hdmf.backends.hdf5.h5_utils module¶

class hdmf.backends.hdf5.h5_utils.H5Dataset(dataset, io)¶

Bases: hdmf.query.HDMFDataset

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

io¶

regionref¶

ref¶

shape¶

class hdmf.backends.hdf5.h5_utils.DatasetOfReferences(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.H5Dataset, hdmf.query.ReferenceResolver

An extension of the base ReferenceResolver class to add more abstract methods for subclasses that will read HDF5 references

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

get_object(h5obj)¶: A class that maps an HDF5 object to a Builder or Container

invert()¶: Return an object that defers reference resolution but in the opposite direction.

class hdmf.backends.hdf5.h5_utils.BuilderResolverMixin¶

Bases: hdmf.query.BuilderResolver

A mixin for adding to HDF5 reference-resolving types the get_object method that returns Builders

get_object(h5obj)¶: A class that maps an HDF5 object to a Builder

class hdmf.backends.hdf5.h5_utils.ContainerResolverMixin¶

Bases: hdmf.query.ContainerResolver

A mixin for adding to HDF5 reference-resolving types the get_object method that returns Containers

get_object(h5obj)¶: A class that maps an HDF5 object to a Container

class hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset(dataset, io, types)¶

Bases: hdmf.backends.hdf5.h5_utils.DatasetOfReferences

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset types (`list` or `tuple`) – the IO object that was used to read the underlying dataset

types¶

dtype¶

__getitem__(arg)¶

resolve(manager)¶

class hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.DatasetOfReferences

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

__getitem__(arg)¶

dtype¶

class hdmf.backends.hdf5.h5_utils.AbstractH5RegionDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

__getitem__(arg)¶

dtype¶

class hdmf.backends.hdf5.h5_utils.ContainerH5TableDataset(dataset, io, types)¶

Bases: hdmf.backends.hdf5.h5_utils.ContainerResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset types (`list` or `tuple`) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.BuilderH5TableDataset(dataset, io, types)¶

Bases: hdmf.backends.hdf5.h5_utils.BuilderResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5TableDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset types (`list` or `tuple`) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.ContainerH5ReferenceDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.ContainerResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.BuilderH5ReferenceDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.BuilderResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5ReferenceDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.ContainerH5RegionDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.ContainerResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5RegionDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.BuilderH5RegionDataset(dataset, io)¶

Bases: hdmf.backends.hdf5.h5_utils.BuilderResolverMixin, hdmf.backends.hdf5.h5_utils.AbstractH5RegionDataset

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

Parameters:	dataset (`Dataset` or `Array`) – the HDF5 file lazily evaluate io (HDF5IO) – the IO object that was used to read the underlying dataset

classmethod get_inverse_class()¶

Return the class the represents the ReferenceResolver that resolves refernces 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.backends.hdf5.h5_utils.H5SpecWriter(group)¶

Bases: hdmf.spec.write.SpecWriter

Parameters:	group (`Group`) – the HDF5 file to write specs to

static stringify(spec)¶: Converts a spec into a JSON string to write to a dataset

write_spec(spec, path)¶

write_namespace(namespace, path)¶

class hdmf.backends.hdf5.h5_utils.H5SpecReader(group)¶

Bases: hdmf.spec.namespace.SpecReader

Class that reads cached JSON-formatted namespace and spec data from an HDF5 group.

Parameters:	group (`Group`) – the HDF5 group to read specs from

read_spec(spec_path)¶

read_namespace(ns_path)¶

class hdmf.backends.hdf5.h5_utils.H5RegionSlicer(dataset, region)¶

Bases: hdmf.region.RegionSlicer

Parameters:	dataset (`Dataset` or `H5Dataset`) – the HDF5 dataset to slice region (`RegionReference`) – the region reference to use to slice

__getitem__(idx)¶: Must be implemented by subclasses

class hdmf.backends.hdf5.h5_utils.H5DataIO(data=None, maxshape=None, chunks=None, compression=None, compression_opts=None, fillvalue=None, shuffle=None, fletcher32=None, link_data=False, allow_plugin_filters=False)¶

Bases: hdmf.data_utils.DataIO

Wrap data arrays for write via HDF5IO to customize I/O behavior, such as compression and chunking for data arrays.

Parameters:

data (ndarray or list or tuple or Dataset or Iterable) – the data to be written. NOTE: If an h5py.Dataset is used, all other settings but link_data will be ignored as the dataset will either be linked to or copied as is in H5DataIO.
maxshape (tuple) – Dataset will be resizable up to this shape (Tuple). Automatically enables chunking.Use None for the axes you want to be unlimited.
chunks (bool or tuple) – Chunk shape or True to enable auto-chunking
compression (str or bool or int) – Compression strategy. If a bool is given, then gzip compression will be used by default.http://docs.h5py.org/en/latest/high/dataset.html#dataset-compression
compression_opts (int or tuple) – Parameter for compression filter
fillvalue (None) – Value to be returned when reading uninitialized parts of the dataset
shuffle (bool) – Enable shuffle I/O filter. http://docs.h5py.org/en/latest/high/dataset.html#dataset-shuffle
fletcher32 (bool) – Enable fletcher32 checksum. http://docs.h5py.org/en/latest/high/dataset.html#dataset-fletcher32
link_data (bool) – If data is an h5py.Dataset should it be linked to or copied. NOTE: This parameter is only allowed if data is an h5py.Dataset
allow_plugin_filters (bool) – Enable passing dynamically loaded filters as compression parameter

get_io_params()¶: Returns a dict with the I/O parameters specifiedin in this DataIO.

static filter_available(filter, allow_plugin_filters)¶

Check if a given I/O filter is available

Parameters:	filter (String, int) – String with the name of the filter, e.g., gzip, szip etc. int with the registered filter ID, e.g. 307 allow_plugin_filters – bool indicating whether the given filter can be dynamically loaded
Returns:	bool indicating wether the given filter is available

link_data¶

io_settings¶

valid¶: bool indicating if the data object is valid