. currentmodule:: silx.io

commonh5: Helpers for writing h5py-like API

This module contains generic objects, emulating h5py groups, datasets and files. They are used in spech5 and fabioh5.

Classes

class Node(name, parent=None, attrs=None)[source]

This is the base class for all spech5 and fabioh5 classes. It represents a tree node, and knows its parent node (parent). The API mimics a h5py node, with following attributes: file, attrs, name, and basename.

property h5_class

Returns the HDF5 class which is mimicked by this class.

Return type

H5Type

property h5py_class

Returns the h5py classes which is mimicked by this class. It can be one of h5py.File, h5py.Group or h5py.Dataset

This should not be used anymore. Prefer using h5_class

Return type

Class

property parent

Returns the parent of the node.

Return type

Node

property file

Returns the file node of this node.

Return type

Node

property attrs

Returns HDF5 attributes of this node.

Return type

dict

property name

Returns the HDF5 name of this node.

property basename

Returns the HDF5 basename of this node.

class File(name=None, mode=None, attrs=None)[source]

Bases: Group

This class is the special Group that is the root node of the tree structure. It mimics h5py.File.

property h5_class

Returns the h5py.File class

close()[source]

Close the object, and free up associated resources.

class Group(name, parent=None, attrs=None)[source]

Bases: Node

This class mimics a h5py.Group.

get(name, default=None, getclass=False, getlink=False)[source]

Retrieve an item or other information.

If getlink only is true, the returned value is always h5py.HardLink, because this implementation do not use links. Like the original implementation.

Parameters

  • name (str) – name of the item

  • default (object) – default value returned if the name is not found

  • getclass (bool) – if true, the returned object is the class of the object found

  • getlink (bool) – if true, links object are returned instead of the target

Returns

An object, else None

Return type

object

__getitem__(name)[source]

Return a child from his name.

Parameters

name (str) – name of a member or a path throug members using ‘/’ separator. A ‘/’ as a prefix access to the root item of the tree.

Return type

Node

__contains__(name)[source]

Returns true if name is an existing child of this group.

Return type

bool

__len__()[source]

Returns the number of children contained in this group.

Return type

int

__iter__()[source]

Iterate over member names

keys()[source]

Returns an iterator over the children’s names in a group.

values()[source]

Returns an iterator over the children nodes (groups and datasets) in a group.

New in version 0.6.

items()[source]

Returns items iterator containing name-node mapping.

Return type

iterator

visit(func, visit_links=False)[source]

Recursively visit all names in this group and subgroups. See the documentation for h5py.Group.visit for more help.

Parameters

func (callable) – Callable (function, method or callable object)

visititems(func, visit_links=False)[source]

Recursively visit names and objects in this group. See the documentation for h5py.Group.visititems for more help.

Parameters

  • func (callable) – Callable (function, method or callable object)

  • visit_links (bool) – If False, ignore links. If True, call func(name) for links and recurse into target groups.

property name

Returns the HDF5 name of this node.

property basename

Returns the HDF5 basename of this node.

property file

Returns the file node of this node.

Return type

Node

property attrs

Returns HDF5 attributes of this node.

Return type

dict

property h5py_class

Returns the h5py classes which is mimicked by this class. It can be one of h5py.File, h5py.Group or h5py.Dataset

This should not be used anymore. Prefer using h5_class

Return type

Class

property parent

Returns the parent of the node.

Return type

Node

class Dataset(name, data, parent=None, attrs=None)[source]

Bases: Node

This class handles a numpy data object, as a mimicry of a h5py.Dataset.

property h5_class

Returns the HDF5 class which is mimicked by this class.

Return type

H5Type

property dtype

Returns the numpy datatype exposed by this dataset.

Return type

numpy.dtype

property shape

Returns the shape of the data exposed by this dataset.

Return type

tuple

property size

Returns the size of the data exposed by this dataset.

Return type

int

property value

Returns the data exposed by this dataset.

Deprecated by h5py. It is prefered to use indexing [()].

Return type

numpy.ndarray

property compression

Returns compression as provided by h5py.Dataset.

There is no compression.

property compression_opts

Returns compression options as provided by h5py.Dataset.

There is no compression.

property chunks

Returns chunks as provided by h5py.Dataset.

There is no chunks.

property is_virtual

Checks virtual data as provided by h5py.Dataset

virtual_sources()[source]

Returns virtual dataset sources as provided by h5py.Dataset.

Return type

list

property external

Returns external sources as provided by h5py.Dataset.

Return type

list or None