hdmf.common package¶
Subpackages¶
Submodules¶
- hdmf.common.alignedtable module
AlignedDynamicTable
AlignedDynamicTable.category_tables
AlignedDynamicTable.categories
AlignedDynamicTable.add_category
AlignedDynamicTable.get_category
AlignedDynamicTable.add_column
AlignedDynamicTable.add_row
AlignedDynamicTable.get_colnames
AlignedDynamicTable.to_dataframe
AlignedDynamicTable.__getitem__
AlignedDynamicTable.get
AlignedDynamicTable.has_foreign_columns
AlignedDynamicTable.get_foreign_columns
AlignedDynamicTable.get_linked_tables
AlignedDynamicTable.data_type
AlignedDynamicTable.namespace
- hdmf.common.hierarchicaltable module
- hdmf.common.multi module
- hdmf.common.resources module
KeyTable
Key
ResourceTable
Resource
EntityTable
Entity
ObjectTable
Object
ObjectKeyTable
ObjectKey
ExternalResources
ExternalResources.keys
ExternalResources.resources
ExternalResources.entities
ExternalResources.objects
ExternalResources.object_keys
ExternalResources.assert_external_resources_equal
ExternalResources.get_key
ExternalResources.get_resource
ExternalResources.add_ref
ExternalResources.get_object_resources
ExternalResources.get_keys
ExternalResources.to_dataframe
ExternalResources.to_sqlite
ExternalResources.to_tsv
ExternalResources.from_tsv
ExternalResources.data_type
ExternalResources.namespace
- hdmf.common.sparse module
- hdmf.common.table module
VectorData
VectorIndex
ElementIdentifiers
DynamicTable
DynamicTable.description
DynamicTable.id
DynamicTable.colnames
DynamicTable.columns
DynamicTable.add_row
DynamicTable.add_column
DynamicTable.create_region
DynamicTable.__getitem__
DynamicTable.get
DynamicTable.get_foreign_columns
DynamicTable.has_foreign_columns
DynamicTable.get_linked_tables
DynamicTable.to_dataframe
DynamicTable.from_dataframe
DynamicTable.copy
DynamicTable.data_type
DynamicTable.namespace
DynamicTableRegion
EnumData
Module contents¶
This package will contain functions, classes, and objects for reading and writing data in according to the HDMF-common specification
- hdmf.common.register_class(data_type, namespace='hdmf-common', container_cls=None)¶
- Register an Container class to use for reading and writing a data_type from a specification
If container_cls is not specified, returns a decorator for registering an Container subclass as the class for data_type in namespace.
- hdmf.common.register_map(container_cls, mapper_cls=None)¶
- Register an ObjectMapper to use for a Container class type
If mapper_cls is not specified, returns a decorator for registering an ObjectMapper class as the mapper for container_cls. If mapper_cls specified, register the class as the mapper for container_cls
- hdmf.common.load_namespaces(namespace_path)¶
Load namespaces from file
- hdmf.common.available_namespaces()¶
- hdmf.common.get_class(data_type, namespace)¶
Get the class object of the Container subclass corresponding to a given neurdata_type.
- hdmf.common.get_type_map(extensions=None)¶
- Get a BuildManager to use for I/O using the given extensions. If no extensions are provided,
return a BuildManager that uses the core namespace
- hdmf.common.get_manager(extensions=None)¶
- Get a BuildManager to use for I/O using the given extensions. If no extensions are provided,
return a BuildManager that uses the core namespace
- hdmf.common.validate(io, namespace='hdmf-common', experimental=False)¶
Validate an file against a namespace
- hdmf.common.get_hdf5io(path=None, mode='r', manager=None, comm=None, file=None, driver=None)¶
A convenience method for getting an HDF5IO object using an HDMF-common build manager if none is provided.
- Parameters
mode (
str
) – the mode to open the HDF5 file with, one of (“w”, “r”, “r+”, “a”, “w-”, “x”). See h5py.File for more details.manager (
TypeMap
orBuildManager
) – the BuildManager or a TypeMap to construct a BuildManager to use for I/Ocomm (Intracomm) – the MPI communicator to use for parallel I/O
file (
File
or S3File) – a pre-existing h5py.File objectdriver (
str
) – driver for h5py to use when opening HDF5 file