Groups (zarr.hierarchy
)¶
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zarr.hierarchy.
group
(store=None, overwrite=False, chunk_store=None, cache_attrs=True, synchronizer=None, path=None)¶ Create a group.
Parameters: store : MutableMapping or string, optional
Store or path to directory in file system.
overwrite : bool, optional
If True, delete any pre-existing data in store at path before creating the group.
chunk_store : MutableMapping, optional
Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.
cache_attrs : bool, optional
If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
path : string, optional
Group path within store.
Returns: g : zarr.hierarchy.Group
Examples
Create a group in memory:
>>> import zarr >>> g = zarr.group() >>> g <zarr.hierarchy.Group '/'>
Create a group with a different store:
>>> store = zarr.DirectoryStore('data/example.zarr') >>> g = zarr.group(store=store, overwrite=True) >>> g <zarr.hierarchy.Group '/'>
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zarr.hierarchy.
open_group
(store, mode='a', cache_attrs=True, synchronizer=None, path=None)¶ Open a group using file-mode-like semantics.
Parameters: store : MutableMapping or string
Store or path to directory in file system or name of zip file.
mode : {‘r’, ‘r+’, ‘a’, ‘w’, ‘w-‘}, optional
Persistence mode: ‘r’ means read only (must exist); ‘r+’ means read/write (must exist); ‘a’ means read/write (create if doesn’t exist); ‘w’ means create (overwrite if exists); ‘w-‘ means create (fail if exists).
cache_attrs : bool, optional
If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
path : string, optional
Group path within store.
Returns: g : zarr.hierarchy.Group
Examples
>>> import zarr >>> root = zarr.open_group('data/example.zarr', mode='w') >>> foo = root.create_group('foo') >>> bar = root.create_group('bar') >>> root <zarr.hierarchy.Group '/'> >>> root2 = zarr.open_group('data/example.zarr', mode='a') >>> root2 <zarr.hierarchy.Group '/'> >>> root == root2 True
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class
zarr.hierarchy.
Group
(store, path=None, read_only=False, chunk_store=None, cache_attrs=True, synchronizer=None)¶ Instantiate a group from an initialized store.
Parameters: store : MutableMapping
Group store, already initialized.
path : string, optional
Group path.
read_only : bool, optional
True if group should be protected against modification.
chunk_store : MutableMapping, optional
Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.
cache_attrs : bool, optional
If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
Attributes
store
A MutableMapping providing the underlying storage for the group. path
Storage path. name
Group name following h5py convention. read_only
A boolean, True if modification operations are not permitted. chunk_store
A MutableMapping providing the underlying storage for array chunks. synchronizer
Object used to synchronize write access to groups and arrays. attrs
A MutableMapping containing user-defined attributes. info
Return diagnostic information about the group. Methods
__len__
()Number of members. __iter__
()Return an iterator over group member names. __contains__
(item)Test for group membership. __getitem__
(item)Obtain a group member. group_keys
()Return an iterator over member names for groups only. groups
()Return an iterator over (name, value) pairs for groups only. array_keys
()Return an iterator over member names for arrays only. arrays
()Return an iterator over (name, value) pairs for arrays only. visit
(func)Run func
on each object’s path.visitkeys
(func)An alias for visit()
.visitvalues
(func)Run func
on each object.visititems
(func)Run func
on each object’s path and the object itself.tree
([expand, level])Provide a print
-able display of the hierarchy.create_group
(name[, overwrite])Create a sub-group. require_group
(name[, overwrite])Obtain a sub-group, creating one if it doesn’t exist. create_groups
(*names, **kwargs)Convenience method to create multiple groups in a single call. require_groups
(*names)Convenience method to require multiple groups in a single call. create_dataset
(name, **kwargs)Create an array. require_dataset
(name, shape[, dtype, exact])Obtain an array, creating if it doesn’t exist. create
(name, **kwargs)Create an array. empty
(name, **kwargs)Create an array. zeros
(name, **kwargs)Create an array. ones
(name, **kwargs)Create an array. full
(name, fill_value, **kwargs)Create an array. array
(name, data, **kwargs)Create an array. empty_like
(name, data, **kwargs)Create an array. zeros_like
(name, data, **kwargs)Create an array. ones_like
(name, data, **kwargs)Create an array. full_like
(name, data, **kwargs)Create an array. info
Return diagnostic information about the group. move
(source, dest)Move contents from one path to another relative to the Group. -
__len__
()¶ Number of members.
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__iter__
()¶ Return an iterator over group member names.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> d1 = g1.create_dataset('baz', shape=100, chunks=10) >>> d2 = g1.create_dataset('quux', shape=200, chunks=20) >>> for name in g1: ... print(name) bar baz foo quux
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__contains__
(item)¶ Test for group membership.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> d1 = g1.create_dataset('bar', shape=100, chunks=10) >>> 'foo' in g1 True >>> 'bar' in g1 True >>> 'baz' in g1 False
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__getitem__
(item)¶ Obtain a group member.
Parameters: item : string
Member name or path.
Examples
>>> import zarr >>> g1 = zarr.group() >>> d1 = g1.create_dataset('foo/bar/baz', shape=100, chunks=10) >>> g1['foo'] <zarr.hierarchy.Group '/foo'> >>> g1['foo/bar'] <zarr.hierarchy.Group '/foo/bar'> >>> g1['foo/bar/baz'] <zarr.core.Array '/foo/bar/baz' (100,) float64>
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group_keys
()¶ Return an iterator over member names for groups only.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> d1 = g1.create_dataset('baz', shape=100, chunks=10) >>> d2 = g1.create_dataset('quux', shape=200, chunks=20) >>> sorted(g1.group_keys()) ['bar', 'foo']
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groups
()¶ Return an iterator over (name, value) pairs for groups only.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> d1 = g1.create_dataset('baz', shape=100, chunks=10) >>> d2 = g1.create_dataset('quux', shape=200, chunks=20) >>> for n, v in g1.groups(): ... print(n, type(v)) bar <class 'zarr.hierarchy.Group'> foo <class 'zarr.hierarchy.Group'>
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array_keys
()¶ Return an iterator over member names for arrays only.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> d1 = g1.create_dataset('baz', shape=100, chunks=10) >>> d2 = g1.create_dataset('quux', shape=200, chunks=20) >>> sorted(g1.array_keys()) ['baz', 'quux']
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arrays
()¶ Return an iterator over (name, value) pairs for arrays only.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> d1 = g1.create_dataset('baz', shape=100, chunks=10) >>> d2 = g1.create_dataset('quux', shape=200, chunks=20) >>> for n, v in g1.arrays(): ... print(n, type(v)) baz <class 'zarr.core.Array'> quux <class 'zarr.core.Array'>
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visit
(func)¶ Run
func
on each object’s path.- Note: If
func
returnsNone
(or doesn’t return), - iteration continues. However, if
func
returns anything else, it ceases and returns that value.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> g4 = g3.create_group('baz') >>> g5 = g3.create_group('quux') >>> def print_visitor(name): ... print(name) >>> g1.visit(print_visitor) bar bar/baz bar/quux foo >>> g3.visit(print_visitor) baz quux
- Note: If
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visitvalues
(func)¶ Run
func
on each object.- Note: If
func
returnsNone
(or doesn’t return), - iteration continues. However, if
func
returns anything else, it ceases and returns that value.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> g4 = g3.create_group('baz') >>> g5 = g3.create_group('quux') >>> def print_visitor(obj): ... print(obj) >>> g1.visitvalues(print_visitor) <zarr.hierarchy.Group '/bar'> <zarr.hierarchy.Group '/bar/baz'> <zarr.hierarchy.Group '/bar/quux'> <zarr.hierarchy.Group '/foo'> >>> g3.visitvalues(print_visitor) <zarr.hierarchy.Group '/bar/baz'> <zarr.hierarchy.Group '/bar/quux'>
- Note: If
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visititems
(func)¶ Run
func
on each object’s path and the object itself.- Note: If
func
returnsNone
(or doesn’t return), - iteration continues. However, if
func
returns anything else, it ceases and returns that value.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> g4 = g3.create_group('baz') >>> g5 = g3.create_group('quux') >>> def print_visitor(name, obj): ... print((name, obj)) >>> g1.visititems(print_visitor) ('bar', <zarr.hierarchy.Group '/bar'>) ('bar/baz', <zarr.hierarchy.Group '/bar/baz'>) ('bar/quux', <zarr.hierarchy.Group '/bar/quux'>) ('foo', <zarr.hierarchy.Group '/foo'>) >>> g3.visititems(print_visitor) ('baz', <zarr.hierarchy.Group '/bar/baz'>) ('quux', <zarr.hierarchy.Group '/bar/quux'>)
- Note: If
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tree
(expand=False, level=None)¶ Provide a
print
-able display of the hierarchy.Parameters: expand : bool, optional
Only relevant for HTML representation. If True, tree will be fully expanded.
level : int, optional
Maximum depth to descend into hierarchy.
Notes
Please note that this is an experimental feature. The behaviour of this function is still evolving and the default output and/or parameters may change in future versions.
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> g4 = g3.create_group('baz') >>> g5 = g3.create_group('quux') >>> d1 = g5.create_dataset('baz', shape=100, chunks=10) >>> g1.tree() / ├── bar │ ├── baz │ └── quux │ └── baz (100,) float64 └── foo >>> g1.tree(level=2) / ├── bar │ ├── baz │ └── quux └── foo >>> g3.tree() bar ├── baz └── quux └── baz (100,) float64
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create_group
(name, overwrite=False)¶ Create a sub-group.
Parameters: name : string
Group name.
overwrite : bool, optional
If True, overwrite any existing array with the given name.
Returns: g : zarr.hierarchy.Group
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') >>> g4 = g1.create_group('baz/quux')
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require_group
(name, overwrite=False)¶ Obtain a sub-group, creating one if it doesn’t exist.
Parameters: name : string
Group name.
overwrite : bool, optional
Overwrite any existing array with given name if present.
Returns: g : zarr.hierarchy.Group
Examples
>>> import zarr >>> g1 = zarr.group() >>> g2 = g1.require_group('foo') >>> g3 = g1.require_group('foo') >>> g2 == g3 True
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create_groups
(*names, **kwargs)¶ Convenience method to create multiple groups in a single call.
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require_groups
(*names)¶ Convenience method to require multiple groups in a single call.
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create_dataset
(name, **kwargs)¶ Create an array.
Parameters: name : string
Array name.
data : array_like, optional
Initial data.
shape : int or tuple of ints
Array shape.
chunks : int or tuple of ints, optional
Chunk shape. If not provided, will be guessed from shape and dtype.
dtype : string or dtype, optional
NumPy dtype.
compressor : Codec, optional
Primary compressor.
fill_value : object
Default value to use for uninitialized portions of the array.
order : {‘C’, ‘F’}, optional
Memory layout to be used within each chunk.
synchronizer : zarr.sync.ArraySynchronizer, optional
Array synchronizer.
filters : sequence of Codecs, optional
Sequence of filters to use to encode chunk data prior to compression.
overwrite : bool, optional
If True, replace any existing array or group with the given name.
cache_metadata : bool, optional
If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded prior to all data access and modification operations (may incur overhead depending on storage and data access pattern).
Returns: a : zarr.core.Array
Examples
>>> import zarr >>> g1 = zarr.group() >>> d1 = g1.create_dataset('foo', shape=(10000, 10000), ... chunks=(1000, 1000)) >>> d1 <zarr.core.Array '/foo' (10000, 10000) float64> >>> d2 = g1.create_dataset('bar/baz/qux', shape=(100, 100, 100), ... chunks=(100, 10, 10)) >>> d2 <zarr.core.Array '/bar/baz/qux' (100, 100, 100) float64>
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require_dataset
(name, shape, dtype=None, exact=False, **kwargs)¶ Obtain an array, creating if it doesn’t exist. Other kwargs are as per
zarr.hierarchy.Group.create_dataset()
.Parameters: name : string
Array name.
shape : int or tuple of ints
Array shape.
dtype : string or dtype, optional
NumPy dtype.
exact : bool, optional
If True, require dtype to match exactly. If false, require dtype can be cast from array dtype.
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create
(name, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.create()
.
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empty
(name, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.empty()
.
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zeros
(name, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.zeros()
.
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ones
(name, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.ones()
.
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full
(name, fill_value, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.full()
.
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array
(name, data, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.array()
.
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empty_like
(name, data, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.empty_like()
.
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zeros_like
(name, data, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.zeros_like()
.
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ones_like
(name, data, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.ones_like()
.
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full_like
(name, data, **kwargs)¶ Create an array. Keyword arguments as per
zarr.creation.full_like()
.
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move
(source, dest)¶ Move contents from one path to another relative to the Group.
Parameters: source : string
Name or path to a Zarr object to move.
dest : string
New name or path of the Zarr object.
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