Source code for dask.array.tiledb_io

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))


[docs]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 -------- >>> import tempfile, tiledb >>> import dask.array as da, numpy as np >>> uri = tempfile.NamedTemporaryFile().name >>> _ = tiledb.from_numpy(uri, np.arange(0,9).reshape(3,3)) # create a tiledb array >>> tdb_ar = da.from_tiledb(uri) # read back the array >>> tdb_ar.shape (3, 3) >>> tdb_ar.mean().compute() 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)
[docs]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)