def to_tiledb(
darray,
uri,
compute=True,
return_stored=False,
storage_options=None,
key=None,
**kwargs,
):
"""Save array to the TileDB storage format
Save 'array' using the TileDB storage manager, to any TileDB-supported URI,
including local disk, S3, or HDFS.
See https://docs.tiledb.io for more information about TileDB.
Parameters
----------
darray: dask.array
A dask array to write.
uri:
Any supported TileDB storage location.
storage_options: dict
Dict containing any configuration options for the TileDB backend.
see https://docs.tiledb.io/en/stable/tutorials/config.html
compute, return_stored: see ``store()``
key: str or None
Encryption key
Returns
-------
None
Unless ``return_stored`` is set to ``True`` (``False`` by default)
Notes
-----
TileDB only supports regularly-chunked arrays.
TileDB `tile extents`_ correspond to form 2 of the dask
`chunk specification`_, and the conversion is
done automatically for supported arrays.
Examples
--------
>>> import dask.array as da, tempfile
>>> uri = tempfile.NamedTemporaryFile().name
>>> data = da.random.random(5,5)
>>> da.to_tiledb(data, uri)
>>> import tiledb
>>> tdb_ar = tiledb.open(uri)
>>> all(tdb_ar == data)
True
.. _chunk specification: https://docs.tiledb.io/en/stable/tutorials/tiling-dense.html
.. _tile extents: http://docs.dask.org/en/latest/array-chunks.html
"""
import tiledb
tiledb_config = storage_options or dict()
# encryption key, if any
key = key or tiledb_config.pop("key", None)
if not core._check_regular_chunks(darray.chunks):
raise ValueError(
"Attempt to save array to TileDB with irregular "
"chunking, please call `arr.rechunk(...)` first."
)
if isinstance(uri, str):
chunks = [c[0] for c in darray.chunks]
# create a suitable, empty, writable TileDB array
tdb = tiledb.empty_like(
uri, darray, tile=chunks, config=tiledb_config, key=key, **kwargs
)
elif isinstance(uri, tiledb.Array):
tdb = uri
# sanity checks
if not ((darray.dtype == tdb.dtype) and (darray.ndim == tdb.ndim)):
raise ValueError(
"Target TileDB array layout is not compatible with source array"
)
else:
raise ValueError(
"'uri' must be string pointing to supported TileDB store location "
"or an open, writable TileDB array."
)
if not (tdb.isopen and tdb.iswritable):
raise ValueError("Target TileDB array is not open and writable.")
return darray.store(tdb, lock=False, compute=compute, return_stored=return_stored)
def to_tiledb(darray, uri, compute=True, return_stored=False,
storage_options=None, **kwargs):
"""Save array to the TileDB storage format
Save 'array' using the TileDB storage manager, to any TileDB-supported URI,
including local disk, S3, or HDFS.
See https://docs.tiledb.io for more information about TileDB.
Parameters
----------
darray: dask.array
A dask array to write.
uri:
Any supported TileDB storage location.
storage_options: dict
Dict containing any configuration options for the TileDB backend.
see https://docs.tiledb.io/en/stable/tutorials/config.html
compute, return_stored: see ``store()``
Returns
-------
None
Unless ``return_stored`` is set to ``True`` (``False`` by default)
Notes
-----
TileDB only supports regularly-chunked arrays.
TileDB `tile extents`_ correspond to form 2 of the dask
`chunk specification`_, and the conversion is
done automatically for supported arrays.
Examples
--------
>>> import dask.array as da, tempfile # doctest: +SKIP
>>> uri = tempfile.NamedTemporaryFile().name # doctest: +SKIP
>>> data = da.random.random(5,5) # doctest: +SKIP
>>> da.to_tiledb(data, uri) # doctest: +SKIP
>>> import tiledb # doctest: +SKIP
>>> tdb_ar = tiledb.open(uri) # doctest: +SKIP
>>> all(tdb_ar == data) # doctest: +SKIP
True
.. _chunk specification: https://docs.tiledb.io/en/stable/tutorials/tiling-dense.html
.. _tile extents: http://docs.dask.org/en/latest/array-chunks.html
"""
import tiledb
tiledb_config = storage_options or dict()
# encryption key, if any
key = tiledb_config.pop('key', None)
if not core._check_regular_chunks(darray.chunks):
raise ValueError('Attempt to save array to TileDB with irregular '
'chunking, please call `arr.rechunk(...)` first.')
if isinstance(uri, str):
chunks = [c[0] for c in darray.chunks]
key = kwargs.pop('key', None)
# create a suitable, empty, writable TileDB array
tdb = tiledb.empty_like(uri, darray, tile=chunks, config=tiledb_config, key=key, **kwargs)
elif isinstance(uri, tiledb.Array):
tdb = uri
# sanity checks
if not ((darray.shape == tdb.shape) and
(darray.dtype == tdb.dtype) and
(darray.ndim == tdb.ndim)):
raise ValueError("Target TileDB array layout is not compatible with "
"source array")
else:
raise ValueError("'uri' must be string pointing to supported TileDB store location "
"or an open, writable TileDB array.")
if not (tdb.isopen and tdb.iswritable):
raise ValueError("Target TileDB array is not open and writable.")
return darray.store(tdb, lock=False, compute=compute,
return_stored=return_stored)