hdmf_zarr.zarr_utils module

Utilities for the Zarr I/O backend, e.g., for wrapping Zarr arrays on read, wrapping arrays for configuring write, or writing the spec among others

class hdmf_zarr.zarr_utils.ZarrDataset(dataset, io)

Bases: HDMFDataset

Extension of HDMFDataset to add Zarr compatibility

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

property io

property shape

class hdmf_zarr.zarr_utils.DatasetOfReferences(dataset, io)

Bases: ZarrDataset, ReferenceResolver

An extension of the base ReferenceResolver class to add more abstract methods for subclasses that will read Zarr references

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

abstract get_object(zarr_obj)

A class that maps an Zarr object to a Builder or Container

invert()

Return an object that defers reference resolution but in the opposite direction.

class hdmf_zarr.zarr_utils.BuilderResolverMixin

Bases: BuilderResolver

A mixin for adding to Zarr reference-resolving types the get_object method that returns Builders

get_object(zarr_obj)

A class that maps an Zarr object to a Builder

class hdmf_zarr.zarr_utils.ContainerResolverMixin

Bases: ContainerResolver

A mixin for adding to Zarr reference-resolvinAbstractZarrReferenceDatasetg types the get_object method that returns Containers

get_object(zarr_obj)

A class that maps an Zarr object to a Container

class hdmf_zarr.zarr_utils.AbstractZarrTableDataset(dataset, io, types)

Bases: DatasetOfReferences

Extension of DatasetOfReferences to serve as the base class for resolving Zarr references in compound datasets to either Builders and Containers.

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

• types (list or tuple) – the list/tuple of reference types

property types

property dtype

__getitem__(arg)

resolve(manager)

class hdmf_zarr.zarr_utils.AbstractZarrReferenceDataset(dataset, io)

Bases: DatasetOfReferences

Extension of DatasetOfReferences to serve as the base class for resolving Zarr references in datasets to either Builders and Containers.

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

__getitem__(arg)

property dtype

class hdmf_zarr.zarr_utils.AbstractZarrRegionDataset(dataset, io)

Bases: AbstractZarrReferenceDataset

Extension of DatasetOfReferences to serve as the base class for resolving Zarr references in datasets to either Builders and Containers.

Note: Region References are not yet supported.

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

__getitem__(arg)

property dtype

class hdmf_zarr.zarr_utils.ContainerZarrTableDataset(dataset, io, types)

Bases: ContainerResolverMixin, AbstractZarrTableDataset

A reference-resolving dataset for resolving references inside tables (i.e. compound dtypes) that returns resolved references as Containers

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

• types (list or tuple) – the list/tuple of reference types

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.

class hdmf_zarr.zarr_utils.BuilderZarrTableDataset(dataset, io, types)

Bases: BuilderResolverMixin, AbstractZarrTableDataset

A reference-resolving dataset for resolving references inside tables (i.e. compound dtypes) that returns resolved references as Builders

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

• types (list or tuple) – the list/tuple of reference types

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.

class hdmf_zarr.zarr_utils.ContainerZarrReferenceDataset(dataset, io)

Bases: ContainerResolverMixin, AbstractZarrReferenceDataset

A reference-resolving dataset for resolving object references that returns resolved references as Containers

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.

class hdmf_zarr.zarr_utils.BuilderZarrReferenceDataset(dataset, io)

Bases: BuilderResolverMixin, AbstractZarrReferenceDataset

A reference-resolving dataset for resolving object references that returns resolved references as Builders

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.

class hdmf_zarr.zarr_utils.ContainerZarrRegionDataset(dataset, io)

Bases: ContainerResolverMixin, AbstractZarrRegionDataset

A reference-resolving dataset for resolving region references that returns resolved references as Containers

Note: Region References are not yet supported.

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.

class hdmf_zarr.zarr_utils.BuilderZarrRegionDataset(dataset, io)

Bases: BuilderResolverMixin, AbstractZarrRegionDataset

A reference-resolving dataset for resolving region references that returns resolved references as Builders.

Note: Region References are not yet supported.

Parameters:

• dataset (ndarray or Array or Array) – the Zarr file lazily evaluate

• io (ZarrIO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()

Return the class the represents the ReferenceResolver that resolves references to the opposite type.

BuilderResolver.get_inverse_class should return a class that subclasses ContainerResolver.

ContainerResolver.get_inverse_class should return a class that subclasses BuilderResolver.