Index

_

__init__() (HedLabMetaData method) (HedNWBValidator method) (HedTags method) (HedValueVector method)

A

add_context_and_filter() (ErrorHandler method) add_definitions() (DefinitionDict method) (DefValidator method) add_note() (HedFileError method) add_row() (HedTags method) (HedValueVector method) add_type() (HedTypeManager method) add_unit() (UnitClassEntry method) aggregate_code_counts() (ErrorHandler static method) all_children() (HedTags method) (HedValueVector method) all_hed_columns (Sidecar property) all_objects (HedTags property) (HedValueVector property) AllowedCharacter (HedKey attribute) annotation quickstart recipe recipe for NWB what is HED AnnotationProperty (HedKey attribute) annotations assembly

API new append() (HedGroup method) (HedString method) (HedTags method) (HedValueVector method) AppFactory (class in hedweb.app_factory) args (HedFileError attribute) assemble() (BaseInput method) (EventOperations method) (SpreadsheetInput method) (TabularInput method) assembly curly braces attribute_has_property() (HedSchemaEntry method) (HedTagEntry method) (UnitClassEntry method) (UnitEntry method) attributes (HedSchema property) Attributes (HedSectionKey attribute) attributes (HedTag property)

B

background_color (WordCloudConfig attribute), [1], [2] BACKUP_DICTIONARY (BackupManager attribute) BACKUP_ROOT (BackupManager attribute) BackupManager (class in remodeler.backup_manager) BAD_COLUMN_NAMES (HedExceptions attribute) BAD_HED_LIBRARY_NAME (HedExceptions attribute) BAD_PARAMETERS (HedExceptions attribute) BAD_WITH_STANDARD (HedExceptions attribute) BAD_WITH_STANDARD_MULTIPLE_VALUES (HedExceptions attribute) BASE_ARRAY (RemodelerValidator attribute) base_tag (HedTag property) base_tag_has_attribute() (HedTag method) (HedTagEntry method) BaseInput (class in hed.models.base_input) BaseOp (class in remodeler.operations.base_op) BaseOperations (class in hedweb.base_operations)

BaseSummary (class in remodeler.operations.base_summary) best practices, [1], [2] BIDS annotation conversion to NWB dataset validation how HED works sidecar validation BIDS dataset BidsDataset (class in hed.tools.bids.bids_dataset) BidsDataset class BidsFile (class in hed.tools.bids.bids_file) BidsFileGroup (class in hed.tools.bids.bids_file_group) BidsSidecarFile (class in hed.tools.bids.bids_sidecar_file) BidsTabularFile (class in hed.tools.bids.bids_tabular_file) BLANK_HED_STRING (SidecarErrors attribute) BoolRange (HedKey attribute)

C

cache_local_versions() (in module hed.schema.hed_cache) cache_xml_versions() (in module hed.schema.hed_cache) can_save() (HedSchema method) CANNOT_PARSE_JSON (HedExceptions attribute) CANNOT_PARSE_RDF (HedExceptions attribute) CANNOT_PARSE_XML (HedExceptions attribute) casefold() (HedGroup method) (HedString method) (HedTag method) CHARACTER_INVALID (ValidationErrors attribute) check_compliance check_compliance() (HedSchema method) (HedSchemaGroup method) check_for_banned_tags() (OnsetValidator static method) check_for_definitions() (DefinitionDict method) (DefValidator method) check_if_in_original() (HedGroup method) (HedString method) check_quality() (EventOperations method) check_reserved_compatibility() (ReservedChecker method) check_tag_formatting() (HedValidator method) check_tag_requirements() (ReservedChecker method) children (HedTags property) (HedValueVector property) (UnitClassEntry property) clear_contents() (BidsFile method) (BidsSidecarFile method) (BidsTabularFile method) CLI CLOSING_GROUP_CHARACTER (HedString attribute) color_func() (ColormapColorFunc method) color_range (WordCloudConfig attribute), [1], [2] color_step_range (WordCloudConfig attribute), [1], [2] colormap matplotlib plasma viridis colormap (WordCloudConfig attribute), [1], [2] ColormapColorFunc (class in hedvis.generators.word_cloud_util) COLUMN (ErrorContext attribute) column_data (Sidecar property) column_metadata() (BaseInput method) (SpreadsheetInput method) (TabularInput method) columns (BaseInput property) (SpreadsheetInput property) (TabularInput property) columns_info_results() (in module hedweb.routes)

combine_dataframe() (BaseInput static method) (SpreadsheetInput static method) (TabularInput static method) COMMA_MISSING (ValidationErrors attribute) command-line interface common issues compare() (SchemaOperations method) ComplianceSummary compress_strings() (EventManager static method) conditions HED annotations configuration API dictionary container_source (HedTags property) (HedValueVector property) contents (BidsFile property) (BidsSidecarFile property) (BidsTabularFile property) contour_color (WordCloudConfig attribute), [1], [2] contour_width (WordCloudConfig attribute), [1], [2] contributing ConversionFactor (HedKey attribute) convert() (SchemaOperations method) (StringOperations method) convert_hed_versions() (in module hedweb.web_util) convert_to_form() (BaseInput method) (SpreadsheetInput method) (TabularInput method) convert_to_long() (BaseInput method) (SpreadsheetInput method) (TabularInput method) convert_to_short() (BaseInput method) (SpreadsheetInput method) (TabularInput method) ConvertColumnsOp (class in remodeler.operations.convert_columns_op) copy() (HedGroup method) (HedString method) (HedTag method) create_app() (AppFactory static method) create_backup() (BackupManager method) create_column_selections() (in module hedweb.columns) create_file_dict() (FileDictionary method) create_file_group() (BidsFileGroup static method) create_wordcloud create_wordcloud() (in module hedvis.generators.word_cloud), [1] CURLY_BRACE_UNSUPPORTED_HERE (ValidationErrors attribute) CUSTOM_TITLE (ErrorContext attribute) customization

D

data (HedTags property) (HedValueVector property) data preparation data_type (HedTags attribute) (HedValueVector attribute) datafile_dict (BidsFileGroup attribute) dataframe (BaseInput property) (SpreadsheetInput property) (TabularInput property) dataframe_a (BaseInput property) (SpreadsheetInput property) (TabularInput property) dataframe_from_worksheet() (in module hedweb.columns) dataset HED-annotated dataset_description.json debugging def_dict (Sidecar property) DEF_EXPAND_INVALID (ValidationErrors attribute) DEF_INVALID (ValidationErrors attribute) DEFAULT_BACKUP_NAME (BackupManager attribute) default_color_func() (in module hedvis.generators.word_cloud_util), [1] default_unit (HedTag property) DefaultUnits (HedKey attribute) DEFINITION_INVALID (ValidationErrors attribute) DefinitionDict (class in hed.models.definition_dict) definitions DefValidator (class in hed.validator.def_validator) dependencies optional DeprecatedFrom (HedKey attribute) description (HedTags property) (HedValueVector property) design concepts

design matrices HED developer guide schema development; library schemas; HED workflow development dictionary Dispatcher (class in remodeler.dispatcher) DISPLAY_INDENT (BaseSummary attribute) do_op() (BaseOp method) (ConvertColumnsOp method) (FactorColumnOp method) (FactorHedTagsOp method) (FactorHedTypeOp method) (MergeConsecutiveOp method) (NumberGroupsOp method) (NumberRowsOp method) (RemapColumnsOp method) (RemoveColumnsOp method) (RemoveRowsOp method) (RenameColumnsOp method) (ReorderColumnsOp method) (SplitRowsOp method) (SummarizeColumnNamesOp method) (SummarizeColumnValuesOp method) (SummarizeDefinitionsOp method) (SummarizeHedTagsOp method) (SummarizeHedTypeOp method) (SummarizeHedValidationOp method) (SummarizeSidecarFromEventsOp method) documentation building dot_str() (SequenceMap method) dump_summary() (BaseSummary static method) DUPLICATE_COLUMN_BETWEEN_SOURCES (ValidationErrors attribute) DUPLICATE_COLUMN_IN_LIST (ValidationErrors attribute) duplicate_names (HedSchemaSection property)

E

edge_to_str() (SequenceMap method) ELEMENT_DEPRECATED (ValidationErrors attribute) ElementDomain (HedKey attribute) entity_dict (BidsFile attribute) ERROR (ErrorSeverity attribute) error handling ErrorContext (class in hed.errors.error_types) ErrorHandler (class in hed.errors.error_reporter) errors empty word cloud font not found import mask not applied types errors_to_str() (Dispatcher static method) ErrorSeverity (class in hed.errors.error_types) event files EventManager (class in hed.tools.analysis.event_manager) EventOperations (class in hedweb.event_operations) events struct array tabular input

events file events_results() (in module hedweb.routes) examples, [1] EXCEL_EXTENSION (BaseInput attribute) (SpreadsheetInput attribute) (TabularInput attribute) expand_defs() (BaseInput method) (HedString method) (SpreadsheetInput method) (TabularInput method) expandable (HedTag property) expanded (HedTag property) ext (BidsFile attribute) extend() (HedTags method) (HedValueVector method) extension (HedTag property) ExtensionAllowed (HedKey attribute) extract_sidecar_template() (TabularSummary method) extract_summary() (TabularSummary static method)

F

FactorColumnOp (class in remodeler.operations.factor_column_op) FactorHedTagsOp (class in remodeler.operations.factor_hed_tags_op) FactorHedTypeOp (class in remodeler.operations.factor_hed_type_op) fields (HedTags property) (HedValueVector property) file_dict (FileDictionary property) file_extension_is_valid() (in module hedweb.web_util) file_groups (BidsDataset attribute) file_list (FileDictionary property) FILE_NAME (ErrorContext attribute) FILE_NOT_FOUND (HedExceptions attribute) file_path (BidsFile attribute) FileDictionary (class in hed.tools.analysis.file_dictionary) filter_edges() (SequenceMap method) filter_issues() (in module hedweb.web_util) filter_issues_by_count() (ErrorHandler static method) filter_issues_by_severity() (ErrorHandler static method) finalize_dictionaries() (HedSchema method) finalize_entry() (HedSchemaEntry method) (HedTagEntry method) (UnitClassEntry method) (UnitEntry method) find_def_tags() (HedGroup method) (HedString method) find_exact_tags() (HedGroup method) (HedString method) find_placeholder_tag() (HedGroup method) (HedString method)

find_tag_entry() (HedSchema method) (HedSchemaGroup method) find_tags() (HedGroup method) (HedString method) find_tags_with_term() (HedGroup method) (HedString method) find_top_level_tags() (HedString method) find_wildcard_tags() (HedGroup method) (HedString method) font custom font size font_path, [1] (WordCloudConfig attribute), [1], [2] form_has_file() (in module hedweb.web_util) form_has_option() (in module hedweb.web_util) form_has_url() (in module hedweb.web_util) format_error() (ErrorHandler static method) (SchemaOperations static method) format_error_from_context() (ErrorHandler static method) format_error_with_context() (ErrorHandler method) from_dataframes() (in module hed.schema.hed_schema_io) from_dict() (VisualizationConfig class method), [1] (WordCloudConfig class method), [1] from_hed_strings() (HedString static method) from_string() (in module hed.schema.hed_schema_io) funding

G

generate_contour_svg() (in module hedvis.generators.word_cloud_util), [1] generate_download_file_from_text() (in module hedweb.web_util) generate_download_spreadsheet() (in module hedweb.web_util) generate_download_zip_file() (in module hedweb.web_util) generate_filename() (in module hedweb.web_util) generate_new_id() (HedTags method) (HedValueVector method) generate_sidecar() (EventOperations method) generate_text_response() (in module hedweb.web_util) GENERIC_ERROR (HedExceptions attribute) get() (DefinitionDict method) (DefValidator method) (HedSchemaSection method) (HedTags method) (HedValueVector method) get_all_groups() (HedGroup method) (HedString method) get_all_tags() (HedGroup method) (HedString method) get_ancestor() (HedTags method) (HedValueVector method) get_ancestors() (HedTags method) (HedValueVector method) get_as_dataframes() (HedSchema method) get_as_form() (HedGroup method) (HedString method) get_as_indented() (HedGroup method) (HedString method) get_as_json_string() (HedSchema method) (Sidecar method) get_as_long() (HedGroup method) (HedString method) get_as_mediawiki_string() (HedSchema method) get_as_original() (HedString method) get_as_short() (HedGroup method) (HedString method) get_as_strings() (DefinitionDict static method) (DefValidator static method) get_as_xml_string() (HedSchema method) get_backup() (BackupManager method) get_backup_files() (BackupManager method) get_backup_path() (BackupManager method) get_cache_directory() (in module hed.schema.hed_cache) get_candidates() (in module hed.tools.bids.bids_util) get_code_counts() (ErrorHandler static method) get_column_numbers() (in module hedweb.columns) get_column_refs() (BaseInput method) (Sidecar method) (SpreadsheetInput method) (TabularInput method) get_columns_info() (TabularSummary static method) get_columns_request() (in module hedweb.columns) get_conversion_factor() (UnitEntry method) get_data_file() (Dispatcher method) get_def_dict get_def_dict() (BaseInput method) (Sidecar method) (SpreadsheetInput method) (TabularInput method) get_def_information() (ReservedChecker method) get_definition_entry() (DefinitionDict method) (DefValidator method) get_derivative_unit_entry() (UnitClassEntry method) get_details_dict() (BaseSummary method) get_edge_list() (SequenceMap method) get_entity() (BidsFile method) (BidsSidecarFile method) (BidsTabularFile method) get_entries_with_attribute() (HedSchemaSection method) get_exception_message() (in module hedweb.web_util) get_extras() (HedSchema method) get_factor_vectors() (HedTypeManager method) get_fields_conf() (HedTags class method) (HedValueVector class method) get_file_group() (BidsDataset method) get_file_key() (BackupManager method) get_file_path() (FileDictionary method) get_first_group() (HedGroup method) (HedString method) get_formatted_version() (HedSchema method) (HedSchemaGroup method) get_group_requirements() (ReservedChecker method) get_hed_obj() (HedTagManager method)

get_hed_objs() (EventOperations method) (HedTagManager method) get_hed_schema_from_pull_down() (in module hedweb.web_util) get_hed_version_path() (in module hed.schema.hed_cache) get_hed_versions() (in module hed.schema.hed_cache) get_hed_xml_version() (in module hed.schema.hed_schema_io) get_incompatible() (ReservedChecker method) get_individual() (BaseSummary method) get_input_from_form() (ProcessForm static method) get_input_schema() (ProcessServices static method) get_instance() (ReservedChecker static method) get_key() (BidsFile method) (BidsSidecarFile method) (BidsTabularFile method) get_library_data() (in module hed.schema.hed_cache) get_list() (ProcessServices static method) get_merged_sidecar() (in module hed.tools.bids.bids_util) get_normalized_str() (HedTag method) get_number_unique() (TabularSummary method) get_option() (in module hedweb.web_util) get_original_hed_string() (HedGroup method) (HedString method) get_parameter_string() (ProcessServices static method) get_parsed_name() (in module hedweb.web_util) get_parser() (in module remodeler.cli.run_remodel) (in module remodeler.cli.run_remodel_backup) (in module remodeler.cli.run_remodel_restore) get_printable_issue_string() (in module hed.errors.error_reporter) get_process() (ProcessServices static method) get_read_io() (HedTags method) (HedValueVector method) get_reserved() (ReservedChecker method) get_save_header_attributes() (HedSchema method) get_schema() (Dispatcher static method) (in module hedweb.schema_operations) (ProcessForm static method) get_schema_from_description() (in module hed.tools.bids.bids_util) get_schema_versions() (HedSchema method) (HedSchemaGroup method) (in module hedweb.web_util) get_service_info() (ProcessServices static method) get_services_list() (ProcessServices static method) get_sidecar() (in module remodeler.cli.run_remodel) (TabularInput method) get_static_url_path() (AppFactory static method) get_stripped_unit_value() (HedTag method) get_summaries() (Dispatcher method) get_summary() (BaseSummary method) (BidsDataset method) (HedType method) (TabularSummary method) get_summary_details() (BaseSummary method) get_summary_save_dir() (Dispatcher method) get_tag_attribute_names_old() (HedSchema method) get_tag_columns() (in module hedweb.columns) get_tag_entry() (HedSchema method) (HedSchemaGroup method) get_tag_unit_class_units() (HedTag method) get_tags_with_attribute() (HedSchema method) (HedSchemaGroup method) get_task() (BackupManager static method) get_text_summary() (BaseSummary method) get_text_summary_details() (BaseSummary method) get_type() (HedTypeManager method) get_type_def_names() (HedType method) (HedTypeManager method) get_type_defs() (EventManager method) get_type_factors() (HedType method) get_type_list() (HedType static method) get_type_tag_factor() (HedTypeManager method) get_type_value_factors() (HedType method) get_type_value_level_info() (HedType method) get_type_value_names() (HedType method) get_worksheet() (BaseInput method) (SpreadsheetInput method) (TabularInput method) getHedAnnotations usage getHedTools getting started, [1] group_by_suffix() (in module hed.tools.bids.bids_util) groups() (HedGroup method) (HedString method)

H

handle_backup() (in module remodeler.cli.run_remodel) handle_error() (in module hedweb.web_util) handle_http_error() (in module hedweb.web_util) has_attribute() (HedSchemaEntry method) (HedTag method) (HedTagEntry method) (UnitClassEntry method) (UnitEntry method) has_column_names (BaseInput property) (SpreadsheetInput property) (TabularInput property) has_duplicates() (HedSchema method) HED JavaScript TypeScript MATLAB HEDTools MCP TypeScript resources validation, [1] hed (HedValueVector property) HED IDs hed-validator hed.schema.hed_cache module hed.schema.hed_schema_io module hed.tools.bids.bids_util module HED_BLANK_COLUMN (ValidationErrors attribute) HED_COLUMN_MISSING (ValidationErrors attribute) HED_COLUMN_NAME (TabularInput attribute) HED_DEF_EXPAND_INVALID (ValidationErrors attribute) HED_DEF_EXPAND_UNMATCHED (ValidationErrors attribute) HED_DEF_EXPAND_VALUE_EXTRA (ValidationErrors attribute) HED_DEF_EXPAND_VALUE_MISSING (ValidationErrors attribute) HED_DEF_UNMATCHED (ValidationErrors attribute) HED_DEF_VALUE_EXTRA (ValidationErrors attribute) HED_DEF_VALUE_MISSING (ValidationErrors attribute) HED_GROUP_EMPTY (ValidationErrors attribute) HED_LIBRARY_UNMATCHED (ValidationErrors attribute) HED_MISSING_REQUIRED_COLUMN (ValidationErrors attribute) HED_MULTIPLE_TOP_TAGS (ValidationErrors attribute) HED_PLACEHOLDER_OUT_OF_CONTEXT (ValidationErrors attribute) HED_RESERVED_TAG_GROUP_ERROR (ValidationErrors attribute) HED_RESERVED_TAG_REPEATED (ValidationErrors attribute) HED_SCHEMA_NODE_NAME_INVALID (HedExceptions attribute) HED_STRING (ErrorContext attribute) HED_TAG_GROUP_TAG (ValidationErrors attribute) HED_TAG_REPEATED (ValidationErrors attribute) HED_TAG_REPEATED_GROUP (ValidationErrors attribute) HED_TAGS_NOT_ALLOWED (ValidationErrors attribute) HED_TOP_LEVEL_TAG (ValidationErrors attribute) HED_UNKNOWN_COLUMN (ValidationErrors attribute) HedExceptions (class in hed.errors.exceptions) HedFileError (class in hed.errors.exceptions) HedGroup (class in hed.models.hed_group) HedID (HedKey attribute) HedKey (class in hed.schema.hed_schema_constants) HedLabMetaData (class in ndx_hed) HedNWBValidator (class in ndx_hed.utils.hed_nwb_validator) hedpy hedpy schema HedSchema (class in hed.schema.hed_schema)

HedSchemaEntry (class in hed.schema.hed_schema_entry) HedSchemaGroup (class in hed.schema.hed_schema_group) HedSchemaSection (class in hed.schema.hed_schema_section) HedSectionKey (class in hed.schema.hed_schema_constants) HedString (class in hed.models.hed_string) HedString class HedTag (class in hed.models.hed_tag) HedTagCounts HedTagEntry (class in hed.schema.hed_schema_entry) HedTagManager (class in hed.tools.analysis.hed_tag_manager) HedTags basic usage standalone usage HedTags (class in ndx_hed) HedTagVisualizer (class in hedvis.core.tag_visualizer), [1] HedTools object hedtools, [1] HedType (class in hed.tools.analysis.hed_type) HedTypeManager (class in hed.tools.analysis.hed_type_manager) HedValidator (class in hed.validator.hed_validator) HedValueVector usage HedValueVector (class in ndx_hed) hedvis, [1] hedvis.core.sequence_map module hedvis.core.tag_visualizer module hedvis.core.visualization_config module hedvis.generators.word_cloud module hedvis.generators.word_cloud_util module hedweb.app_factory module hedweb.base_operations module hedweb.columns module hedweb.event_operations module hedweb.process_form module hedweb.process_service module hedweb.routes module hedweb.schema_operations module hedweb.sidecar_operations module hedweb.spreadsheet_operations module hedweb.string_operations module hedweb.web_util module height (WordCloudConfig attribute), [1], [2] Hierarchical Event Descriptors

I

imports basic IN_LIBRARY_IN_UNMERGED (HedExceptions attribute) INDIVIDUAL_SUMMARIES_PATH (BaseSummary attribute) InLibrary (HedKey attribute) installation, [1], [2], [3] Python, [1] web services INVALID_DATAFRAME (HedExceptions attribute) INVALID_EXTENSION (HedExceptions attribute) INVALID_FILE_FORMAT (HedExceptions attribute) INVALID_HED_FORMAT (HedExceptions attribute) INVALID_LIBRARY_PREFIX (HedExceptions attribute) INVALID_PARENT_NODE (ValidationErrors attribute) INVALID_POUND_SIGNS_CATEGORY (SidecarErrors attribute) INVALID_POUND_SIGNS_VALUE (SidecarErrors attribute) INVALID_TAG_CHARACTER (ValidationErrors attribute) INVALID_VALUE_CLASS_CHARACTER (ValidationErrors attribute)

INVALID_VALUE_CLASS_VALUE (ValidationErrors attribute) is_basic_tag() (HedTag method) is_column_ref() (HedTag method) is_group (HedGroup property) (HedString property) is_hed() (BidsSidecarFile static method) is_placeholder() (HedTag method) is_sidecar_for() (BidsSidecarFile method) is_takes_value_tag() (HedTag method) is_unit_class_tag() (HedTag method) is_value_class_tag() (HedTag method) issues (DefinitionDict property) (DefValidator property) items() (DefinitionDict method) (DefValidator method) (HedSchemaSection method) iter_errors() (in module hed.errors.error_reporter) iter_files() (FileDictionary method)

J

JavaScript TypeScript, HED validation JavaScript library

JSON sidecar template creation JSON sidecar Jupyter notebooks

K

key_diffs() (FileDictionary method)

key_list (FileDictionary property) keys() (HedSchemaSection method)

L

lang library library (HedSchema property) library schema LINE (ErrorContext attribute) load_and_resize_mask() (in module hedvis.generators.word_cloud), [1] load_schema load_schema() (in module hed.schema.hed_schema_io) load_schema_version load_schema_version() (in module hed.schema.hed_schema_io)

load_sidecar_file() (Sidecar method) load_sidecar_files() (Sidecar method) loaded_workbook (BaseInput property) (SpreadsheetInput property) (TabularInput property) long_tag (HedTag property) lower() (HedGroup method) (HedString method) (HedTag method)

M

main() (in module remodeler.cli.run_remodel) (in module remodeler.cli.run_remodel_backup) (in module remodeler.cli.run_remodel_restore) make_backup() (BackupManager method) make_combined_dicts() (TabularSummary static method) make_file_dict() (FileDictionary static method) make_key() (FileDictionary static method) Mask image mask image mask_path (WordCloudConfig attribute), [1], [2] matches_criteria() (in module hed.tools.bids.bids_util) MATLAB interface MATLAB HEDTools MAX_CATEGORICAL (SummarizeColumnValuesOp attribute) max_font_size (WordCloudConfig attribute), [1], [2] MCP TypeScript, HED validation MCP server merge_all_info() (BaseSummary method) merge_sidecar_list() (BidsSidecarFile static method) MergeConsecutiveOp (class in remodeler.operations.merge_consecutive_op) merged (HedSchema property) MESSAGE_STRINGS (RemodelerValidator attribute) migration dependencies

min_font_size (WordCloudConfig attribute), [1], [2] Model Context Protocol modified (HedTags property) (HedValueVector property) module hed.schema.hed_cache hed.schema.hed_schema_io hed.tools.bids.bids_util hedvis.core.sequence_map hedvis.core.tag_visualizer hedvis.core.visualization_config hedvis.generators.word_cloud hedvis.generators.word_cloud_util hedweb.app_factory hedweb.base_operations hedweb.columns hedweb.event_operations hedweb.process_form hedweb.process_service hedweb.routes hedweb.schema_operations hedweb.sidecar_operations hedweb.spreadsheet_operations hedweb.string_operations hedweb.web_util ndx_hed.utils.bids2nwb remodeler.cli.run_remodel remodeler.cli.run_remodel_backup remodeler.cli.run_remodel_restore

N

name (BaseInput property) NAME (BaseOp property) (ConvertColumnsOp attribute) (FactorColumnOp attribute) (FactorHedTagsOp attribute) (FactorHedTypeOp attribute) name (FileDictionary property) (HedSchema property) (HedSchemaGroup property) (HedTags property) (HedValueVector property) NAME (MergeConsecutiveOp attribute) (NumberGroupsOp attribute) (NumberRowsOp attribute) (RemapColumnsOp attribute) (RemoveColumnsOp attribute) (RemoveRowsOp attribute) (RenameColumnsOp attribute) (ReorderColumnsOp attribute) name (SequenceMap attribute) NAME (SplitRowsOp attribute) name (SpreadsheetInput property) NAME (SummarizeColumnNamesOp attribute) (SummarizeColumnValuesOp attribute) (SummarizeDefinitionsOp attribute) (SummarizeHedTagsOp attribute) (SummarizeHedTypeOp attribute) (SummarizeHedValidationOp attribute) (SummarizeSidecarFromEventsOp attribute)

name (TabularInput property) namespace (HedTags attribute) (HedValueVector attribute) ndx-events integration ndx-hed installation ndx_hed.utils.bids2nwb module needs_sorting (BaseInput property) (SpreadsheetInput property) (TabularInput property) neurodata_type (HedTags attribute) (HedValueVector attribute) next steps NWB annotation NO_VALID_TAG_FOUND (ValidationErrors attribute) NODE_NAME_EMPTY (ValidationErrors attribute) normalize_boolean() (in module hedweb.process_service) NumberGroupsOp (class in remodeler.operations.number_groups_op) NumberRowsOp (class in remodeler.operations.number_rows_op) NumericRange (HedKey attribute) NWB annotation how HED works saving files what is NWB

O

object_id (HedTags property) (HedValueVector property) ONSET_TOLERANCE (SpreadsheetValidator attribute) onsets (BaseInput property) (SpreadsheetInput property) (TabularInput property) ONSETS_UNORDERED (ValidationErrors attribute)

OnsetValidator (class in hed.validator.onset_validator) OPENING_GROUP_CHARACTER (HedString attribute) OPERATION_DICT (RemodelerValidator attribute) optimization org_base_tag (HedTag property) org_tag (HedTag property) output_files() (FileDictionary method) output_formats (VisualizationConfig attribute), [1], [2]

P

package_results() (in module hedweb.web_util) package_spreadsheet() (ProcessServices static method) pandas DataFrame, [1] PARAMETER_SPECIFICATION_TEMPLATE (RemodelerValidator attribute) PARAMS (BaseOp property) (ConvertColumnsOp attribute) (FactorColumnOp attribute) (FactorHedTagsOp attribute) (FactorHedTypeOp attribute) (MergeConsecutiveOp attribute) (NumberGroupsOp attribute) (NumberRowsOp attribute) (RemapColumnsOp attribute) (RemoveColumnsOp attribute) (RemoveRowsOp attribute) (RenameColumnsOp attribute) (ReorderColumnsOp attribute) (SplitRowsOp attribute) (SummarizeColumnNamesOp attribute) (SummarizeColumnValuesOp attribute) (SummarizeDefinitionsOp attribute) (SummarizeHedTagsOp attribute) (SummarizeHedTypeOp attribute) (SummarizeHedValidationOp attribute) (SummarizeSidecarFromEventsOp attribute) parent (HedTagEntry property) (HedTags property) (HedValueVector property) parent_name (HedTagEntry property) PARENTHESES_MISMATCH (ValidationErrors attribute) parse_arguments() (in module remodeler.cli.run_remodel) parse_bids_filename() (in module hed.tools.bids.bids_util)

parse_operations() (Dispatcher static method) parse_tasks() (in module remodeler.cli.run_remodel) parse_version_list() (in module hed.schema.hed_schema_io) pattern_doubleslash (HedValidator attribute) performance pip pip extras PLACEHOLDER_INVALID (ValidationErrors attribute) pop_error_context() (ErrorHandler method) post_proc_data() (Dispatcher static method) prefer_horizontal (WordCloudConfig attribute), [1], [2] prep() (SequenceMap static method) prep_data() (Dispatcher static method) process() (BaseOperations method) (EventOperations method) (ProcessServices static method) (SchemaOperations method) (SidecarOperations method) (SpreadsheetOperations method) (StringOperations method) ProcessForm (class in hedweb.process_form) ProcessServices (class in hedweb.process_service) properties (HedSchema property) Properties (HedSectionKey attribute) push_error_context() (ErrorHandler method) pyenv PyPI pyproject.toml Python direct calls installation

Q

queries

R

random_color_darker() (in module hedvis.generators.word_cloud_util) read_io (HedTags property) (HedValueVector property) Recommended (HedKey attribute) RelatedTag (HedKey attribute) RELATIVE_BACKUP_LOCATION (BackupManager attribute) relative_scaling (WordCloudConfig attribute), [1], [2] RemapColumnsOp (class in remodeler.operations.remap_columns_op) remodel() (EventOperations method) remodeler.cli.run_remodel module remodeler.cli.run_remodel_backup module remodeler.cli.run_remodel_restore module RemodelerValidator (class in remodeler.remodeler_validator) REMODELING_SUMMARY_PATH (Dispatcher attribute) remove() (HedGroup method) (HedString method) remove_definitions() (HedString method) remove_refs() (HedString method) RemoveColumnsOp (class in remodeler.operations.remove_columns_op) RemoveRowsOp (class in remodeler.operations.remove_rows_op) RenameColumnsOp (class in remodeler.operations.rename_columns_op) render_events_form() (in module hedweb.routes) render_home_page() (in module hedweb.routes) render_schemas_form() (in module hedweb.routes) render_services_form() (in module hedweb.routes) render_sidecars_form() (in module hedweb.routes) render_spreadsheets_form() (in module hedweb.routes) render_strings_form() (in module hedweb.routes) ReorderColumnsOp (class in remodeler.operations.reorder_columns_op) replace() (HedGroup static method) (HedString static method)

replace_placeholder() (HedTag method) replace_tag_references() (ErrorHandler static method) RequireChild (HedKey attribute) Required (HedKey attribute) REQUIRED_TAG_MISSING (ValidationErrors attribute) requirements files deprecated Reserved (HedKey attribute) reserved_category_values (SidecarValidator attribute) reserved_column_names (SidecarValidator attribute) reserved_reqs_path (ReservedChecker attribute) ReservedChecker (class in hed.validator.reserved_checker) reset_column_mapper() (TabularInput method) reset_error_context() (ErrorHandler method) reset_mapper() (BaseInput method) (SpreadsheetInput method) (TabularInput method) reset_parent() (HedTags method) (HedValueVector method) resources NWB and HED restore_backup() (BackupManager method) root_path (BidsDataset attribute) Rooted (HedKey attribute) ROOTED_TAG_DOES_NOT_EXIST (HedExceptions attribute) ROOTED_TAG_HAS_PARENT (HedExceptions attribute) ROOTED_TAG_INVALID (HedExceptions attribute) ROW (ErrorContext attribute) run_basic_checks() (HedValidator method) run_full_string_checks() (HedValidator method) run_operations() (Dispatcher method) run_ops() (in module remodeler.cli.run_remodel)

S

save() (BaseSummary method) save_as_dataframes() (HedSchema method) save_as_json() (HedSchema method) (Sidecar method) save_as_mediawiki() (HedSchema method) save_as_xml() (HedSchema method) save_directory (VisualizationConfig attribute), [1], [2] save_summaries() (Dispatcher method) save_visualizations() (BaseSummary method) scale_adjustment (WordCloudConfig attribute), [1], [2] schema conversion development IDs library loading release validation, [1] schema (BidsDataset attribute) schema management schema reference standard schema; library schemas; versions; formats; HED usage schema validation schema_83_props (HedSchema property) (HedSchemaGroup property) SCHEMA_ATTRIBUTE (ErrorContext attribute) SCHEMA_DUPLICATE_FROM_LIBRARY (SchemaErrors attribute) SCHEMA_DUPLICATE_LIBRARY (HedExceptions attribute) SCHEMA_DUPLICATE_NAMES (HedExceptions attribute) SCHEMA_DUPLICATE_NODE (SchemaErrors attribute) SCHEMA_DUPLICATE_PREFIX (HedExceptions attribute) schema_for_namespace() (HedSchema method) (HedSchemaGroup method) SCHEMA_HEADER_INVALID (HedExceptions attribute) SCHEMA_HEADER_MISSING (HedExceptions attribute) SCHEMA_INVALID (HedExceptions attribute) SCHEMA_INVALID_CHILD (SchemaErrors attribute) SCHEMA_INVALID_SIBLING (SchemaErrors attribute) SCHEMA_LIBRARY_INVALID (HedExceptions attribute) SCHEMA_LOAD_FAILED (HedExceptions attribute) schema_namespace (HedSchema property) (HedTag property) SCHEMA_SECTION (ErrorContext attribute) SCHEMA_SECTION_MISSING (HedExceptions attribute) SCHEMA_TAG (ErrorContext attribute) SCHEMA_TAG_TSV_BAD_PARENT (HedExceptions attribute) SCHEMA_UNKNOWN_HEADER_ATTRIBUTE (HedExceptions attribute) SCHEMA_VERSION_INVALID (HedExceptions attribute) schema_version_results() (in module hedweb.routes) schema_versions_results() (in module hedweb.routes) SchemaErrors (class in hed.errors.error_types) SchemaOperations (class in hedweb.schema_operations) schemas_results() (in module hedweb.routes) SchemaValidator score library scripts search applications HED object-based text-based search() (EventOperations method) (StringOperations method) searchHed usage searching HED annotations section_key (HedSchemaEntry property) (HedSchemaSection property) (HedTagEntry property) (UnitClassEntry property) (UnitEntry property) semantics annotation separate_issues() (in module hed.errors.error_reporter) SequenceMap (class in hedvis.core.sequence_map) series_a (BaseInput property) (SpreadsheetInput property) (TabularInput property) series_filtered (BaseInput property) (SpreadsheetInput property) (TabularInput property) services_results() (in module hedweb.routes) set_cache_directory() (in module hed.schema.hed_cache) set_cell() (BaseInput method) (SpreadsheetInput method) (TabularInput method) set_contents() (BidsFile method) (BidsSidecarFile method) (BidsTabularFile method) set_data_io() (HedTags method) (HedValueVector method) set_definitions() (ProcessServices static method) set_input_from_dict() (BaseOperations method) (EventOperations method) (SchemaOperations method) (SidecarOperations method) (SpreadsheetOperations method) (StringOperations method)

set_input_from_request() (ProcessServices static method) set_input_objects() (ProcessForm static method) (ProcessServices static method) set_json_files() (ProcessForm static method) set_modified() (HedTags method) (HedValueVector method) set_parameters() (ProcessServices static method) set_queries() (ProcessForm static method) (ProcessServices static method) set_remodel_parameters() (ProcessServices static method) set_schema_from_request() (ProcessForm static method) set_schema_from_version() (ProcessForm static method) set_schema_prefix() (HedSchema method) set_sidecar() (BidsTabularFile method) (ProcessServices static method) set_tsv_schema() (ProcessForm static method) shape (HedTags property) (HedValueVector property) short_base_tag (HedTag property) short_tag (HedTag property) shrink_defs() (BaseInput method) (HedString method) (SpreadsheetInput method) (TabularInput method) sidecar Sidecar (class in hed.models.sidecar) Sidecar class sidecar file sidecar validation SIDECAR_AND_OTHER_COLUMNS (ValidationErrors attribute) SIDECAR_BRACES_INVALID (SidecarErrors attribute) SIDECAR_COLUMN_NAME (ErrorContext attribute) sidecar_convert() (SidecarOperations method) sidecar_dict (BidsFileGroup attribute) sidecar_dir_dict (BidsFileGroup attribute) sidecar_extract() (SidecarOperations method) SIDECAR_HED_USED (SidecarErrors attribute) SIDECAR_INVALID (ValidationErrors attribute) SIDECAR_KEY_MISSING (ValidationErrors attribute) SIDECAR_KEY_NAME (ErrorContext attribute) sidecar_merge() (SidecarOperations method) SIDECAR_NA_USED (SidecarErrors attribute) sidecar_validate() (SidecarOperations method) SidecarErrors (class in hed.errors.error_types) SidecarOperations (class in hedweb.sidecar_operations) sidecars_results() (in module hedweb.routes) SidecarValidator (class in hed.validator.sidecar_validator) SIUnit (HedKey attribute) SIUnitModifier (HedKey attribute) SIUnitSymbolModifier (HedKey attribute) sort() (HedGroup method) (HedString method) sort_issues() (in module hed.errors.error_reporter) sorted() (HedGroup method) (HedString method) span (HedGroup property) (HedString property) split_hed_string() (HedString static method) split_into_groups() (HedString static method) SplitRowsOp (class in remodeler.operations.split_rows_op) spreadsheet templates spreadsheet_convert() (SpreadsheetOperations method) spreadsheet_validate() (SpreadsheetOperations method) SpreadsheetInput (class in hed.models.spreadsheet_input) SpreadsheetOperations (class in hedweb.spreadsheet_operations) spreadsheets_results() (in module hedweb.routes) SpreadsheetValidator (class in hed.validator.spreadsheet_validator) str_list_to_hed() (EventManager method) StringOperations (class in hedweb.string_operations) StringRange (HedKey attribute) strings_results() (in module hedweb.routes) STYLE_WARNING (ValidationErrors attribute) suffix (BidsFile attribute) (BidsFileGroup attribute) SuggestedTag (HedKey attribute) summarize() (BidsFileGroup method) summarize_all() (HedTypeManager method) SummarizeColumnNamesOp (class in remodeler.operations.summarize_column_names_op) SummarizeColumnValuesOp (class in remodeler.operations.summarize_column_values_op) SummarizeDefinitionsOp (class in remodeler.operations.summarize_definitions_op) SummarizeHedTagsOp (class in remodeler.operations.summarize_hed_tags_op) SummarizeHedTypeOp (class in remodeler.operations.summarize_hed_type_op) SummarizeHedValidationOp (class in remodeler.operations.summarize_hed_validation_op) SummarizeSidecarFromEventsOp (class in remodeler.operations.summarize_sidecar_from_events_op) summary column values experimental design HED HED tags SUMMARY_TYPE (SummarizeColumnNamesOp attribute) (SummarizeColumnValuesOp attribute) (SummarizeDefinitionsOp attribute) (SummarizeHedTagsOp attribute) (SummarizeHedTypeOp attribute) (SummarizeHedValidationOp attribute) (SummarizeSidecarFromEventsOp attribute) SVG format

T

TABLE_NAME (ErrorContext attribute) tabular data TabularInput, [1] (class in hed.models.tabular_input) TabularSummary (class in hed.tools.analysis.tabular_summary) tag filtering, [1] tag (HedTag property) tag counts tag frequency, [1] tag template TAG_EMPTY (ValidationErrors attribute) tag_exists_in_schema() (HedTag method) TAG_EXPRESSION_REPEATED (ValidationErrors attribute) TAG_EXTENDED (ValidationErrors attribute) TAG_EXTENSION_INVALID (ValidationErrors attribute) TAG_GROUP_ERROR (ValidationErrors attribute) TAG_INVALID (ValidationErrors attribute) tag_modified() (HedTag method) TAG_NAMESPACE_PREFIX_INVALID (ValidationErrors attribute) TAG_NOT_UNIQUE (ValidationErrors attribute) TAG_REQUIRES_CHILD (ValidationErrors attribute) TagDomain (HedKey attribute) TagGroup (HedKey attribute) TagRange (HedKey attribute) tags (HedSchema property) Tags (HedSectionKey attribute) tags() (HedGroup method) (HedString method) TakesValue (HedKey attribute)

TEMPORAL_ANCHORS (SpreadsheetValidator attribute) TEMPORAL_TAG_ERROR (ValidationErrors attribute) TEXT_EXTENSION (BaseInput attribute) (SpreadsheetInput attribute) (TabularInput attribute) TILDES_UNSUPPORTED (ValidationErrors attribute) to_csv() (BaseInput method) (SpreadsheetInput method) (TabularInput method) to_dict() (VisualizationConfig method), [1] (WordCloudConfig method), [1] to_excel() (BaseInput method) (SpreadsheetInput method) (TabularInput method) tool overview TopLevelTagGroup (HedKey attribute) total_events (HedType property) transform() (HedTags method) (HedValueVector method) troubleshooting, [1], [2] tsv files TSV_COLUMN_MISSING (ValidationErrors attribute) tutorial, [1] type_hierarchy() (HedTags class method) (HedValueVector class method) type_variables (HedType property) types (HedTypeManager property) TypeScript HED JavaScript HED MCP

U

unfold_context() (EventManager method) Unique (HedKey attribute) unit_classes (HedSchema property) (HedTag property) unit_modifiers (HedSchema property) UnitClass (HedKey attribute) UnitClassDomain (HedKey attribute) UnitClassEntry (class in hed.schema.hed_schema_entry) UnitClasses (HedSectionKey attribute) UnitClassRange (HedKey attribute) UnitDomain (HedKey attribute) UnitEntry (class in hed.schema.hed_schema_entry) UnitModifierDomain (HedKey attribute) UnitModifiers (HedSectionKey attribute)

UnitPrefix (HedKey attribute) UnitRange (HedKey attribute) units (HedSchema property) Units (HedSectionKey attribute) UNITS_INVALID (ValidationErrors attribute) UnitSymbol (HedKey attribute) UNKNOWN_COLUMN_TYPE (SidecarErrors attribute) update() (SequenceMap method) (TabularSummary method) update_entity() (in module hed.tools.bids.bids_util) update_summary() (BaseSummary method) (TabularSummary method) URL_ERROR (HedExceptions attribute) use_mask (WordCloudConfig attribute), [1], [2] user guide, [1], [2]

V

val_error_unknown() (ErrorHandler method) valid_operations (in module remodeler.operations.valid_operations) valid_prefixes (HedSchema property) (HedSchemaGroup property) validate method validate() (BaseInput method) (BidsDataset method) (BidsFileGroup method) (EventOperations method) (HedString method) (HedValidator method) (RemodelerValidator method) (SchemaOperations method) (Sidecar method) (SidecarValidator method) (SpreadsheetInput method) (SpreadsheetValidator method) (StringOperations method) (TabularInput method) validate_datafiles() (BidsFileGroup method) validate_def_tags() (DefValidator method) validate_def_value_units() (DefValidator method) validate_input_data() (BaseOp static method) (ConvertColumnsOp static method) (FactorColumnOp static method) (FactorHedTagsOp static method) (FactorHedTypeOp static method) (MergeConsecutiveOp static method) (NumberGroupsOp static method) (NumberRowsOp static method) (RemapColumnsOp static method) (RemoveColumnsOp static method) (RemoveRowsOp static method) (RenameColumnsOp static method) (ReorderColumnsOp static method) (SplitRowsOp static method) (SummarizeColumnNamesOp static method) (SummarizeColumnValuesOp static method) (SummarizeDefinitionsOp static method) (SummarizeHedTagsOp static method) (SummarizeHedTypeOp static method) (SummarizeHedValidationOp static method) (SummarizeSidecarFromEventsOp static method)

validate_onset_offset() (DefValidator method) validate_sidecars() (BidsFileGroup method) validate_structure() (SidecarValidator method) validate_temporal_relations() (OnsetValidator method) validate_units() (HedValidator method) validateEvents validateSidecar validateTags validation BIDS HED, [1], [2] HED strings JavaScript MCP NWB strategies what is validation tools, [1] validation workflow ValidationErrors (class in hed.errors.error_types) value_as_default_unit() (HedTag method) value_classes (HedSchema property) (HedTag property) VALUE_INVALID (ValidationErrors attribute) ValueClass (HedKey attribute) ValueClassDomain (HedKey attribute) ValueClasses (HedSectionKey attribute) ValueClassRange (HedKey attribute) values() (HedSchemaSection method) VALUES_PER_LINE (SummarizeColumnValuesOp attribute) version (HedSchema property) version management VERSION_DEPRECATED (ValidationErrors attribute) version_number (HedSchema property) visualization publication-ready VisualizationConfig (class in hedvis.core.visualization_config), [1] visualize_from_counts() (HedTagVisualizer method), [1] visualize_from_dataframe visualize_from_dataframe() (HedTagVisualizer method), [1] visualize_from_tabular() (HedTagVisualizer method), [1]

W

walk_back() (in module hed.tools.bids.bids_util) WARNING (ErrorSeverity attribute) web services width (WordCloudConfig attribute), [1], [2] WIKI_DELIMITERS_INVALID (HedExceptions attribute) WIKI_LINE_INVALID (HedExceptions attribute) WIKI_LINE_START_INVALID (HedExceptions attribute) WIKI_SEPARATOR_INVALID (HedExceptions attribute) with_standard (HedSchema property) with_traceback() (HedFileError method) Word cloud word cloud shaped

word frequency, [1] word_cloud (VisualizationConfig attribute), [1], [2] word_cloud_to_svg word_cloud_to_svg() (in module hedvis.generators.word_cloud), [1] WordCloudConfig (class in hedvis.core.visualization_config), [1] workflows worksheet_name (BaseInput property) (SpreadsheetInput property) (TabularInput property) WRONG_HED_DATA_TYPE (SidecarErrors attribute)