Index

_

_abc_impl (cytotable.warehouse.iceberg.TinyCatalog attribute) _arrow_type_cast_if_specified() (in module cytotable.utils) _build_file_index() (in module cytotable.warehouse.images) _build_join_tree() (in module cytotable.joins) _build_path() (in module cytotable.sources) _build_stable_image_crop_id() (in module cytotable.warehouse.images) _build_stable_object_id() (in module cytotable.warehouse.images) _build_stable_source_image_id() (in module cytotable.warehouse.images) _cache_cloudpath_to_local() (in module cytotable.utils) _classify_group() (in module cytotable.joins) _collect_crop_rows() (in module cytotable.warehouse.images) _collect_source_rows() (in module cytotable.warehouse.images) _collect_tables() (in module cytotable.joins) _column_has_invalid_values() (in module cytotable.joins) _column_sort() (in module cytotable.utils) _concat_join_sources() (in module cytotable.convert) _concat_source_group() (in module cytotable.convert) _count_unique_source_image_names() (in module cytotable.warehouse.images) _crop_ome_arrow() (in module cytotable.warehouse.images) _crop_shard_worker() (in module cytotable.warehouse.images) _dedup_table_by_first_occurrence() (in module cytotable.warehouse.images) _default_identifying_columns() (in module cytotable.joins) _default_parsl_config() (in module cytotable.utils) _detect_key_columns() (in module cytotable.joins) _detect_source_page_key() (in module cytotable.joins) _duckdb_reader() (in module cytotable.utils) _Edge (class in cytotable.joins) _edge_conditions() (in module cytotable.joins) _ensure_thread_executor() (in module cytotable.utils) _expand_path() (in module cytotable.utils) _extract_crop_key_field_names() (in module cytotable.warehouse.images) _extract_image_key_field_names() (in module cytotable.warehouse.images) _extract_image_key_fields() (in module cytotable.warehouse.images) _extract_key_fields() (in module cytotable.warehouse.images) _extract_npz_to_parquet() (in module cytotable.utils) _file_is_more_than_one_line() (in module cytotable.sources) _filter_source_filepaths() (in module cytotable.sources) _find_matching_segmentation_path() (in module cytotable.warehouse.images) _find_reference_edges() (in module cytotable.joins) _find_referenced_table() (in module cytotable.joins) _gather_sources() (in module cytotable.sources) _gather_tablenumber_checksum() (in module cytotable.utils) _generate_pagesets() (in module cytotable.utils) _get_cytotable_version() (in module cytotable.utils) _get_source_filepaths() (in module cytotable.sources) _get_table_columns_and_types() (in module cytotable.convert) _get_table_keyset_pagination_sets() (in module cytotable.convert) _glob_follow_symlinks() (in module cytotable.utils) _glob_pattern_matches() (in module cytotable.utils) _image_crop_table_parallel() (in module cytotable.warehouse.images)

_infer_source_datatype() (in module cytotable.sources) _infer_source_group_common_schema() (in module cytotable.convert) _infer_source_page_keys() (in module cytotable.joins) _invalid_page_key_condition() (in module cytotable.joins) _join_source_pageset() (in module cytotable.convert) _JoinStep (class in cytotable.joins) _local_image_io_path() (in module cytotable.warehouse.images) _measure_edge_match() (in module cytotable.joins) _natural_sort() (in module cytotable.utils) _normalize_file_value() (in module cytotable.warehouse.images) _parsl_loaded() (in module cytotable.utils) _paths_sql() (in module cytotable.joins) _pick_column() (in module cytotable.joins) _prep_cast_column_data_types() (in module cytotable.convert) _prepare_join_sql() (in module cytotable.convert) _prepend_column_name() (in module cytotable.convert) _raise_if_sqlite_readonly_error() (in module cytotable.utils) _raw_source_select_sql() (in module cytotable.joins) _read_ome_arrow() (in module cytotable.warehouse.images) _read_registry() (cytotable.warehouse.iceberg.TinyCatalog method) _relative_index_key() (in module cytotable.warehouse.images) _remove_empty_dirs() (in module cytotable.utils) _render_join_sql() (in module cytotable.joins) _require_ome_arrow() (in module cytotable.warehouse.images) _resolve_image_columns() (in module cytotable.warehouse.images) _resolve_image_worker_count() (in module cytotable.warehouse.images) _resolve_indexed_path() (in module cytotable.warehouse.images) _resolve_source_page_keys() (in module cytotable.utils) _rows_to_crop_table() (in module cytotable.warehouse.images) _rows_to_source_table() (in module cytotable.warehouse.images) _run_export_workflow() (in module cytotable.convert) _select_base_table() (in module cytotable.joins) _set_tablenumber() (in module cytotable.convert) _shared_key_pairs() (in module cytotable.joins) _source_image_table_parallel() (in module cytotable.warehouse.images) _source_pageset_to_parquet() (in module cytotable.convert) _source_shard_worker() (in module cytotable.warehouse.images) _sql_string_literal() (in module cytotable.joins) _sqlite_mixed_type_query_to_parquet() (in module cytotable.utils) _strip_null_fields_from_type() (in module cytotable.warehouse.images) _strip_null_fields_from_value() (in module cytotable.warehouse.images) _TableInfo (class in cytotable.joins) _unwrap_source() (in module cytotable.utils) _unwrap_value() (in module cytotable.utils) _validate_edges() (in module cytotable.joins) _validate_rendered_sql() (in module cytotable.joins) _validated_bbox_values() (in module cytotable.warehouse.images) _walk_and_match() (in module cytotable.utils) _write_parquet_table_with_metadata() (in module cytotable.utils) _write_registry() (cytotable.warehouse.iceberg.TinyCatalog method) _write_row_shards() (in module cytotable.warehouse.images)

A

add_object_id_to_profiles_frame() (in module cytotable.warehouse.images)

B

base_table (cytotable.joins.InferredJoin attribute) BBoxColumns (class in cytotable.warehouse.images)

by_basename (cytotable.warehouse.images.FileIndex attribute) by_relative (cytotable.warehouse.images.FileIndex attribute) by_stem (cytotable.warehouse.images.FileIndex attribute)

C

catalog() (in module cytotable.warehouse.iceberg) cloud_glob() (in module cytotable.utils) commit_table() (cytotable.warehouse.iceberg.TinyCatalog method) config (in module cytotable.presets) convert() (in module cytotable.convert) create_namespace() (cytotable.warehouse.iceberg.TinyCatalog method) create_table() (cytotable.warehouse.iceberg.TinyCatalog method) cytotable.convert module cytotable.exceptions module cytotable.joins module

cytotable.sources module cytotable.utils module cytotable.warehouse.access module cytotable.warehouse.iceberg module cytotable.warehouse.images module CytoTableException

D

DatatypeException describe_iceberg_warehouse() (in module cytotable.warehouse.iceberg)

drop_namespace() (cytotable.warehouse.iceberg.TinyCatalog method) drop_table() (cytotable.warehouse.iceberg.TinyCatalog method) drop_view() (cytotable.warehouse.iceberg.TinyCatalog method)

E

edges (cytotable.joins.InferredJoin attribute)

evaluate_futures() (in module cytotable.utils)

F

FileIndex (class in cytotable.warehouse.images)

find_anndata_metadata_field_names() (in module cytotable.utils)

I

image_crop_table_from_joined_chunk() (in module cytotable.warehouse.images) infer_join_sql() (in module cytotable.joins)

InferredJoin (class in cytotable.joins) is_infer_joins_sentinel() (in module cytotable.joins)

L

list_iceberg_tables() (in module cytotable.warehouse.iceberg) list_namespaces() (cytotable.warehouse.iceberg.TinyCatalog method) list_tables() (cytotable.warehouse.iceberg.TinyCatalog method) (in module cytotable.warehouse.access)

list_views() (cytotable.warehouse.iceberg.TinyCatalog method) load_namespace_properties() (cytotable.warehouse.iceberg.TinyCatalog method) load_table() (cytotable.warehouse.iceberg.TinyCatalog method)

M

map_pyarrow_type() (in module cytotable.utils) module cytotable.convert cytotable.exceptions cytotable.joins cytotable.sources cytotable.utils cytotable.warehouse.access cytotable.warehouse.iceberg cytotable.warehouse.images

N

NoInputDataException

O

object_id() (in module cytotable.warehouse.images)

P

page_key (cytotable.joins.InferredJoin attribute)

Parsl_AppBase_init_for_docs() (in module cytotable.utils) profile_with_images_frame() (in module cytotable.warehouse.images)

R

read_iceberg_table() (in module cytotable.warehouse.iceberg) read_table() (in module cytotable.warehouse.access)

register_table() (cytotable.warehouse.iceberg.TinyCatalog method) rename_table() (cytotable.warehouse.iceberg.TinyCatalog method) resolve_bbox_columns() (in module cytotable.warehouse.images)

S

SchemaException source_image_table_from_joined_chunk() (in module cytotable.warehouse.images)

sql (cytotable.joins.InferredJoin attribute) SQLiteReadOnlyException

T

table_exists() (cytotable.warehouse.iceberg.TinyCatalog method)

TinyCatalog (class in cytotable.warehouse.iceberg)

U

update_namespace_properties() (cytotable.warehouse.iceberg.TinyCatalog method)

V

view_exists() (cytotable.warehouse.iceberg.TinyCatalog method)

W

write_iceberg_warehouse() (in module cytotable.warehouse.iceberg)

X

x_max (cytotable.warehouse.images.BBoxColumns attribute)

x_min (cytotable.warehouse.images.BBoxColumns attribute)

Y

y_max (cytotable.warehouse.images.BBoxColumns attribute)

y_min (cytotable.warehouse.images.BBoxColumns attribute)