hdmf package

Subpackages

• hdmf.backends package
  • Subpackages
    • hdmf.backends.hdf5 package
      • Submodules
      • Module contents
  • Submodules
    • hdmf.backends.errors module
      • UnsupportedOperation
    • hdmf.backends.io module
      • HDMFIO
    • hdmf.backends.utils module
      • WriteStatusTracker
      • NamespaceToBuilderHelper
    • hdmf.backends.warnings module
      • BrokenLinkWarning
  • Module contents
• hdmf.build package
  • Submodules
    • hdmf.build.builders module
      • Builder
      • BaseBuilder
      • GroupBuilder
      • DatasetBuilder
      • LinkBuilder
      • ReferenceBuilder
    • hdmf.build.classgenerator module
      • ClassGenerator
      • TypeDoesNotExistError
      • CustomClassGenerator
      • MCIClassGenerator
    • hdmf.build.errors module
      • BuildError
      • OrphanContainerBuildError
      • ReferenceTargetNotBuiltError
      • ContainerConfigurationError
      • ConstructError
    • hdmf.build.manager module
      • Proxy
      • BuildManager
      • TypeSource
      • TypeMap
    • hdmf.build.objectmapper module
      • ObjectMapper
    • hdmf.build.warnings module
      • BuildWarning
      • IncorrectQuantityBuildWarning
      • IncorrectDatasetShapeBuildWarning
      • MissingRequiredBuildWarning
      • MissingRequiredWarning
      • OrphanContainerWarning
      • DtypeConversionWarning
  • Module contents
• hdmf.common package
  • Subpackages
    • hdmf.common.io package
      • Submodules
      • Module contents
  • Submodules
    • hdmf.common.alignedtable module
      • AlignedDynamicTable
    • hdmf.common.hierarchicaltable module
      • to_hierarchical_dataframe
      • drop_id_columns
      • flatten_column_index
    • hdmf.common.multi module
      • SimpleMultiContainer
    • hdmf.common.resources module
      • KeyTable
      • Key
      • EntityTable
      • Entity
      • FileTable
      • File
      • ObjectTable
      • Object
      • ObjectKeyTable
      • EntityKeyTable
      • EntityKey
      • ObjectKey
      • HERD
    • hdmf.common.sparse module
      • CSRMatrix
    • hdmf.common.table module
      • VectorData
      • VectorIndex
      • ElementIdentifiers
      • DynamicTable
      • DynamicTableRegion
      • EnumData
  • Module contents
    • load_type_config
    • get_loaded_type_config
    • unload_type_config
    • register_class
    • register_map
    • load_namespaces
    • available_namespaces
    • get_class
    • get_type_map
    • get_manager
    • validate
    • get_hdf5io
• hdmf.spec package
  • Submodules
    • hdmf.spec.catalog module
      • SpecCatalog
    • hdmf.spec.namespace module
      • SpecNamespace
      • SpecReader
      • YAMLSpecReader
      • NamespaceCatalog
    • hdmf.spec.spec module
      • DtypeHelper
      • ConstructableDict
      • Spec
      • RefSpec
      • AttributeSpec
      • BaseStorageSpec
      • DtypeSpec
      • DatasetSpec
      • LinkSpec
      • GroupSpec
    • hdmf.spec.write module
      • SpecWriter
      • YAMLSpecWriter
      • NamespaceBuilder
      • SpecFileBuilder
      • export_spec
  • Module contents
• hdmf.testing package
  • Submodules
    • hdmf.testing.testcase module
      • TestCase
      • H5RoundTripMixin
    • hdmf.testing.utils module
      • remove_test_file
    • hdmf.testing.validate_spec module
      • validate_spec
      • main
  • Module contents
• hdmf.validate package
  • Submodules
    • hdmf.validate.errors module
      • Error
      • DtypeError
      • MissingError
      • ExpectedArrayError
      • ShapeError
      • MissingDataType
      • IllegalLinkError
      • IncorrectDataType
      • IncorrectQuantityError
    • hdmf.validate.validator module
      • check_type
      • get_iso8601_regex
      • get_string_format
      • EmptyArrayError
      • get_type
      • check_shape
      • ValidatorMap
      • Validator
      • AttributeValidator
      • BaseStorageValidator
      • DatasetValidator
      • GroupValidator
      • SpecMatches
      • SpecMatcher
  • Module contents

Submodules

• hdmf.container module
  • HERDManager
    • HERDManager.link_resources
    • HERDManager.get_linked_resources
  • AbstractContainer
    • AbstractContainer.data_type
    • AbstractContainer.get_fields_conf
    • AbstractContainer.read_io
    • AbstractContainer.get_read_io
    • AbstractContainer.name
    • AbstractContainer.get_ancestor
    • AbstractContainer.all_children
    • AbstractContainer.all_objects
    • AbstractContainer.get_ancestors
    • AbstractContainer.fields
    • AbstractContainer.object_id
    • AbstractContainer.generate_new_id
    • AbstractContainer.modified
    • AbstractContainer.set_modified
    • AbstractContainer.children
    • AbstractContainer.type_hierarchy
    • AbstractContainer.container_source
    • AbstractContainer.parent
    • AbstractContainer.reset_parent
  • Container
    • Container.css_style
    • Container.js_script
    • Container.set_data_io
    • Container.data_type
    • Container.namespace
  • Data
    • Data.data
    • Data.shape
    • Data.set_data_io
    • Data.transform
    • Data.__getitem__
    • Data.get
    • Data.append
    • Data.extend
    • Data.data_type
    • Data.namespace
  • MultiContainerInterface
  • Row
    • Row.idx
    • Row.table
  • RowGetter
    • RowGetter.__getitem__
  • Table
    • Table.columns
    • Table.add_row
    • Table.which
    • Table.__getitem__
    • Table.to_dataframe
    • Table.from_dataframe
• hdmf.data_utils module
  • append_data
  • extend_data
  • AbstractDataChunkIterator
    • AbstractDataChunkIterator.__iter__
    • AbstractDataChunkIterator.__next__
    • AbstractDataChunkIterator.recommended_chunk_shape
    • AbstractDataChunkIterator.recommended_data_shape
    • AbstractDataChunkIterator.dtype
    • AbstractDataChunkIterator.maxshape
  • GenericDataChunkIterator
    • GenericDataChunkIterator._get_data
    • GenericDataChunkIterator._get_maxshape
    • GenericDataChunkIterator._get_dtype
    • GenericDataChunkIterator.recommended_chunk_shape
    • GenericDataChunkIterator.recommended_data_shape
    • GenericDataChunkIterator.maxshape
    • GenericDataChunkIterator.dtype
  • DataChunkIterator
    • DataChunkIterator.from_iterable
    • DataChunkIterator.next
    • DataChunkIterator.recommended_chunk_shape
    • DataChunkIterator.recommended_data_shape
    • DataChunkIterator.maxshape
    • DataChunkIterator.dtype
  • DataChunk
    • DataChunk.astype
    • DataChunk.dtype
    • DataChunk.get_min_bounds
  • assertEqualShape
  • ShapeValidatorResult
    • ShapeValidatorResult.SHAPE_ERROR
  • DataIO
    • DataIO.get_io_params
    • DataIO.data
    • DataIO.dtype
    • DataIO.shape
    • DataIO.append
    • DataIO.extend
    • DataIO.__getitem__
    • DataIO.valid
  • InvalidDataIOError
• hdmf.monitor module
  • NotYetExhausted
  • DataChunkProcessor
    • DataChunkProcessor.recommended_chunk_shape
    • DataChunkProcessor.recommended_data_shape
    • DataChunkProcessor.get_final_result
    • DataChunkProcessor.process_data_chunk
    • DataChunkProcessor.compute_final_result
  • NumSampleCounter
    • NumSampleCounter.process_data_chunk
    • NumSampleCounter.compute_final_result
• hdmf.query module
  • HDMFDataset
    • HDMFDataset.__getitem__
    • HDMFDataset.dataset
    • HDMFDataset.dtype
    • HDMFDataset.next
    • HDMFDataset.append
  • ReferenceResolver
    • ReferenceResolver.get_inverse_class
    • ReferenceResolver.invert
  • BuilderResolver
  • ContainerResolver
• hdmf.term_set module
  • TermSet
    • TermSet.validate
    • TermSet.view_set
    • TermSet.__getitem__
  • TermSetWrapper
    • TermSetWrapper.value
    • TermSetWrapper.field
    • TermSetWrapper.termset
    • TermSetWrapper.dtype
    • TermSetWrapper.__getitem__
    • TermSetWrapper.append
    • TermSetWrapper.extend
  • TypeConfigurator
    • TypeConfigurator.get_config
    • TypeConfigurator.load_type_config
    • TypeConfigurator.unload_type_config
• hdmf.utils module
  • AllowPositional
    • AllowPositional.ALLOWED
    • AllowPositional.WARNING
    • AllowPositional.ERROR
  • docval_macro
  • get_docval_macro
  • check_type
  • get_docval
  • docval
  • getargs
  • popargs
  • popargs_to_dict
  • ExtenderMeta
    • ExtenderMeta.pre_init
    • ExtenderMeta.post_init
  • get_data_shape
  • pystr
  • to_uint_array
  • is_ragged
  • get_basic_array_info
  • generate_array_html_repr
  • LabelledDict
    • LabelledDict.label
    • LabelledDict.key_attr
    • LabelledDict.__getitem__
    • LabelledDict.add
    • LabelledDict.pop
    • LabelledDict.popitem
    • LabelledDict.clear
    • LabelledDict.setdefault
    • LabelledDict.update
  • StrDataset
    • StrDataset.__getitem__

Module contents