Skip to content

groups.rst

Latest commit

 

History

History
145 lines (117 loc) · 4.42 KB

groups.rst

File metadata and controls

145 lines (117 loc) · 4.42 KB
.. only:: doctest

   >>> import shutil
   >>> shutil.rmtree('data', ignore_errors=True)

Working with groups

Zarr supports hierarchical organization of arrays via groups. As with arrays, groups can be stored in memory, on disk, or via other storage systems that support a similar interface.

To create a group, use the :func:`zarr.group` function:

>>> import zarr
>>> store = zarr.storage.MemoryStore()
>>> root = zarr.create_group(store=store)
>>> root
<Group memory://...>

Groups have a similar API to the Group class from h5py. For example, groups can contain other groups:

>>> foo = root.create_group('foo')
>>> bar = foo.create_group('bar')

Groups can also contain arrays, e.g.:

>>> z1 = bar.create_array(name='baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32')
>>> z1
<Array memory://.../foo/bar/baz shape=(10000, 10000) dtype=int32>

Members of a group can be accessed via the suffix notation, e.g.:

>>> root['foo']
<Group memory://.../foo>

The '/' character can be used to access multiple levels of the hierarchy in one call, e.g.:

>>> root['foo/bar']
<Group memory://.../foo/bar>
>>> root['foo/bar/baz']
<Array memory://.../foo/bar/baz shape=(10000, 10000) dtype=int32>

The :func:`zarr.Group.tree` method can be used to print a tree representation of the hierarchy, e.g.:

>>> root.tree()
/
└── foo
    └── bar
        └── baz (10000, 10000) int32
<BLANKLINE>

The :func:`zarr.open_group` function provides a convenient way to create or re-open a group stored in a directory on the file-system, with sub-groups stored in sub-directories, e.g.:

>>> root = zarr.open_group('data/group.zarr', mode='w')
>>> root
<Group file://data/group.zarr>
>>>
>>> z = root.create_array(name='foo/bar/baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32')
>>> z
<Array file://data/group.zarr/foo/bar/baz shape=(10000, 10000) dtype=int32>

For more information on groups see the :class:`zarr.Group` API docs.

Array and group diagnostics

Diagnostic information about arrays and groups is available via the info property. E.g.:

>>> store = zarr.storage.MemoryStore()
>>> root = zarr.group(store=store)
>>> foo = root.create_group('foo')
>>> bar = foo.create_array(name='bar', shape=1000000, chunks=100000, dtype='int64')
>>> bar[:] = 42
>>> baz = foo.create_array(name='baz', shape=(1000, 1000), chunks=(100, 100), dtype='float32')
>>> baz[:] = 4.2
>>> root.info
Name        :
Type        : Group
Zarr format : 3
Read-only   : False
Store type  : MemoryStore
>>> foo.info
Name        : foo
Type        : Group
Zarr format : 3
Read-only   : False
Store type  : MemoryStore
>>> bar.info_complete()
Type               : Array
Zarr format        : 3
Data type          : DataType.int64
Shape              : (1000000,)
Chunk shape        : (100000,)
Order              : C
Read-only          : False
Store type         : MemoryStore
Filters            : ()
Serializer         : BytesCodec(endian=<Endian.little: 'little'>)
Compressors        : (ZstdCodec(level=0, checksum=False),)
No. bytes          : 8000000 (7.6M)
No. bytes stored   : 1432
Storage ratio      : 5586.6
Chunks Initialized : 0
>>> baz.info
Type               : Array
Zarr format        : 3
Data type          : DataType.float32
Shape              : (1000, 1000)
Chunk shape        : (100, 100)
Order              : C
Read-only          : False
Store type         : MemoryStore
Filters            : ()
Serializer         : BytesCodec(endian=<Endian.little: 'little'>)
Compressors        : (ZstdCodec(level=0, checksum=False),)
No. bytes          : 4000000 (3.8M)

Groups also have the :func:`zarr.Group.tree` method, e.g.:

>>> root.tree()
/
└── foo
    ├── bar (1000000,) int64
    └── baz (1000, 1000) float32
<BLANKLINE>

Note

:func:`zarr.Group.tree` requires the optional rich dependency. It can be installed with the [tree] extra.