Add N5 Support

docs/release.rst

@@ -96,6 +96,10 @@ Enhancements
   the existing :class:`zarr.storage.DirectoryStore` class but nests chunk files
   for multidimensional arrays into sub-directories. :issue:`155`, :issue:`177`.
 
+* **New storage class for N5 containers**. The :class:`zarr.n5.N5Store` has been
+  added, which uses :class:`zarr.storage.NestedDirectoryStore` to support
+  reading and writing from and to N5 containers.
+
 * **New tree() method for printing hierarchies**. The ``Group`` class has a new
   :func:`zarr.hierarchy.Group.tree` method which enables a tree representation of
   a group hierarchy to be printed. Also provides an interactive tree

docs/tutorial.rst

@@ -729,6 +729,21 @@ group (requires `lmdb <http://lmdb.readthedocs.io/>`_ to be installed)::
     >>> z[:] = 42
     >>> store.close()
 
+For compatibility with the `N5<https://github.com/saalfeldlab/n5`_ data format,
+Zarr also provides an N5 backend. Similar to the zip storage class, an
+:class:`zarr.n5.N5Store` can be instantiated directly::
+
+    >>> store = zarr.N5Store('data/example.n5', mode='w')
+    >>> root = zarr.group(store=store)
+    >>> z = root.zeros('foo/bar', shape=(1000, 1000), chunks=(100, 100), dtype='i4')
+    >>> z[:] = 42
+    >>> store.close()
+
+For convenience, the N5 backend will automatically be chosen when the filename
+ends with `.n5`::
+
+    >>> root = zarr.open('data/example.n5', mode='w')
+
 Distributed/cloud storage
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 

zarr/__init__.py

@@ -14,5 +14,6 @@
 from zarr.convenience import (open, save, save_array, save_group, load, copy_store,
                               copy, copy_all, tree, consolidate_metadata,
                               open_consolidated)
+from zarr.n5 import N5Store
 from zarr.errors import CopyError, MetadataError, PermissionError
 from zarr.version import version as __version__

zarr/creation.py

@@ -9,6 +9,7 @@
 from zarr.core import Array
 from zarr.storage import (DirectoryStore, init_array, contains_array, contains_group,
                           default_compressor, normalize_storage_path, ZipStore)
+from zarr.n5 import N5Store
 from numcodecs.registry import codec_registry
 from zarr.errors import err_contains_array, err_contains_group, err_array_not_found
 
@@ -132,6 +133,8 @@ def normalize_store_arg(store, clobber=False, default=dict):
         if store.endswith('.zip'):
             mode = 'w' if clobber else 'a'
             return ZipStore(store, mode=mode)
+        elif store.endswith('.n5'):
+            return N5Store(store)
         else:
             return DirectoryStore(store)
     else: