplutil) convert_omni_to_aim() (in module iplaimconvert) convert_or_move_raw_float32_pixels_file_to() (in module lupoutil) copy_array_to_image() (openclutil.CLKernel method)

copy_image_to_array() (openclutil.CLKernel method) count (plyio.PlyHeaderElement attribute) create_activity_log_event() (in module xfworkerutil) create_empty_file() (in module fileioutil) create_output_bitmap() (xfworkerutil.XFWorkerJob method) create_output_contours() (xfworkerutil.XFWorkerJob method) create_output_csv() (xfworkerutil.XFWorkerJob method) create_output_entity() (xfworkerutil.XFWorkerJob method) create_output_foreign_file() (xfworkerutil.XFWorkerJob method) create_output_gi_result() (xfworkerutil.XFWorkerJob method) create_output_html_document() (xfworkerutil.XFWorkerJob method) create_output_image() (xfworkerutil.XFWorkerJob method) create_output_image_pair_list() (xfworkerutil.XFWorkerJob method) create_output_image_voi() (xfworkerutil.XFWorkerJob method) create_output_mesh() (xfworkerutil.XFWorkerJob method) create_output_path() (xfworkerutil.XFWorkerJob method) create_output_registration_result() (xfworkerutil.XFWorkerJob method) create_output_rotated_image_voi() (xfworkerutil.XFWorkerJob method) create_output_snapshot() (xfworkerutil.XFWorkerJob method) create_output_snapshot_metadata() (xfworkerutil.XFWorkerJob method) create_output_spectra() (xfworkerutil.XFWorkerJob method) create_output_video() (xfworkerutil.XFWorkerJob method) create_parameter() (in module xfworkerutil) create_related_path() (xfworkerutil.TemporaryWorkingDirectory method) (xfworkerutil.XFWorkerJob method) create_temp_path() (xfworkerutil.TemporaryWorkingDirectory method) (xfworkerutil.XFWorkerJob method) create_xf_job() (in module xfworkerutil) create_xf_task() (in module xfworkerutil)

D

D1TbinCmp (in module aimio) D1Tchar (in module aimio) D1TcharCmp (in module aimio) D1Tint (in module aimio) D1Tpixel (in module aimio) D1Tshort (in module aimio) D1Tuchar (in module aimio) D1Tushort (in module aimio) data_offset (aimio.AimReader attribute) Database debug_print_lifsnapshot() (in module lifsnapshot) debug_print_mlsd_header() (in module mlsdio) default_pixel_calibration_unit_type (omni.Image property) default_unit_type (aimio.Calibrations attribute) delete() (network.Connection method) delete_empty_directory_on_filestorage() (in module network) delete_file_on_filestorage() (in module network)

dens_intercept (aimio.Calibrations attribute) dens_slope (aimio.Calibrations attribute) dens_unit (aimio.Calibrations attribute) dens_valid (aimio.Calibrations attribute) Dependency Package derive_image() (omni.Image method) derive_segments() (omni.Image method) detect_lupo_version() (in module lupoutil) detect_major_ipl_version() (in module iplutil) dimensions (omni.Image property) DirectAccessHeader (class in network) download_additional_input_files() (xfworkerutil.XFWorkerJob method) download_input_file() (xfworkerutil.XFWorkerJob method) download_related_input_file() (xfworkerutil.XFWorkerJob method) download_xf_dependency_package_config_file() (xfworkerutil.XFWorkerJob method) download_xf_task_type_config_file() (xfworkerutil.XFWorkerJob method) download_xf_userdata_file() (xfworkerutil.XFWorkerJob method) download_xf_workflow_config_file() (xfworkerutil.XFWorkerJob method)

E

EGObjMode (class in gobjio) EGObjType (class in gobjio) element_size() (plyio.PlyHeaderElement method) ensure_pixels_loaded() (omni.Image method)

Entity error() (xfworkerutil.XFWorkerJob method) escape() (in module ffmpegutil) extract_raw_pixels_file() (in module lupoutil) extract_raw_uint8_pixels_file() (in module lupoutil)

F

ffmpegutil module ffprobe_avg_frame_rate() (in module ffmpegutil) ffprobe_json() (in module ffmpegutil) ffprobe_json_format() (in module ffmpegutil) ffprobe_json_streams() (in module ffmpegutil) File Storage Service file_exists_on_filestorage() (in module network) fileioutil module files (omnimesh.MeshGroup property) find_xf_task_type() (xfworkerutil.XFWorkerJob method) find_xf_task_types() (xfworkerutil.XFWorkerJob method) finish() (xfworkerutil.XFWorkerJob method) Follower Task format (omni.Image property) (omnimesh.Mesh property)

format_version() (in module xfworkerutil) format_vms_style_time() (in module vmsutil) from_chunks() (lifsnapshot.AlphaLUTHardcoded static method) (lifsnapshot.Camera static method) (lifsnapshot.ClipPlane static method) (lifsnapshot.ClipPlaneCollection static method) (lifsnapshot.ColorLUTHardcoded static method) (lifsnapshot.LightEnv static method) (lifsnapshot.MeshGroup static method) (lifsnapshot.MeshSet static method) (lifsnapshot.WindowLevel static method) from_numpy_array() (omni.Image static method) from_vms_string() (in module vmsutil) from_vms_time() (in module vmsutil) FSS

G

get() (network.Connection method) get_aim_size() (in module aimio) get_alpha_lut_hardcoded() (lifsnapshot.SnapshotView method) get_alpha_window_level() (lifsnapshot.SnapshotView method) get_background_color() (lifsnapshot.SnapshotView method) get_bool() (lifsnapshot.Chunk method) get_camera() (lifsnapshot.SnapshotView method) get_clip_planes() (lifsnapshot.SnapshotView method) get_color() (lifsnapshot.Chunk method) get_color_lut_hardcoded() (lifsnapshot.SnapshotView method) get_coordinates() (gobjio.GObjCompressedContour method) get_current_task() (xfworkerutil.XFWorkerJob method) get_debug_info() (xfworkerutil.XFWorkerJob method) get_error_response_json_message() (network.Connection method) get_exe_path() (in module imagejutil) (in module lupoutil) get_existing_job_sort_orders() (xfworkerutil.XFWorkerJob method) get_file_from_filestorage() (in module network) get_file_size_from_filestorage() (in module network) get_float() (iplutil.ParsedIPLParameter method) get_float32_lut() (lifsnapshot.AlphaLUTHardcoded method) get_float64() (lifsnapshot.Chunk method) get_float64_2d() (lifsnapshot.Chunk method) get_float64_3d() (lifsnapshot.Chunk method) get_int32() (lifsnapshot.Chunk method) get_int32_2d() (lifsnapshot.Chunk method) get_int32_3d() (lifsnapshot.Chunk method) get_int64() (lifsnapshot.Chunk method) get_ipl_exe_path() (in module iplutil) get_ipl_image_path() (xfworkerutil.XFWorkerJob method) get_json() (network.Connection method) get_light_env() (lifsnapshot.SnapshotView method) get_matplotlib_cmap() (lifsnapshot.ColorLUTHardcoded method) get_mesh_set() (lifsnapshot.SnapshotView method) get_mesh_view() (lifsnapshot.Snapshot method) get_mpi_ntask_default() (in module runutil) get_new_source_job_sort_order() (in module xfsortorder) get_new_source_job_sort_orders() (in module xfsortorder) get_new_source_job_sort_orders_directly_after() (in module xfsortorder) get_omni_image() (xfworkerutil.XFWorkerJob method) get_or_extract_raw_float32_pixels_file() (in module lupoutil) get_or_extract_raw_pixels_file() (in module lupoutil) get_or_extract_raw_uint8_pixels_file() (in module lupoutil) get_parameter_file_references() (in module xfworkerutil) get_parameter_file_token() (in module xfworkerutil) get_regex_pattern_full_line() (iplutil.IPLParameterParser method) get_regex_pattern_one_of() (iplutil.IPLParameterParser method) get_relative_voi_pos_of_target_image() (omni.Image method) get_run_entity() (xfworkerutil.XFWorkerJob method) get_sns_meas_dir_token() (in module network) get_sns_meas_file_token() (in module network)

get_sns_server_connection() (in module xfworkerutil) get_sns_token() (in module network) get_str() (lifsnapshot.Chunk method) get_transform() (lifsnapshot.Chunk method) get_uint32() (lifsnapshot.Chunk method) get_uint8() (lifsnapshot.Chunk method) get_virtualpath_dirname() (in module network) get_virtualpath_filename() (in module network) get_vr_dual_view() (lifsnapshot.Snapshot method) get_vr_view() (lifsnapshot.Snapshot method) get_window_level() (lifsnapshot.SnapshotView method) get_xf_combined_query() (in module xfworkerutil) get_xf_default_sns_server_connection_params() (in module xfworkerutil) get_xf_dependency_package_config_token() (in module xfworkerutil) get_xf_job() (in module xfworkerutil) get_xf_job_log_token() (in module xfworkerutil) get_xf_job_result_token() (in module xfworkerutil) get_xf_jobs_by_task() (in module xfworkerutil) get_xf_jobs_by_workflow() (in module xfworkerutil) get_xf_parameter_float_sequence() (in module xfworkerutil) get_xf_parameter_paired_float_sequences() (in module xfworkerutil) get_xf_parameter_sequence() (in module xfworkerutil) get_xf_project() (in module xfworkerutil) get_xf_projects() (in module xfworkerutil) get_xf_task() (in module xfworkerutil) get_xf_task_config_token() (in module xfworkerutil) get_xf_task_type() (in module xfworkerutil) get_xf_task_type_config_token() (in module xfworkerutil) get_xf_task_types() (in module xfworkerutil) get_xf_tasks_by_workflow() (in module xfworkerutil) get_xf_userdata_token() (in module xfworkerutil) get_xf_workflow() (in module xfworkerutil) get_xf_workflow_config_token() (in module xfworkerutil) get_xf_workflow_run() (in module xfworkerutil) get_xf_workflows_by_project() (in module xfworkerutil) get_xml_element_text() (network.AuthorizationToken method) get_xml_optional_element_text() (network.AuthorizationToken method) GObjBase (class in gobjio) GObjCommonStruct (class in gobjio) GObjCompressedContour (class in gobjio) GObjCompressedContourHeaderStruct (class in gobjio) GObjEllipse (class in gobjio) GObjFile (class in gobjio) GObjHeaderStruct (class in gobjio) gobjio module GObjParent (class in gobjio) GObjParentTransformStruct (class in gobjio) GObjReader (class in gobjio) GObjRectangle (class in gobjio) groups (omnimesh.Mesh property)

H

has_attributes() (plyio.PlyMesh method) head_response() (network.Connection method) header (aimio.AimReader attribute) Header (class in labspecio)

header_elements (plyio.PlyMesh attribute) HierarchyChunk (class in lifsnapshot) hook_exceptions() (xfworkerutil.XFWorkerJob method) hu_valid (aimio.Calibrations attribute)

I

Image (class in omni) image_relations (omni.Image property) imagejutil module ImageRelation (class in omni) import_from_aim() (in module omni) import_from_isq() (in module omni) import_from_mlsd() (in module omni) indices (plyio.PlyMesh attribute) indirect_base_unit_type (omni.Calibration property) inherit_env() (in module runutil) inherit_metadata() (omni.Image method) Interactive Task intercept (omni.Calibration property) invalid_pixels (omni.Image property) InvalidLIFSnapshot InvalidPixels (class in omni) IPL ipl_args() (in module iplutil) iplaimconvert module

IPLParameterParser (class in iplutil) IplStdoutChecker (class in iplutil) iplutil module is_bulk_chunk_type() (in module lifsnapshot) is_chunk_type_mode() (in module lifsnapshot) is_direct_access_possible() (network.DirectAccessHeader method) is_generic_chunk_type() (in module lifsnapshot) is_hierarchic_chunk_type() (in module lifsnapshot) is_lupo_version_compatible() (in module lupoutil) is_mpi_installed() (in module runutil) is_standard_chunk_type() (in module lifsnapshot) is_under() (xfworkerutil.TemporaryWorkingDirectory method) isotropic_pixel_size_mm() (omni.Image method) IsqCalibration (class in isqio) IsqExtendedHeader (class in isqio) IsqHeader (class in isqio) isqio module IsqReader (class in isqio) ItemChunk (class in lifsnapshot)

J

Job	job_serial (xfworkerutil.XFWorkerArguments property)

K

kind (plyio.PlyHeaderProperty attribute)

L

LabSpecError labspecio module lifsnapshot module LightEnv (class in lifsnapshot) list_files_and_folders_on_filestorage() (in module network) list_files_on_filestorage() (in module network) load() (omni.Image static method) (omnimesh.Mesh static method) load_aim() (in module aimio)

load_job() (xfworkerutil.XFWorkerJob method) load_lifsnapshot() (in module lifsnapshot) log (aimio.AimReader attribute) log_time() (in module logutil) logutil module Lucid LUPO LUPO lupo_version_not_expected_message() (in module lupoutil) lupoutil module

M

many_after_last() (in module xfsortorder) many_after_prefix() (in module xfsortorder) many_between() (in module xfsortorder) Mesh (class in omnimesh) MeshGroup (class in lifsnapshot) (class in omnimesh) MeshSet (class in lifsnapshot) mlsdio module MLSDReader (class in mlsdio) module aimio ffmpegutil fileioutil gobjio imagejutil iplaimconvert iplutil isqio labspecio lifsnapshot logutil lupoutil mlsdio network omni omnimesh openclutil plyio runutil vmsutil xfsortorder xfworkerutil

mu_scaling (aimio.Calibrations attribute) mu_valid (aimio.Calibrations attribute) mu_water (aimio.Calibrations attribute)

N

name (omni.PixelValueObject property) (omnimesh.MeshGroup property) (plyio.PlyHeaderElement attribute) (plyio.PlyHeaderProperty attribute)

network module normals (plyio.PlyMesh attribute)

O

offset (aimio.AimReader attribute) OMNI omni module

omnimesh module openclutil module overwrite_bytes() (in module fileioutil)

P

Package parse() (iplutil.IPLParameterParser method) parse_calibrations() (aimio.ProcessingLog method) parse_ipl_parameter() (in module iplutil) parse_ipl_translated_symbol() (in module iplutil) parse_ipl_whitespace_parameter() (in module iplutil) parse_max_data_value() (aimio.ProcessingLog method) parse_min_data_value() (aimio.ProcessingLog method) parse_parameter_units() (aimio.ProcessingLog method) parse_version() (in module xfworkerutil) ParsedIPLParameter (class in iplutil) percent_encode_relaxed_virtualpath() (in module network) PipeProcessInfo (class in runutil) pixel_calibrations (omni.Image property) pixel_calibrations_of_unit_type() (omni.Image method) pixel_max_value (omni.Image property) pixel_min_value (omni.Image property) pixel_size_mm (omni.Image property) pixel_size_mm_3d (omni.Image property) pixel_type (omni.Image property) pixel_value (omni.PixelValueObject property) pixel_value_objects (omni.Image property)

pixels (omni.Image property) pixels_compression (omni.Image property) pixels_count (omni.Image property) pixels_file_data_offset (omni.Image property) pixels_filename (omni.Image property) PixelValueObject (class in omni) PlyHeaderElement (class in plyio) PlyHeaderProperty (class in plyio) plyio module PlyMesh (class in plyio) pos (aimio.AimReader attribute) positions (plyio.PlyMesh property) post() (network.Connection method) post_json() (network.Connection method) PostgreSQL Processing Task ProcessingLog (class in aimio) progress() (xfworkerutil.XFWorkerJob method) properties (plyio.PlyHeaderElement attribute) put() (network.Connection method) put_file_to_filestorage() (in module network) put_json() (network.Connection method)

Q

quote_for_cmd_exe() (in module runutil) quote_for_subprocess() (in module runutil)

quote_naively() (in module runutil) quoted_path() (in module iplutil)

R

raw_stddev_to_calibrated_stddev() (omni.Calibration method) raw_to_calibrated() (omni.Calibration method) raw_variance_to_calibrated_variance() (omni.Calibration method) read_chunk_header() (in module lifsnapshot) read_chunks() (in module lifsnapshot) read_compact() (in module lifsnapshot) read_header() (in module lifsnapshot) read_leb128() (in module mlsdio) read_pixels() (aimio.AimReader method) read_ply() (in module plyio) read_ply_header_line() (in module plyio) read_unpack() (in module lifsnapshot) remove() (xfworkerutil.TemporaryWorkingDirectory method) remove_image_relation() (omni.Image method) request_with_retry() (network.Connection method) res_nano (aimio.AimReader attribute) resave_all() (omni.Image method) resave_compressed() (omni.Image method) RFC RFC 5280 Run

run() (in module runutil) run_crop_pad_target_voi() (in module lupoutil) run_ffmpeg() (in module ffmpegutil) run_ffprobe() (in module ffmpegutil) run_imagej_script() (in module imagejutil) run_ipl() (in module iplutil) run_ipl_content() (in module iplutil) run_label_components() (in module lupoutil) run_label_components_intersected_by_seed() (in module lupoutil) run_lupo() (in module lupoutil) run_lupo_mpi() (in module lupoutil) run_lupom() (in module lupoutil) run_morph_dilate_erode() (in module lupoutil) run_morph_open_close() (in module lupoutil) run_mpi() (in module runutil) run_pad_only_target_voi() (in module lupoutil) run_pipe() (in module runutil) run_reconstruction() (in module runutil) run_rscript() (in module runutil) runutil module

S

save_aim() (in module aimio) save_all() (omni.Image method) save_derived_image() (omni.Image method) save_derived_segments() (omni.Image method) save_job() (xfworkerutil.XFWorkerJob method) save_metadata() (omni.Image method) (omnimesh.Mesh method) save_pixels() (omni.Image method) save_pixels_as() (omni.Image method) Section (class in labspecio) SectionHeader (class in labspecio) SectionType (class in labspecio) Segments() (in module omni) segments_type (omni.Image property) select_device() (in module openclutil) Sequence Server server_auth (xfworkerutil.XFWorkerArguments property) server_connection() (xfworkerutil.XFWorkerJob method) server_host (xfworkerutil.XFWorkerArguments property) server_port (xfworkerutil.XFWorkerArguments property) set_default_image_relation() (omni.Image method) set_error_message() (xfworkerutil.XFWorkerJob method) set_estimated_duration() (xfworkerutil.XFWorkerJob method)

set_file_size() (in module fileioutil) set_image_relation() (omni.Image method) set_or_add_voi_pixel_position() (omni.ImageRelation method) set_output_units() (xfworkerutil.XFWorkerJob method) single() (in module xfsortorder) size (aimio.AimReader attribute) (omni.Image property) (plyio.PlyHeaderProperty attribute) size_3d (omni.Image property) size_3d_tuple (omni.Image property) size_mm (omnimesh.Mesh property) slices_read (aimio.AimReader attribute) slope (omni.Calibration property) Snapshot (class in lifsnapshot) SnapshotView (class in lifsnapshot) SNS sns_translate_logical() (in module network) Source Task spawn_xf_job_basic() (xfworkerutil.XFWorkerJob method) spawn_xf_task_basic() (xfworkerutil.XFWorkerJob method) spawn_xf_task_type_basic() (xfworkerutil.XFWorkerJob method) startupinfo() (in module runutil) subdir() (xfworkerutil.TemporaryWorkingDirectory method) SWAP switch_to_interactive_mode() (xfworkerutil.XFWorkerJob method)

T

Task Task Type Task Type Package TemporaryWorkingDirectory (class in xfworkerutil) to_header_line() (plyio.PlyHeaderElement method) (plyio.PlyHeaderProperty method) try_get_direct_access_path() (in module network)

try_parse_ply_header_element() (in module plyio) try_parse_ply_header_property() (in module plyio) try_parse_response_header() (network.DirectAccessHeader static method) try_parse_virtualpath_schema_sns_measurement() (in module network) type (omni.Calibration property) (omni.Image property) (omni.ImageRelation property) (omni.InvalidPixels property)

U

UnexpectedStatusError unit_name (omni.Calibration property) unit_type (omni.Calibration property) unprocessed_delete_response() (network.Connection method) unprocessed_get_response() (network.Connection method) unprocessed_head_response() (network.Connection method) unprocessed_post_response() (network.Connection method) unprocessed_put_response() (network.Connection method)

update_xf_job() (in module xfworkerutil) update_xf_project() (in module xfworkerutil) update_xf_task() (in module xfworkerutil) update_xf_workflow() (in module xfworkerutil) upload_omni_output() (xfworkerutil.XFWorkerJob method) upload_omni_output_only_metadata() (xfworkerutil.XFWorkerJob method) upload_output_file() (xfworkerutil.XFWorkerJob method) upload_xf_userdata_file() (xfworkerutil.XFWorkerJob method) User Data

V

vax_to_ieee_float32() (in module vmsutil) vax_to_ieee_float64() (in module vmsutil) verify_pixel_type() (omni.Image method) version_to_string() (in module lupoutil) vertices (plyio.PlyMesh attribute) virtualpath_join_file() (in module network)

virtualpath_join_folder() (in module network) virtualpath_parent_folder() (in module network) vmsutil module VOI voi_pixel_position (omni.ImageRelation property) Volume Of Interest

W

Web Admin Web Portal WindowLevel (class in lifsnapshot) Worker

Workflow Workflow Package write_pixels() (aimio.AimWriter method) write_ply() (in module plyio) write_ply_header_line() (in module plyio)

X

XamFlow XamFlow Desktop XamFlow Server XamFlow Worker Service XamFlow Workstation XF XF Desktop XF Server

XF Worker XF Workstation xfsortorder module XFWorkerArguments (class in xfworkerutil) XFWorkerJob (class in xfworkerutil) xfworkerutil module