Index

_

__getitem__() (hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset method) (hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset method) (hdmf.build.builders.GroupBuilder method) (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.multi.SimpleMultiContainer method) (hdmf.common.table.DynamicTable method) (hdmf.common.table.DynamicTableRegion method) (hdmf.common.table.EnumData method) (hdmf.common.table.VectorIndex method) (hdmf.container.Data method) (hdmf.container.RowGetter method) (hdmf.container.Table method) (hdmf.data_utils.DataIO method) (hdmf.query.HDMFDataset method) (hdmf.term_set.TermSet method) (hdmf.term_set.TermSetWrapper method) (hdmf.utils.LabelledDict method) (hdmf.utils.StrDataset method)

__iter__() (hdmf.data_utils.AbstractDataChunkIterator method) __next__() (hdmf.data_utils.AbstractDataChunkIterator method) _get_data() (hdmf.data_utils.GenericDataChunkIterator method) _get_dtype() (hdmf.data_utils.GenericDataChunkIterator method) _get_maxshape() (hdmf.data_utils.GenericDataChunkIterator method)

A

AbstractContainer (class in hdmf.container) AbstractDataChunkIterator (class in hdmf.data_utils) AbstractH5ReferenceDataset (class in hdmf.backends.hdf5.h5_utils) AbstractH5TableDataset (class in hdmf.backends.hdf5.h5_utils) add() (hdmf.utils.LabelledDict method) (hdmf.validate.validator.SpecMatches method) add_attribute() (hdmf.spec.spec.BaseStorageSpec method) add_candidate() (hdmf.build.manager.Proxy method) add_category() (hdmf.common.alignedtable.AlignedDynamicTable method) add_column() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) add_container() (hdmf.common.multi.SimpleMultiContainer method) add_dataset() (hdmf.spec.spec.GroupSpec method) add_group() (hdmf.spec.spec.GroupSpec method) add_link() (hdmf.spec.spec.GroupSpec method) add_meanings_table() (hdmf.common.table.DynamicTable method) add_namespace() (hdmf.spec.namespace.NamespaceCatalog method) add_ref() (hdmf.common.resources.HERD method) add_ref_container() (hdmf.common.resources.HERD method) add_ref_termset() (hdmf.common.resources.HERD method) add_row() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.resources.EntityKeyTable method) (hdmf.common.resources.EntityTable method) (hdmf.common.resources.FileTable method) (hdmf.common.resources.KeyTable method) (hdmf.common.resources.ObjectKeyTable method) (hdmf.common.resources.ObjectTable method) (hdmf.common.table.DynamicTable method) (hdmf.common.table.EnumData method) (hdmf.common.table.MeaningsTable method) (hdmf.common.table.VectorData method) (hdmf.common.table.VectorIndex method) (hdmf.container.Table method) add_source() (hdmf.spec.write.NamespaceBuilder method) add_spec() (hdmf.spec.write.NamespaceBuilder method) (hdmf.spec.write.SpecFileBuilder method) add_vector() (hdmf.common.table.VectorIndex method)

additional_allowed (hdmf.spec.spec.DtypeHelper attribute) addl (hdmf.spec.spec.DtypeHelper attribute) AlignedDynamicTable (class in hdmf.common.alignedtable) AlignedDynamicTableMap (class in hdmf.common.io.alignedtable) all_children() (hdmf.container.AbstractContainer method) all_objects (hdmf.container.AbstractContainer property) allow (hdmf.spec.spec.DtypeHelper attribute) allowable (hdmf.spec.spec.DtypeHelper attribute) ALLOWED (hdmf.utils.AllowPositional attribute) AllowPositional (class in hdmf.utils) append() (hdmf.backends.hdf5.h5_utils.H5Dataset method) (hdmf.backends.hdf5.h5_utils.HDF5IODataChunkIteratorQueue method) (hdmf.container.Data method) (hdmf.data_utils.DataIO method) (hdmf.query.HDMFDataset method) (hdmf.term_set.TermSetWrapper method) append_data() (in module hdmf.data_utils) apply_generator_to_field() (hdmf.build.classgenerator.CustomClassGenerator class method) (hdmf.build.classgenerator.MCIClassGenerator class method) (hdmf.common.io.table.DynamicTableGenerator class method) assert_external_resources_equal() (hdmf.common.resources.HERD static method) assertBuilderEqual() (hdmf.testing.testcase.TestCase method) assertContainerEqual() (hdmf.testing.testcase.TestCase method) assertEqualShape() (in module hdmf.data_utils) assertRaisesWith() (hdmf.testing.testcase.TestCase method) assertValidDtype() (hdmf.spec.spec.DtypeSpec static method) assertWarnsWith() (hdmf.testing.testcase.TestCase method) assign_to_specs() (hdmf.validate.validator.SpecMatcher method) astype() (hdmf.data_utils.DataChunk method) attr_columns() (hdmf.common.io.table.DynamicTableMap method) attributes (hdmf.build.builders.BaseBuilder property) (hdmf.spec.spec.BaseStorageSpec property) AttributeSpec (class in hdmf.spec.spec) AttributeValidator (class in hdmf.validate.validator) author (hdmf.spec.namespace.SpecNamespace property) auto_register() (hdmf.spec.catalog.SpecCatalog method) available_namespaces() (in module hdmf.common) aws_region (hdmf.backends.hdf5.h5tools.HDF5IO property)

B

BaseBuilder (class in hdmf.build.builders) BaseStorageSpec (class in hdmf.spec.spec) BaseStorageValidator (class in hdmf.validate.validator) BrokenLinkWarning build() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) (hdmf.build.objectmapper.ObjectMapper method) build_const_args() (hdmf.spec.spec.AttributeSpec class method) (hdmf.spec.spec.BaseStorageSpec class method) (hdmf.spec.spec.ConstructableDict class method) (hdmf.spec.spec.DatasetSpec class method) (hdmf.spec.spec.DtypeSpec class method) (hdmf.spec.spec.GroupSpec class method) (hdmf.spec.spec.Spec class method)

build_namespace() (hdmf.spec.namespace.SpecNamespace class method) build_spec() (hdmf.spec.spec.ConstructableDict class method) Builder (class in hdmf.build.builders) builder (hdmf.build.builders.LinkBuilder property) (hdmf.build.builders.ReferenceBuilder property) BuilderH5ReferenceDataset (class in hdmf.backends.hdf5.h5_utils) BuilderH5TableDataset (class in hdmf.backends.hdf5.h5_utils) BuilderResolver (class in hdmf.query) BuilderResolverMixin (class in hdmf.backends.hdf5.h5_utils) BuildError BuildManager (class in hdmf.build.manager) BuildWarning

C

can_read() (hdmf.backends.hdf5.h5tools.HDF5IO static method) (hdmf.backends.io.HDMFIO static method) catalog (hdmf.spec.namespace.SpecNamespace property) categories (hdmf.common.alignedtable.AlignedDynamicTable property) category_tables (hdmf.common.alignedtable.AlignedDynamicTable property) check_dtype() (hdmf.spec.spec.DtypeHelper static method) check_shape() (in module hdmf.validate.validator) check_type() (in module hdmf.utils) (in module hdmf.validate.validator) check_valid_dtype() (hdmf.spec.spec.DtypeSpec static method) children (hdmf.container.AbstractContainer property) chunks (hdmf.build.builders.DatasetBuilder property) ClassGeneratorManager (class in hdmf.build.classgenerator) clear() (hdmf.utils.LabelledDict method) clear_cache() (hdmf.build.manager.BuildManager method) close() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) close_linked_files() (hdmf.backends.hdf5.h5tools.HDF5IO method) colnames (hdmf.common.table.DynamicTable property) columns (hdmf.common.table.DynamicTable property) (hdmf.container.Table property) comm (hdmf.backends.hdf5.h5tools.HDF5IO property) compute_default_chunk_shape() (hdmf.backends.hdf5.h5tools.HDF5IO static method) construct() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) (hdmf.build.objectmapper.ObjectMapper method) construct_helper() (hdmf.common.io.resources.HERDMap method) ConstructableDict (class in hdmf.spec.spec)

ConstructError constructor_arg() (hdmf.build.objectmapper.ObjectMapper static method) constructor_args (hdmf.build.objectmapper.ObjectMapper attribute) (hdmf.common.io.alignedtable.AlignedDynamicTableMap attribute) (hdmf.common.io.multi.SimpleMultiContainerMap attribute) (hdmf.common.io.resources.HERDMap attribute) (hdmf.common.io.table.DynamicTableMap attribute) contact (hdmf.spec.namespace.SpecNamespace property) Container (class in hdmf.container) container_source (hdmf.container.AbstractContainer property) ContainerConfigurationError ContainerH5ReferenceDataset (class in hdmf.backends.hdf5.h5_utils) ContainerH5TableDataset (class in hdmf.backends.hdf5.h5_utils) ContainerResolver (class in hdmf.query) ContainerResolverMixin (class in hdmf.backends.hdf5.h5_utils) containers (hdmf.common.multi.SimpleMultiContainer property) containers_attr() (hdmf.common.io.multi.SimpleMultiContainerMap method) containers_carg() (hdmf.common.io.multi.SimpleMultiContainerMap method) convert_dt_name() (hdmf.build.objectmapper.ObjectMapper class method) convert_dtype() (hdmf.build.objectmapper.ObjectMapper class method) convert_namespace() (hdmf.backends.utils.NamespaceToBuilderHelper class method) copy() (hdmf.common.table.DynamicTable method) copy_mappers() (hdmf.build.manager.TypeMap method) core_namespaces (hdmf.spec.namespace.NamespaceCatalog property) create_region() (hdmf.common.table.DynamicTable method) CSRMatrix (class in hdmf.common.sparse) css_style (hdmf.container.Container property) custom_generators (hdmf.build.classgenerator.ClassGeneratorManager property) CustomClassGenerator (class in hdmf.build.classgenerator)

D

Data (class in hdmf.container) data (hdmf.build.builders.DatasetBuilder property) (hdmf.container.Data property) (hdmf.data_utils.DataIO property) data_type (hdmf.build.manager.Proxy property) (hdmf.build.manager.TypeSource attribute) (hdmf.common.alignedtable.AlignedDynamicTable attribute) (hdmf.common.multi.SimpleMultiContainer attribute) (hdmf.common.resources.HERD attribute) (hdmf.common.sparse.CSRMatrix attribute) (hdmf.common.table.DynamicTable attribute) (hdmf.common.table.DynamicTableRegion attribute) (hdmf.common.table.ElementIdentifiers attribute) (hdmf.common.table.EnumData attribute) (hdmf.common.table.MeaningsTable attribute) (hdmf.common.table.VectorData attribute) (hdmf.common.table.VectorIndex attribute) (hdmf.container.AbstractContainer property) (hdmf.container.Container attribute) (hdmf.container.Data attribute) (hdmf.spec.spec.BaseStorageSpec property) (hdmf.validate.errors.MissingDataType property) data_type_def (hdmf.spec.spec.BaseStorageSpec property) data_type_inc (hdmf.spec.spec.BaseStorageSpec property) (hdmf.spec.spec.LinkSpec property) data_type_inc_resolved (hdmf.spec.spec.BaseStorageSpec property) DataChunk (class in hdmf.data_utils) DataChunkIterator (class in hdmf.data_utils) DataIO (class in hdmf.data_utils) datas_attr() (hdmf.common.io.multi.SimpleMultiContainerMap method) dataset (hdmf.backends.hdf5.h5_utils.H5DataIO property) (hdmf.query.HDMFDataset property) dataset_spec_cls (hdmf.spec.namespace.NamespaceCatalog property) dataset_spec_cls() (hdmf.spec.spec.GroupSpec class method) DatasetBuilder (class in hdmf.build.builders) DatasetOfReferences (class in hdmf.backends.hdf5.h5_utils) datasets (hdmf.build.builders.GroupBuilder property) (hdmf.spec.spec.GroupSpec property) DatasetSpec (class in hdmf.spec.spec) DatasetValidator (class in hdmf.validate.validator)

date (hdmf.spec.namespace.SpecNamespace property) def_key() (hdmf.spec.spec.BaseStorageSpec class method) default_name (hdmf.spec.spec.BaseStorageSpec property) default_value (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.DatasetSpec property) description (hdmf.common.table.DynamicTable property) (hdmf.common.table.VectorData property) dimension_labels (hdmf.build.builders.DatasetBuilder property) dims (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.DatasetSpec property) doc (hdmf.spec.namespace.SpecNamespace property) (hdmf.spec.spec.DtypeSpec property) (hdmf.spec.spec.Spec property) docval() (in module hdmf.utils) docval_macro() (in module hdmf.utils) driver (hdmf.backends.hdf5.h5tools.HDF5IO property) drop_id_columns() (in module hdmf.common.hierarchicaltable) dt (hdmf.spec.spec.DtypeHelper attribute) dt_syn (hdmf.spec.spec.DtypeHelper attribute) dtype (hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset property) (hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset property) (hdmf.build.builders.DatasetBuilder property) (hdmf.data_utils.AbstractDataChunkIterator property) (hdmf.data_utils.DataChunk property) (hdmf.data_utils.DataChunkIterator property) (hdmf.data_utils.DataIO property) (hdmf.data_utils.GenericDataChunkIterator property) (hdmf.query.HDMFDataset property) (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.DatasetSpec property) (hdmf.spec.spec.DtypeSpec property) (hdmf.term_set.TermSetWrapper property) dtype_spec_cls() (hdmf.spec.spec.DatasetSpec class method) DtypeConversionWarning DtypeError (class in hdmf.validate.errors) DtypeHelper (class in hdmf.spec.spec) DtypeSpec (class in hdmf.spec.spec) DynamicTable (class in hdmf.common.table) DynamicTableGenerator (class in hdmf.common.io.table) DynamicTableMap (class in hdmf.common.io.table) DynamicTableRegion (class in hdmf.common.table)

E

ElementIdentifiers (class in hdmf.common.table) elements (hdmf.common.table.EnumData property) EmptyArrayError entities (hdmf.common.resources.HERD property) entities() (hdmf.common.io.resources.HERDMap method) Entity (class in hdmf.common.resources) entity_keys (hdmf.common.resources.HERD property) entity_keys() (hdmf.common.io.resources.HERDMap method) EntityKey (class in hdmf.common.resources) EntityKeyTable (class in hdmf.common.resources) EntityTable (class in hdmf.common.resources) EnumData (class in hdmf.common.table) Error (class in hdmf.validate.errors) ERROR (hdmf.utils.AllowPositional attribute)

exhaust_queue() (hdmf.backends.hdf5.h5_utils.HDF5IODataChunkIteratorQueue method) ExpectedArrayError (class in hdmf.validate.errors) export() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) (hdmf.spec.write.NamespaceBuilder method) export_io() (hdmf.backends.hdf5.h5tools.HDF5IO class method) export_spec() (in module hdmf.spec.write) extend() (hdmf.common.table.DynamicTableRegion method) (hdmf.common.table.VectorData method) (hdmf.container.Data method) (hdmf.data_utils.DataIO method) (hdmf.term_set.TermSetWrapper method) extend_data() (in module hdmf.data_utils) ExtenderMeta (class in hdmf.utils) external_resources (hdmf.container.HERDManager property)

F

field (hdmf.term_set.TermSetWrapper property) fields (hdmf.container.AbstractContainer property) File (class in hdmf.common.resources) files (hdmf.common.resources.HERD property) files() (hdmf.common.io.resources.HERDMap method) FileTable (class in hdmf.common.resources)

filter_available() (hdmf.backends.hdf5.h5_utils.H5DataIO static method) flatten_column_index() (in module hdmf.common.hierarchicaltable) from_dataframe() (hdmf.common.table.DynamicTable class method) (hdmf.container.Table class method) from_iterable() (hdmf.data_utils.DataChunkIterator class method) from_zip() (hdmf.common.resources.HERD class method) full_name (hdmf.spec.namespace.SpecNamespace property)

G

generate_array_html_repr() (in module hdmf.utils) generate_class() (hdmf.build.classgenerator.ClassGeneratorManager method) generate_dataset_html() (hdmf.backends.hdf5.h5tools.HDF5IO static method) (hdmf.backends.io.HDMFIO static method) generate_html_repr() (hdmf.common.table.DynamicTable method) generate_new_id() (hdmf.container.AbstractContainer method) GenericDataChunkIterator (class in hdmf.data_utils) get() (hdmf.build.builders.GroupBuilder method) (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) (hdmf.common.table.DynamicTableRegion method) (hdmf.common.table.EnumData method) (hdmf.common.table.VectorData method) (hdmf.common.table.VectorIndex method) (hdmf.container.Data method) get_ancestor() (hdmf.container.AbstractContainer method) get_ancestors() (hdmf.container.AbstractContainer method) get_attr_names() (hdmf.build.objectmapper.ObjectMapper class method) get_attr_spec() (hdmf.build.objectmapper.ObjectMapper method) get_attr_value() (hdmf.build.objectmapper.ObjectMapper method) (hdmf.common.io.table.DynamicTableMap method) get_attribute() (hdmf.build.objectmapper.ObjectMapper method) (hdmf.spec.spec.BaseStorageSpec method) get_basic_array_info() (in module hdmf.utils) get_builder() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.build.manager.BuildManager method) get_builder_dt() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) get_builder_loc() (hdmf.validate.validator.Validator class method) get_builder_name() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) (hdmf.build.objectmapper.ObjectMapper method) get_builder_ns() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) get_carg_spec() (hdmf.build.objectmapper.ObjectMapper method) get_category() (hdmf.common.alignedtable.AlignedDynamicTable method) get_class() (in module hdmf.common) get_cls() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) get_colnames() (hdmf.common.alignedtable.AlignedDynamicTable method) get_config() (hdmf.term_set.TypeConfigurator method) get_const_arg() (hdmf.build.objectmapper.ObjectMapper method) get_container() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.common.multi.SimpleMultiContainer method) get_container_classes() (hdmf.build.manager.TypeMap method) get_container_cls_dt() (hdmf.build.manager.TypeMap method) get_container_name() (hdmf.build.objectmapper.ObjectMapper method) get_container_ns_dt() (hdmf.build.manager.TypeMap method) get_data_shape() (in module hdmf.utils) get_data_type() (hdmf.spec.spec.GroupSpec method) get_data_type_spec() (hdmf.spec.spec.BaseStorageSpec class method) get_dataset() (hdmf.spec.spec.GroupSpec method) get_docval() (in module hdmf.utils) get_docval_macro() (in module hdmf.utils) get_dt_container_cls() (hdmf.build.manager.TypeMap method) get_entity() (hdmf.common.resources.HERD method) get_external_resources() (hdmf.container.HERDManager method) get_fields_conf() (hdmf.container.AbstractContainer class method) get_foreign_columns() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) get_full_hierarchy() (hdmf.spec.catalog.SpecCatalog method) get_group() (hdmf.spec.spec.GroupSpec method) get_hdf5io() (in module hdmf.common) get_hierarchy() (hdmf.spec.catalog.SpecCatalog method) (hdmf.spec.namespace.NamespaceCatalog method) (hdmf.spec.namespace.SpecNamespace method)

get_inverse_class() (hdmf.backends.hdf5.h5_utils.BuilderH5ReferenceDataset class method) (hdmf.backends.hdf5.h5_utils.BuilderH5TableDataset class method) (hdmf.backends.hdf5.h5_utils.ContainerH5ReferenceDataset class method) (hdmf.backends.hdf5.h5_utils.ContainerH5TableDataset class method) (hdmf.query.ReferenceResolver class method) get_io_params() (hdmf.backends.hdf5.h5_utils.H5DataIO method) (hdmf.data_utils.DataIO method) get_iso8601_regex() (in module hdmf.validate.validator) get_key() (hdmf.common.resources.HERD method) get_link() (hdmf.spec.spec.GroupSpec method) get_linked_tables() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) get_loaded_type_config() (in module hdmf.common) get_manager() (in module hdmf.common) get_map() (hdmf.build.manager.TypeMap method) get_meanings() (hdmf.common.table.VectorData method) get_meanings_for_column() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) get_meanings_table() (hdmf.common.table.DynamicTable method) get_min_bounds() (hdmf.data_utils.DataChunk method) get_namespace() (hdmf.spec.namespace.NamespaceCatalog method) get_namespace_sources() (hdmf.spec.namespace.NamespaceCatalog method) get_namespace_spec() (hdmf.spec.spec.BaseStorageSpec class method) get_namespaces() (hdmf.backends.hdf5.h5tools.HDF5IO class method) get_object() (hdmf.backends.hdf5.h5_utils.BuilderResolverMixin method) (hdmf.backends.hdf5.h5_utils.ContainerResolverMixin method) (hdmf.backends.hdf5.h5_utils.DatasetOfReferences method) get_object_entities() (hdmf.common.resources.HERD method) get_object_type() (hdmf.common.resources.HERD method) get_proxy() (hdmf.build.manager.BuildManager method) get_read_io() (hdmf.container.AbstractContainer method) get_registered_types() (hdmf.spec.catalog.SpecCatalog method) (hdmf.spec.namespace.SpecNamespace method) get_source_description() (hdmf.spec.namespace.SpecNamespace method) get_source_files() (hdmf.spec.namespace.SpecNamespace method) get_source_types() (hdmf.spec.namespace.NamespaceCatalog method) get_sources() (hdmf.spec.namespace.NamespaceCatalog method) get_spec() (hdmf.spec.catalog.SpecCatalog method) (hdmf.spec.namespace.NamespaceCatalog method) (hdmf.spec.namespace.SpecNamespace method) get_spec_loc() (hdmf.validate.validator.Validator class method) get_spec_source_dict() (hdmf.spec.namespace.NamespaceCatalog method) get_spec_source_file() (hdmf.spec.catalog.SpecCatalog method) get_string_format() (in module hdmf.validate.validator) get_subspec() (hdmf.build.manager.BuildManager method) (hdmf.build.manager.TypeMap method) get_subtypes() (hdmf.spec.catalog.SpecCatalog method) get_target_data() (hdmf.common.table.VectorIndex method) get_target_type() (hdmf.spec.spec.GroupSpec method) get_type() (hdmf.backends.hdf5.h5tools.HDF5IO class method) (in module hdmf.validate.validator) get_type_map() (in module hdmf.common) get_types() (hdmf.spec.namespace.NamespaceCatalog method) get_validator() (hdmf.validate.validator.ValidatorMap method) get_written() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.utils.WriteStatusTracker method) get_zip_directory() (hdmf.common.resources.HERD class method) getargs() (in module hdmf.utils) group_spec_cls (hdmf.spec.namespace.NamespaceCatalog property) GroupBuilder (class in hdmf.build.builders) groups (hdmf.build.builders.GroupBuilder property) (hdmf.spec.spec.GroupSpec property) GroupSpec (class in hdmf.spec.spec) GroupValidator (class in hdmf.validate.validator)

H

H5DataIO (class in hdmf.backends.hdf5.h5_utils) H5Dataset (class in hdmf.backends.hdf5.h5_utils) H5RoundTripMixin (class in hdmf.testing.testcase) H5SpecReader (class in hdmf.backends.hdf5.h5_utils) H5SpecWriter (class in hdmf.backends.hdf5.h5_utils) has_foreign_columns() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.table.DynamicTable method) has_timezone() (in module hdmf.validate.validator) HDF5IO (class in hdmf.backends.hdf5.h5tools) HDF5IODataChunkIteratorQueue (class in hdmf.backends.hdf5.h5_utils) hdmf module hdmf.backends module hdmf.backends.errors module hdmf.backends.hdf5 module hdmf.backends.hdf5.h5_utils module hdmf.backends.hdf5.h5tools module hdmf.backends.io module hdmf.backends.utils module hdmf.backends.warnings module hdmf.build module hdmf.build.builders module hdmf.build.classgenerator module hdmf.build.errors module hdmf.build.manager module hdmf.build.objectmapper module hdmf.build.warnings module hdmf.common module hdmf.common.alignedtable module hdmf.common.hierarchicaltable module hdmf.common.io module hdmf.common.io.alignedtable module hdmf.common.io.multi module

hdmf.common.io.resources module hdmf.common.io.table module hdmf.common.multi module hdmf.common.resources module hdmf.common.sparse module hdmf.common.table module hdmf.container module hdmf.data_utils module hdmf.query module hdmf.spec module hdmf.spec.catalog module hdmf.spec.namespace module hdmf.spec.spec module hdmf.spec.write module hdmf.term_set module hdmf.testing module hdmf.testing.make_test_files module hdmf.testing.testcase module hdmf.testing.utils module hdmf.testing.validate_spec module hdmf.utils module hdmf.validate module hdmf.validate.errors module hdmf.validate.validator module HDMFDataset (class in hdmf.query) HDMFIO (class in hdmf.backends.io) HERD (class in hdmf.common.resources) HERDManager (class in hdmf.container) HERDMap (class in hdmf.common.io.resources)

I

id (hdmf.common.table.DynamicTable property) id_key() (hdmf.spec.spec.BaseStorageSpec class method) idx (hdmf.container.Row property) IllegalLinkError (class in hdmf.validate.errors) in_export_mode (hdmf.build.manager.BuildManager property) inc_key() (hdmf.spec.spec.BaseStorageSpec class method) inc_spec_resolved (hdmf.spec.spec.BaseStorageSpec property) include_namespace() (hdmf.spec.write.NamespaceBuilder method) include_type() (hdmf.spec.write.NamespaceBuilder method) IncorrectDatasetShapeBuildWarning IncorrectDataType (class in hdmf.validate.errors) IncorrectQuantityBuildWarning IncorrectQuantityError (class in hdmf.validate.errors) InvalidDataIOError invert() (hdmf.backends.hdf5.h5_utils.DatasetOfReferences method) (hdmf.query.ReferenceResolver method) io (hdmf.backends.hdf5.h5_utils.H5Dataset property) io_settings (hdmf.backends.hdf5.h5_utils.H5DataIO property) is_allowed_dtype() (hdmf.spec.spec.DtypeHelper static method) is_array_like() (in module hdmf.utils) is_empty() (hdmf.build.builders.GroupBuilder method) is_inherited_attribute() (hdmf.spec.spec.BaseStorageSpec method) is_inherited_dataset() (hdmf.spec.spec.GroupSpec method)

is_inherited_group() (hdmf.spec.spec.GroupSpec method) is_inherited_link() (hdmf.spec.spec.GroupSpec method) is_inherited_spec() (hdmf.spec.spec.BaseStorageSpec method) (hdmf.spec.spec.GroupSpec method) is_inherited_target_type() (hdmf.spec.spec.GroupSpec method) is_inherited_type() (hdmf.spec.spec.GroupSpec method) is_many() (hdmf.spec.spec.BaseStorageSpec method) (hdmf.spec.spec.LinkSpec method) is_newer_version() (in module hdmf.utils) is_open() (hdmf.backends.hdf5.h5tools.HDF5IO method) is_overridden_attribute() (hdmf.spec.spec.BaseStorageSpec method) is_overridden_dataset() (hdmf.spec.spec.GroupSpec method) is_overridden_group() (hdmf.spec.spec.GroupSpec method) is_overridden_link() (hdmf.spec.spec.GroupSpec method) is_overridden_spec() (hdmf.spec.spec.BaseStorageSpec method) (hdmf.spec.spec.GroupSpec method) is_overridden_target_type() (hdmf.spec.spec.GroupSpec method) is_overridden_type() (hdmf.spec.spec.GroupSpec method) is_ragged() (in module hdmf.utils) is_ref() (hdmf.spec.spec.DtypeSpec static method) is_sub_data_type() (hdmf.build.manager.BuildManager method) (hdmf.spec.namespace.NamespaceCatalog method) is_zarr_array() (in module hdmf.utils) items() (hdmf.build.builders.GroupBuilder method)

J

js_script (hdmf.container.Container property)

K

Key (class in hdmf.common.resources) key_attr (hdmf.utils.LabelledDict property) keys (hdmf.common.resources.HERD property)

keys() (hdmf.build.builders.GroupBuilder method) (hdmf.common.io.resources.HERDMap method) KeyTable (class in hdmf.common.resources)

L

label (hdmf.utils.LabelledDict property) LabelledDict (class in hdmf.utils) link_data (hdmf.backends.hdf5.h5_utils.H5DataIO property) link_resources() (hdmf.container.HERDManager method) link_spec_cls() (hdmf.spec.spec.GroupSpec class method) linkable (hdmf.spec.spec.BaseStorageSpec property) LinkBuilder (class in hdmf.build.builders) links (hdmf.build.builders.GroupBuilder property) (hdmf.spec.spec.GroupSpec property) LinkSpec (class in hdmf.spec.spec) load_namespaces() (hdmf.backends.hdf5.h5tools.HDF5IO class method) (hdmf.backends.io.HDMFIO class method) (hdmf.build.manager.TypeMap method) (hdmf.spec.namespace.NamespaceCatalog method) (in module hdmf.common)

load_namespaces_io() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) load_type_config() (hdmf.term_set.TypeConfigurator method) (in module hdmf.common) location (hdmf.build.builders.BaseBuilder property) (hdmf.build.manager.Proxy property) (hdmf.validate.errors.Error property)

M

main() (in module hdmf.testing.validate_spec) make_herd_1_8_0_file() (in module hdmf.testing.make_test_files) manager (hdmf.backends.io.HDMFIO property) map_attr() (hdmf.build.objectmapper.ObjectMapper method) map_const_arg() (hdmf.build.objectmapper.ObjectMapper method) map_spec() (hdmf.build.objectmapper.ObjectMapper method) matched_spec (hdmf.build.builders.Builder property) matched_spec_shape (hdmf.build.builders.DatasetBuilder property) matches() (hdmf.build.manager.Proxy method) maxshape (hdmf.backends.hdf5.h5_utils.H5DataIO property) (hdmf.build.builders.DatasetBuilder property) (hdmf.data_utils.AbstractDataChunkIterator property) (hdmf.data_utils.DataChunkIterator property) (hdmf.data_utils.GenericDataChunkIterator property) MCIClassGenerator (class in hdmf.build.classgenerator) meanings_tables (hdmf.common.table.DynamicTable property) MeaningsTable (class in hdmf.common.table) merge() (hdmf.build.manager.TypeMap method) (hdmf.spec.namespace.NamespaceCatalog method) MissingDataType (class in hdmf.validate.errors) MissingError (class in hdmf.validate.errors) MissingRequiredBuildWarning MissingRequiredWarning mode (hdmf.backends.hdf5.h5tools.HDF5IO property) modified (hdmf.container.AbstractContainer property) module hdmf hdmf.backends hdmf.backends.errors hdmf.backends.hdf5 hdmf.backends.hdf5.h5_utils hdmf.backends.hdf5.h5tools hdmf.backends.io hdmf.backends.utils hdmf.backends.warnings hdmf.build hdmf.build.builders hdmf.build.classgenerator hdmf.build.errors hdmf.build.manager hdmf.build.objectmapper hdmf.build.warnings hdmf.common hdmf.common.alignedtable hdmf.common.hierarchicaltable hdmf.common.io hdmf.common.io.alignedtable hdmf.common.io.multi hdmf.common.io.resources hdmf.common.io.table hdmf.common.multi hdmf.common.resources hdmf.common.sparse hdmf.common.table hdmf.container hdmf.data_utils hdmf.query hdmf.spec hdmf.spec.catalog hdmf.spec.namespace hdmf.spec.spec hdmf.spec.write hdmf.term_set hdmf.testing hdmf.testing.make_test_files hdmf.testing.testcase hdmf.testing.utils hdmf.testing.validate_spec hdmf.utils hdmf.validate hdmf.validate.errors hdmf.validate.validator

MultiContainerInterface (class in hdmf.container)

N

name (hdmf.build.builders.Builder property) (hdmf.container.AbstractContainer property) (hdmf.spec.namespace.SpecNamespace property) (hdmf.spec.spec.DtypeSpec property) (hdmf.spec.spec.Spec property) (hdmf.spec.write.NamespaceBuilder property) (hdmf.validate.errors.Error property) namespace (hdmf.build.manager.Proxy property) (hdmf.build.manager.TypeSource attribute) (hdmf.common.alignedtable.AlignedDynamicTable attribute) (hdmf.common.multi.SimpleMultiContainer attribute) (hdmf.common.resources.HERD attribute) (hdmf.common.sparse.CSRMatrix attribute) (hdmf.common.table.DynamicTable attribute) (hdmf.common.table.DynamicTableRegion attribute) (hdmf.common.table.ElementIdentifiers attribute) (hdmf.common.table.EnumData attribute) (hdmf.common.table.MeaningsTable attribute) (hdmf.common.table.VectorData attribute) (hdmf.common.table.VectorIndex attribute) (hdmf.container.Container attribute) (hdmf.container.Data attribute) (hdmf.validate.validator.ValidatorMap property)

namespace_catalog (hdmf.build.manager.BuildManager property) (hdmf.build.manager.TypeMap property) NamespaceBuilder (class in hdmf.spec.write) NamespaceCatalog (class in hdmf.spec.namespace) namespaces (hdmf.spec.namespace.NamespaceCatalog property) NamespaceToBuilderHelper (class in hdmf.backends.utils) next() (hdmf.data_utils.DataChunkIterator method) (hdmf.query.HDMFDataset method) no_convert() (hdmf.build.objectmapper.ObjectMapper class method)

O

obj_attrs (hdmf.build.objectmapper.ObjectMapper attribute) (hdmf.common.io.alignedtable.AlignedDynamicTableMap attribute) (hdmf.common.io.multi.SimpleMultiContainerMap attribute) (hdmf.common.io.resources.HERDMap attribute) (hdmf.common.io.table.DynamicTableMap attribute) Object (class in hdmf.common.resources) object_attr() (hdmf.build.objectmapper.ObjectMapper static method) object_id (hdmf.container.AbstractContainer property) object_keys (hdmf.common.resources.HERD property) object_keys() (hdmf.common.io.resources.HERDMap method)

OBJECT_REF_TYPE (hdmf.build.builders.DatasetBuilder attribute) ObjectKey (class in hdmf.common.resources) ObjectKeyTable (class in hdmf.common.resources) ObjectMapper (class in hdmf.build.objectmapper) objects (hdmf.common.resources.HERD property) objects() (hdmf.common.io.resources.HERDMap method) ObjectTable (class in hdmf.common.resources) open() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) OrphanContainerBuildError OrphanContainerWarning

P

parent (hdmf.build.builders.Builder property) (hdmf.container.AbstractContainer property) (hdmf.spec.spec.Spec property) path (hdmf.build.builders.Builder property) (hdmf.spec.spec.Spec property) pop() (hdmf.utils.LabelledDict method) popargs() (in module hdmf.utils) popargs_to_dict() (in module hdmf.utils) popitem() (hdmf.utils.LabelledDict method) post_init() (hdmf.utils.ExtenderMeta class method) post_process() (hdmf.build.classgenerator.CustomClassGenerator class method) (hdmf.build.classgenerator.MCIClassGenerator class method) (hdmf.common.io.table.DynamicTableGenerator class method)

pre_init() (hdmf.utils.ExtenderMeta class method) prebuilt() (hdmf.build.manager.BuildManager method) primary_dtype_synonyms (hdmf.spec.spec.DtypeHelper attribute) process_field_spec() (hdmf.build.classgenerator.CustomClassGenerator class method) (hdmf.build.classgenerator.MCIClassGenerator class method) (hdmf.common.io.table.DynamicTableGenerator class method) Proxy (class in hdmf.build.manager) purge_outdated() (hdmf.build.manager.BuildManager method) pystr() (in module hdmf.utils)

Q

quantity (hdmf.spec.spec.BaseStorageSpec property) (hdmf.spec.spec.LinkSpec property)

queue_ref() (hdmf.build.manager.BuildManager method)

R

read() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) read_builder() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) read_io (hdmf.container.AbstractContainer property) read_namespace() (hdmf.backends.hdf5.h5_utils.H5SpecReader method) (hdmf.spec.namespace.SpecReader method) (hdmf.spec.namespace.YAMLSpecReader method) read_spec() (hdmf.backends.hdf5.h5_utils.H5SpecReader method) (hdmf.spec.namespace.SpecReader method) (hdmf.spec.namespace.YAMLSpecReader method) reason (hdmf.validate.errors.Error property) recommended_chunk_shape() (hdmf.data_utils.AbstractDataChunkIterator method) (hdmf.data_utils.DataChunkIterator method) (hdmf.data_utils.GenericDataChunkIterator method) recommended_data_shape() (hdmf.data_utils.AbstractDataChunkIterator method) (hdmf.data_utils.DataChunkIterator method) (hdmf.data_utils.GenericDataChunkIterator method) recommended_primary_dtypes (hdmf.spec.spec.DtypeHelper attribute) ref (hdmf.backends.hdf5.h5_utils.H5Dataset property) ReferenceBuilder (class in hdmf.build.builders) ReferenceResolver (class in hdmf.query) ReferenceTargetNotBuiltError RefSpec (class in hdmf.spec.spec)

reftype (hdmf.spec.spec.RefSpec property) register_class() (in module hdmf.common) register_container_type() (hdmf.build.manager.TypeMap method) register_generator() (hdmf.build.classgenerator.ClassGeneratorManager method) (hdmf.build.manager.TypeMap method) register_map() (hdmf.build.manager.TypeMap method) (in module hdmf.common) register_spec() (hdmf.spec.catalog.SpecCatalog method) remove_test_file() (in module hdmf.testing.utils) reorder_yaml() (hdmf.spec.write.YAMLSpecWriter method) required (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.BaseStorageSpec property) (hdmf.spec.spec.LinkSpec property) reset_parent() (hdmf.container.AbstractContainer method) resolve() (hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset method) (hdmf.build.manager.Proxy method) resolve_all_specs() (hdmf.spec.namespace.NamespaceCatalog method) resolve_inc_spec() (hdmf.spec.spec.BaseStorageSpec method) (hdmf.spec.spec.DatasetSpec method) (hdmf.spec.spec.GroupSpec method) resolved (hdmf.spec.spec.BaseStorageSpec property) roundtripContainer() (hdmf.testing.testcase.H5RoundTripMixin method) roundtripExportContainer() (hdmf.testing.testcase.H5RoundTripMixin method) Row (class in hdmf.container) RowGetter (class in hdmf.container)

S

schema (hdmf.spec.namespace.SpecNamespace property) set_attribute() (hdmf.build.builders.BaseBuilder method) (hdmf.build.builders.GroupBuilder method) (hdmf.spec.spec.BaseStorageSpec method) set_attributes() (hdmf.backends.hdf5.h5tools.HDF5IO method) set_data_io() (hdmf.container.Container method) (hdmf.container.Data method) set_dataio() (hdmf.backends.hdf5.h5tools.HDF5IO class method) set_dataset() (hdmf.build.builders.GroupBuilder method) (hdmf.spec.spec.GroupSpec method) set_group() (hdmf.build.builders.GroupBuilder method) (hdmf.spec.spec.GroupSpec method) set_init() (hdmf.build.classgenerator.CustomClassGenerator class method) (hdmf.build.classgenerator.MCIClassGenerator class method) set_link() (hdmf.build.builders.GroupBuilder method) (hdmf.spec.spec.GroupSpec method) set_modified() (hdmf.container.AbstractContainer method) set_written() (hdmf.backends.utils.WriteStatusTracker method) setdefault() (hdmf.utils.LabelledDict method) setUp() (hdmf.testing.testcase.H5RoundTripMixin method) setUpContainer() (hdmf.testing.testcase.H5RoundTripMixin method) shape (hdmf.backends.hdf5.h5_utils.H5Dataset property) (hdmf.common.table.DynamicTableRegion property) (hdmf.container.Data property) (hdmf.data_utils.DataIO property) (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.DatasetSpec property)

SHAPE_ERROR (hdmf.data_utils.ShapeValidatorResult attribute) ShapeError (class in hdmf.validate.errors) ShapeValidatorResult (class in hdmf.data_utils) SimpleMultiContainer (class in hdmf.common.multi) SimpleMultiContainerMap (class in hdmf.common.io.multi) simplify_cpd_type() (hdmf.spec.spec.DtypeHelper static method) sort_keys() (hdmf.spec.write.YAMLSpecWriter static method) source (hdmf.backends.io.HDMFIO property) (hdmf.build.builders.Builder property) (hdmf.build.builders.GroupBuilder property) (hdmf.build.manager.Proxy property) (hdmf.spec.namespace.SpecReader property) Spec (class in hdmf.spec.spec) spec (hdmf.build.objectmapper.ObjectMapper property) (hdmf.validate.validator.Validator property) spec_matches (hdmf.validate.validator.SpecMatcher property) spec_namespace_cls (hdmf.spec.namespace.NamespaceCatalog property) SpecCatalog (class in hdmf.spec.catalog) SpecFileBuilder (class in hdmf.spec.write) SpecMatcher (class in hdmf.validate.validator) SpecMatches (class in hdmf.validate.validator) SpecNamespace (class in hdmf.spec.namespace) SpecReader (class in hdmf.spec.namespace) SpecWriter (class in hdmf.spec.write) StrDataset (class in hdmf.utils) stringify() (hdmf.backends.hdf5.h5_utils.H5SpecWriter static method) syn (hdmf.spec.spec.DtypeHelper attribute)

T

Table (class in hdmf.container) table (hdmf.common.table.DynamicTableRegion property) (hdmf.container.Row property) target (hdmf.common.table.MeaningsTable property) (hdmf.common.table.VectorIndex property) target_type (hdmf.spec.spec.LinkSpec property) (hdmf.spec.spec.RefSpec property) tearDown() (hdmf.testing.testcase.H5RoundTripMixin method) TermSet (class in hdmf.term_set) termset (hdmf.term_set.TermSetWrapper property) TermSetWrapper (class in hdmf.term_set) test_roundtrip() (hdmf.testing.testcase.H5RoundTripMixin method) test_roundtrip_export() (hdmf.testing.testcase.H5RoundTripMixin method) TestCase (class in hdmf.testing.testcase) to_dataframe() (hdmf.common.alignedtable.AlignedDynamicTable method) (hdmf.common.resources.HERD method) (hdmf.common.table.DynamicTable method) (hdmf.common.table.DynamicTableRegion method) (hdmf.container.Table method)

to_hierarchical_dataframe() (in module hdmf.common.hierarchicaltable) to_spmat() (hdmf.common.sparse.CSRMatrix method) to_uint_array() (in module hdmf.utils) to_zip() (hdmf.common.resources.HERD method) todict() (hdmf.common.resources.Entity method) (hdmf.common.resources.EntityKey method) (hdmf.common.resources.File method) (hdmf.common.resources.Key method) (hdmf.common.resources.Object method) (hdmf.common.resources.ObjectKey method) transform() (hdmf.container.Data method) type_hierarchy() (hdmf.container.AbstractContainer class method) type_key() (hdmf.spec.spec.BaseStorageSpec class method) type_map (hdmf.build.manager.BuildManager property) TypeConfigurator (class in hdmf.term_set) TypeDoesNotExistError TypeMap (class in hdmf.build.manager) types (hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset property) types_key() (hdmf.spec.namespace.SpecNamespace class method) TypeSource (class in hdmf.build.manager)

U

unload_type_config() (hdmf.term_set.TypeConfigurator method) (in module hdmf.common) unmap() (hdmf.build.objectmapper.ObjectMapper method)

unmatched_builders (hdmf.validate.validator.SpecMatcher property) UnsupportedOperation UNVERSIONED (hdmf.spec.namespace.SpecNamespace attribute) update() (hdmf.utils.LabelledDict method)

V

valid (hdmf.backends.hdf5.h5_utils.H5DataIO property) (hdmf.data_utils.DataIO property) valid_primary_dtypes (hdmf.spec.spec.DtypeHelper attribute) valid_types() (hdmf.validate.validator.ValidatorMap method) validate() (hdmf.term_set.TermSet method) (hdmf.testing.testcase.H5RoundTripMixin method) (hdmf.validate.validator.AttributeValidator method) (hdmf.validate.validator.BaseStorageValidator method) (hdmf.validate.validator.DatasetValidator method) (hdmf.validate.validator.GroupValidator method) (hdmf.validate.validator.Validator method) (hdmf.validate.validator.ValidatorMap method) (in module hdmf.common)

validate_data (hdmf.common.table.DynamicTableRegion property) validate_spec() (in module hdmf.testing.validate_spec) Validator (class in hdmf.validate.validator) ValidatorMap (class in hdmf.validate.validator) value (hdmf.spec.spec.AttributeSpec property) (hdmf.spec.spec.DatasetSpec property) (hdmf.term_set.TermSetWrapper property) values() (hdmf.build.builders.GroupBuilder method) VectorData (class in hdmf.common.table) VectorIndex (class in hdmf.common.table) version (hdmf.spec.namespace.SpecNamespace property) view_set (hdmf.term_set.TermSet property) vmap (hdmf.validate.validator.Validator property)

W

warn_for_ignored_namespaces() (hdmf.spec.namespace.NamespaceCatalog method) WARNING (hdmf.utils.AllowPositional attribute) which() (hdmf.container.Table method) write() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) write_builder() (hdmf.backends.hdf5.h5tools.HDF5IO method) (hdmf.backends.io.HDMFIO method) write_dataset() (hdmf.backends.hdf5.h5tools.HDF5IO method)

write_group() (hdmf.backends.hdf5.h5tools.HDF5IO method) write_link() (hdmf.backends.hdf5.h5tools.HDF5IO method) write_namespace() (hdmf.backends.hdf5.h5_utils.H5SpecWriter method) (hdmf.spec.write.SpecWriter method) (hdmf.spec.write.YAMLSpecWriter method) write_spec() (hdmf.backends.hdf5.h5_utils.H5SpecWriter method) (hdmf.spec.write.SpecWriter method) (hdmf.spec.write.YAMLSpecWriter method) WriteStatusTracker (class in hdmf.backends.utils)

Y

YAMLSpecReader (class in hdmf.spec.namespace)

YAMLSpecWriter (class in hdmf.spec.write)