Index

Symbols

--app_config <app_config> collect_tiles command line option load_slide command line option --app_config_file <app_config_file> luna.pathology.point_annotation.proxy_table.generate command line option --data_config <data_config> dsa_viz command line option --data_config_file <data_config_file> luna.pathology.point_annotation.proxy_table.generate command line option --datastore_id <datastore_id> collect_tiles command line option load_slide command line option --method_param_path <method_param_path> collect_tiles command line option load_slide command line option

--source_type <source_type> dsa_viz command line option -a collect_tiles command line option load_slide command line option luna.pathology.point_annotation.proxy_table.generate command line option -d dsa_viz command line option luna.pathology.point_annotation.proxy_table.generate command line option -m collect_tiles command line option load_slide command line option -s collect_tiles command line option dsa_viz command line option load_slide command line option

A

add() (luna.common.DataStore.DataStore method)

add_contours_for_label() (in module luna.pathology.common.build_geojson)

B

BaseTorchTileClassifier (class in luna.pathology.common.ml) BaseTorchTileDataset (class in luna.pathology.common.ml) bitmask_polygon() (in module luna.pathology.cli.dsa.dsa_viz) bootstrap() (in module luna.common.DataStore)

build_all_geojsons_from_default() (in module luna.pathology.common.build_geojson) build_default_geojson_from_annotation() (in module luna.pathology.common.build_geojson) build_geojson_from_annotation() (in module luna.pathology.common.build_geojson) build_geojson_from_pointclick_json() (in module luna.pathology.common.build_geojson) build_labelset_specific_geojson() (in module luna.pathology.common.build_geojson)

C

check_filepaths_valid() (in module luna.pathology.cli.dsa.dsa_viz) clean_nested_colname() (in module luna.common.utils) clear() (luna.common.config.ConfigSet method) close() (luna.common.Neo4jConnection.Neo4jConnection method) CodeTimer (class in luna.common.CodeTimer) collect_tile_with_datastore() (in module luna.pathology.cli.collect_tile_segment) collect_tiles command line option --app_config <app_config> --datastore_id <datastore_id> --method_param_path <method_param_path> -a -m -s

commute_all_sink_id() (luna.common.Neo4jConnection.Neo4jConnection method) commute_cohort_id_to_spark() (luna.common.Neo4jConnection.Neo4jConnection method) commute_record_id_to_spark() (luna.common.Neo4jConnection.Neo4jConnection method) commute_sink_id_to_spark() (luna.common.Neo4jConnection.Neo4jConnection method) commute_source_id_to_spark() (luna.common.Neo4jConnection.Neo4jConnection method) commute_source_id_to_spark_query() (luna.common.Neo4jConnection.Neo4jConnection method) concatenate_regional_geojsons() (in module luna.pathology.common.build_geojson) CONFIG_LOCATION() (in module luna.common.constants) ConfigSet (class in luna.common.config) create_id_lookup_table() (luna.common.Neo4jConnection.Neo4jConnection method) create_id_lookup_table_where() (luna.common.Neo4jConnection.Neo4jConnection method) create_proxy_table() (in module luna.pathology.point_annotation.proxy_table.generate) createDatastore() (luna.common.DataStore.DataStore method) createNamespace() (luna.common.DataStore.DataStore method)

D

dask_job() (in module luna.common.dask) DataStore (class in luna.common.DataStore) DataStore_v2 (class in luna.common.DataStore) does_not_contain() (in module luna.common.utils) download_point_annotation() (in module luna.pathology.point_annotation.proxy_table.generate) download_sv_point_annotation() (in module luna.pathology.common.slideviewer_client)

download_zip() (in module luna.pathology.common.slideviewer_client) dsa_viz command line option --data_config <data_config> --source_type <source_type> -d -s

E

ensure_datastore() (luna.common.DataStore.DataStore_v2 method)

EnsureByteContext (class in luna.common.EnsureByteContext) (class in luna.pathology.common.EnsureByteContext)

F

fetch_slide_ids() (in module luna.pathology.common.slideviewer_client) find_parents() (in module luna.pathology.common.build_geojson)

format() (luna.common.custom_logger.MultilineFormatter method) forward() (luna.pathology.common.ml.BaseTorchTileClassifier method) (luna.pathology.models.ov_tissuenet.TissueTileNet method)

G

generate_k_function_statistics() (in module luna.pathology.spatial.transforms) generate_uuid() (in module luna.common.utils) generate_uuid_binary() (in module luna.common.utils) generate_uuid_dict() (in module luna.common.utils) get() (luna.common.DataStore.DataStore method) (luna.common.DataStore.DataStore_v2 method) get_absolute_path() (in module luna.common.utils) get_address() (luna.common.Node.Node method) get_all_props() (luna.common.Node.Node method) get_classifier() (in module luna.pathology.models.eng_tissuenet) (in module luna.pathology.models.ov_tissuenet) get_collection_metadata() (in module luna.pathology.cli.dsa.dsa_api_handler) get_collection_uuid() (in module luna.pathology.cli.dsa.dsa_api_handler) get_color() (in module luna.pathology.cli.dsa.utils) get_config_set() (luna.common.config.ConfigSet method) get_continuous_color() (in module luna.pathology.cli.dsa.utils)

get_create_str() (luna.common.Node.Node method) get_item_uuid() (in module luna.pathology.cli.dsa.dsa_api_handler) get_keys() (luna.common.config.ConfigSet method) get_local_dask_directory() (in module luna.common.dask) get_map_str() (luna.common.Node.Node method) get_match_str() (luna.common.Node.Node method) get_method_data() (in module luna.common.utils) get_names() (luna.common.config.ConfigSet method) get_or_create_dask_client() (in module luna.common.dask) get_qualified_name() (luna.common.Node.Node static method) get_slide_annotation() (in module luna.pathology.cli.dsa.dsa_api_handler) get_slide_id() (in module luna.pathology.common.slideviewer_client) get_slides_from_collection() (in module luna.pathology.cli.dsa.dsa_api_handler) get_transform() (in module luna.pathology.models.eng_tissuenet) (in module luna.pathology.models.ov_tissuenet) get_value() (luna.common.config.ConfigSet method)

H

handler() (in module luna.pathology.common.build_geojson)

has_value() (luna.common.config.ConfigSet method) heatmap() (in module luna.pathology.cli.dsa.dsa_viz)

I

init_logger() (in module luna.common.custom_logger)

isAttached() (luna.common.DataStore.DataStore method)

J

JobExecutionError

K

Kfunction() (in module luna.pathology.spatial.stats)

L

load() (in module luna.common.PipelineBuilder) load_slide command line option --app_config <app_config> --datastore_id <datastore_id> --method_param_path <method_param_path> -a -m -s load_slide_with_datastore() (in module luna.pathology.cli.load_slide) luna.common module luna.common.CodeTimer module luna.common.config module luna.common.constants module luna.common.custom_logger module luna.common.dask module luna.common.DataStore module luna.common.EnsureByteContext module luna.common.Neo4jConnection module luna.common.Node module luna.common.PipelineBuilder module luna.common.sparksession module luna.common.utils module luna.pathology module luna.pathology.analysis module luna.pathology.analysis.qupath module luna.pathology.cli module luna.pathology.cli.collect_tile_segment module luna.pathology.cli.dsa module luna.pathology.cli.dsa.dsa_api_handler module

luna.pathology.cli.dsa.dsa_viz module luna.pathology.cli.dsa.utils module luna.pathology.cli.load_slide module luna.pathology.common module luna.pathology.common.build_geojson module luna.pathology.common.EnsureByteContext module luna.pathology.common.ml module luna.pathology.common.slideviewer_client module luna.pathology.models module luna.pathology.models.eng_tissuenet module luna.pathology.models.ov_tissuenet module luna.pathology.point_annotation module luna.pathology.point_annotation.proxy_table module luna.pathology.point_annotation.proxy_table.generate module luna.pathology.point_annotation.proxy_table.generate command line option --app_config_file <app_config_file> --data_config_file <data_config_file> -a -d luna.pathology.point_annotation.refined_table module luna.pathology.proxy_table module luna.pathology.proxy_table.regional_annotation module luna.pathology.refined_table module luna.pathology.refined_table.regional_annotation module luna.pathology.spatial.stats module luna.pathology.spatial.transforms module

M

match_concept_node() (luna.common.Neo4jConnection.Neo4jConnection method) module luna.common luna.common.CodeTimer luna.common.config luna.common.constants luna.common.custom_logger luna.common.dask luna.common.DataStore luna.common.EnsureByteContext luna.common.Neo4jConnection luna.common.Node luna.common.PipelineBuilder luna.common.sparksession luna.common.utils luna.pathology luna.pathology.analysis luna.pathology.analysis.qupath luna.pathology.cli luna.pathology.cli.collect_tile_segment luna.pathology.cli.dsa luna.pathology.cli.dsa.dsa_api_handler luna.pathology.cli.dsa.dsa_viz luna.pathology.cli.dsa.utils luna.pathology.cli.load_slide luna.pathology.common luna.pathology.common.build_geojson luna.pathology.common.EnsureByteContext luna.pathology.common.ml luna.pathology.common.slideviewer_client luna.pathology.models luna.pathology.models.eng_tissuenet luna.pathology.models.ov_tissuenet luna.pathology.point_annotation luna.pathology.point_annotation.proxy_table luna.pathology.point_annotation.proxy_table.generate luna.pathology.point_annotation.refined_table luna.pathology.proxy_table luna.pathology.proxy_table.regional_annotation luna.pathology.refined_table luna.pathology.refined_table.regional_annotation luna.pathology.spatial.stats luna.pathology.spatial.transforms

MultilineFormatter (class in luna.common.custom_logger)

N

Neo4jConnection (class in luna.common.Neo4jConnection)

Node (class in luna.common.Node)

P

predict() (luna.pathology.common.ml.BaseTorchTileClassifier method) preprocess() (luna.pathology.common.ml.BaseTorchTileDataset method) pretty_path() (in module luna.common.Neo4jConnection) PROJECT_LOCATION() (in module luna.common.constants) prop_str() (luna.common.Node.Node static method)

prop_str_repr() (luna.common.Node.Node static method) prune_empty_delayed() (in module luna.common.dask) push_annotation_to_dsa_image() (in module luna.pathology.cli.dsa.dsa_api_handler) put() (luna.common.DataStore.DataStore method) (luna.common.DataStore.DataStore_v2 method)

Q

query() (luna.common.Neo4jConnection.Neo4jConnection method)

qupath_polygon() (in module luna.pathology.cli.dsa.dsa_viz)

R

regional_polygon() (in module luna.pathology.cli.dsa.dsa_viz) replace_token() (in module luna.common.utils) run() (luna.common.DataStore.DataStore static method)

runDaskDistributed() (luna.common.DataStore.DataStore method) runLocal() (luna.common.DataStore.DataStore method) runProcessPoolExecutor() (luna.common.DataStore.DataStore method)

S

save_dsa_annotation() (in module luna.pathology.cli.dsa.dsa_viz) saveAll() (luna.common.DataStore.DataStore method) set_aux() (luna.common.Node.Node method) set_data() (luna.common.Node.Node method) set_namespace() (luna.common.Node.Node method) setDatastore() (luna.common.DataStore.DataStore method) setNamespace() (luna.common.DataStore.DataStore method)

setup() (luna.pathology.common.ml.BaseTorchTileClassifier method) (luna.pathology.common.ml.BaseTorchTileDataset method) spark_session() (luna.common.sparksession.SparkConfig method) SparkConfig (class in luna.common.sparksession) stardist_cell() (in module luna.pathology.cli.dsa.dsa_viz) stardist_polygon() (in module luna.pathology.cli.dsa.dsa_viz) system_check() (in module luna.pathology.cli.dsa.dsa_api_handler)

T

TABLE_LOCATION() (in module luna.common.constants) TABLE_NAME() (in module luna.common.constants) test_connection() (luna.common.Neo4jConnection.Neo4jConnection method) test_count() (luna.common.Neo4jConnection.Neo4jConnection method)

TissueTileNet (class in luna.pathology.models.ov_tissuenet) to_sql_field() (in module luna.common.utils) to_sql_value() (in module luna.common.utils) training (luna.pathology.common.ml.BaseTorchTileClassifier attribute) (luna.pathology.models.ov_tissuenet.TissueTileNet attribute)

U

unzip() (in module luna.pathology.common.slideviewer_client)

V

vectorize_np_array_bitmask_by_pixel_value() (in module luna.pathology.cli.dsa.utils)

W

with_event_loop() (in module luna.common.dask)

write() (luna.common.DataStore.DataStore_v2 method)