def _array_iter(self, keys_only, method, recurse):
if self._version == 2:
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
assert not path.startswith("meta")
if contains_array(self._store, path):
_key = key.rstrip("/")
yield _key if keys_only else (_key, self[key])
elif recurse and contains_group(self._store, path):
group = self[key]
for i in getattr(group, method)(recurse=recurse):
yield i
else:
dir_name = meta_root + self._path
array_sfx = '.array' + self._metadata_key_suffix
for key in sorted(listdir(self._store, dir_name)):
if key.endswith(array_sfx):
key = key[:-len(array_sfx)]
path = self._key_prefix + key
assert not path.startswith("meta")
if key.endswith('.group' + self._metadata_key_suffix):
# skip group metadata keys
continue
if contains_array(self._store, path):
_key = key.rstrip("/")
yield _key if keys_only else (_key, self[key])
elif recurse and contains_group(self._store, path):
group = self[key]
for i in getattr(group, method)(recurse=recurse):
yield i
def group_keys(self):
"""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']
"""
if self._version == 2:
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_group(self._store, path):
yield key
else:
dir_name = meta_root + self._path
group_sfx = '.group' + self._metadata_key_suffix
for key in sorted(listdir(self._store, dir_name)):
if key.endswith(group_sfx):
key = key[:-len(group_sfx)]
path = self._key_prefix + key
if path.endswith(".array" + self._metadata_key_suffix):
# skip array keys
continue
if contains_group(self._store, path, explicit_only=False):
yield key
def arrays(self):
"""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'>
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key, Array(self._store,
path=path,
read_only=self._read_only,
chunk_store=self._chunk_store,
cache_attrs=self.attrs.cache,
synchronizer=self._synchronizer)
def groups(self):
"""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'>
"""
if self._version == 2:
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_group(self._store, path, explicit_only=False):
yield key, Group(self._store,
path=path,
read_only=self._read_only,
chunk_store=self._chunk_store,
cache_attrs=self.attrs.cache,
synchronizer=self._synchronizer,
zarr_version=self._version)
else:
dir_name = meta_root + self._path
group_sfx = '.group' + self._metadata_key_suffix
for key in sorted(listdir(self._store, dir_name)):
if key.endswith(group_sfx):
key = key[:-len(group_sfx)]
path = self._key_prefix + key
if path.endswith(".array" + self._metadata_key_suffix):
# skip array keys
continue
if contains_group(self._store, path, explicit_only=False):
yield key, Group(self._store,
path=path,
read_only=self._read_only,
chunk_store=self._chunk_store,
cache_attrs=self.attrs.cache,
synchronizer=self._synchronizer,
zarr_version=self._version)
def _array_iter(self, keys_only, method, recurse):
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key if keys_only else (key, self[key])
elif recurse and contains_group(self._store, path):
group = self[key]
for i in getattr(group, method)(recurse=recurse):
yield i
def __iter__(self):
"""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
"""
if getattr(self._store, '_store_version', 2) == 2:
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if (contains_array(self._store, path)
or contains_group(self._store, path)):
yield key
else:
# TODO: Should this iterate over data folders and/or metadata
# folders and/or metadata files
dir_path = meta_root + self._key_prefix
name_start = len(dir_path)
keys, prefixes = self._store.list_dir(dir_path)
# yield any groups or arrays
sfx = self._metadata_key_suffix
for key in keys:
len_suffix = len('.group') + len(sfx) # same for .array
if key.endswith(('.group' + sfx, '.array' + sfx)):
yield key[name_start:-len_suffix]
# also yield any implicit groups
for prefix in prefixes:
prefix = prefix.rstrip('/')
# only implicit if there is no .group.sfx file
if not prefix + '.group' + sfx in self._store:
yield prefix[name_start:]
def array_keys(self):
"""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']
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key
def array_keys(self):
"""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']
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key
def arrays(self):
"""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'>
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key, Array(self._store, path=path, read_only=self._read_only,
chunk_store=self._chunk_store,
synchronizer=self._synchronizer)
def __iter__(self):
"""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
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if (contains_array(self._store, path)
or contains_group(self._store, path)):
yield key
def __iter__(self):
"""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
"""
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if (contains_array(self._store, path) or
contains_group(self._store, path)):
yield key
def nchunks_initialized(self):
"""The number of chunks that have been initialized with some data."""
return sum(1 for k in listdir(self._chunk_store, self._path)
if k not in [array_meta_key, attrs_key])
def nchunks_initialized(self):
"""The number of chunks that have been initialized with some data."""
return sum(1 for k in listdir(self._chunk_store, self._path)
if k not in [array_meta_key, attrs_key])