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@normanb @jrbourbeau @jcrist @ihnorton
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from . import core
def _tiledb_to_chunks(tiledb_array):
schema = tiledb_array.schema
return list(schema.domain.dim(i).tile for i in range(schema.ndim))
def from_tiledb(uri, attribute=None, chunks=None, storage_options=None, **kwargs):
"""Load array from the TileDB storage format
See https://docs.tiledb.io for more information about TileDB.
Parameters
----------
uri: TileDB array or str
Location to save the data
attribute: str or None
Attribute selection (single-attribute view on multi-attribute array)
Returns
-------
A Dask Array
Examples
--------
>>> # create a tiledb array
>>> import tiledb, numpy as np, tempfile # doctest: +SKIP
>>> uri = tempfile.NamedTemporaryFile().name # doctest: +SKIP
>>> tiledb.from_numpy(uri, np.arange(0,9).reshape(3,3)) # doctest: +SKIP
<tiledb.libtiledb.DenseArray object at 0x...>
>>> # read back the array
>>> import dask.array as da # doctest: +SKIP
>>> tdb_ar = da.from_tiledb(uri) # doctest: +SKIP
>>> tdb_ar.shape # doctest: +SKIP
(3, 3)
>>> tdb_ar.mean().compute() # doctest: +SKIP
4.0
"""
import tiledb
tiledb_config = storage_options or dict()
key = tiledb_config.pop("key", None)
if isinstance(uri, tiledb.Array):
tdb = uri
else:
tdb = tiledb.open(uri, attr=attribute, config=tiledb_config, key=key)
if tdb.schema.sparse:
raise ValueError("Sparse TileDB arrays are not supported")
if not attribute:
if tdb.schema.nattr > 1:
raise TypeError(
"keyword 'attribute' must be provided"
"when loading a multi-attribute TileDB array"
)
else:
attribute = tdb.schema.attr(0).name
if tdb.iswritable:
raise ValueError("TileDB array must be open for reading")
chunks = chunks or _tiledb_to_chunks(tdb)
assert len(chunks) == tdb.schema.ndim
return core.from_array(tdb, chunks, name="tiledb-%s" % uri)
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.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)
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