tiledbsoma.DenseNDArray

class tiledbsoma.DenseNDArray(handle: _WrapperType_co | DataFrameWrapper | DenseNDArrayWrapper | SparseNDArrayWrapper, *, _dont_call_this_use_create_or_open_instead: str = 'unset')

DenseNDArray is a dense, N-dimensional array, with offset (zero-based) integer indexing on each dimension. DenseNDArray has a user-defined schema, which includes:

• The element type, expressed as an Arrow type indicating the type of data contained within the array.

• The shape of the array, i.e., the number of dimensions and the length of each dimension.

All dimensions must have a positive, non-zero length, and there must be 1 or more dimensions.

Where explicitly referenced in the API, the dimensions are named soma_dim_N, where N is the dimension number (e.g., soma_dim_0), and elements are named soma_data.

Lifecycle

Maturing.

Examples

>>> import tiledbsoma
>>> import pyarrow as pa
>>> import numpy as np
>>> with tiledbsoma.DenseNDArray.create(
...     "./test_dense_ndarray", type=pa.int32(), shape=(2, 3, 4)
... ) as arr:
...     data = pa.Tensor.from_numpy(
...         np.random.default_rng().integers(0, 10, 24).reshape(2, 3, 4)
...     )
...     arr.write((slice(None),), data)
... with tiledbsoma.open("./test_dense_ndarray") as arr:
...     print(arr.schema)
...     print("---")
...     print(arr.read())
...
soma_dim_0: int64
soma_dim_1: int64
soma_dim_2: int64
soma_data: int32
---
<pyarrow.Tensor>
type: int32
shape: (2, 3, 4)
strides: (48, 16, 4)

__init__(handle: _WrapperType_co | DataFrameWrapper | DenseNDArrayWrapper | SparseNDArrayWrapper, *, _dont_call_this_use_create_or_open_instead: str = 'unset')

Internal-only common initializer steps.

This function is internal; users should open TileDB SOMA objects using the create() and open() factory class methods.

Methods

__init__(handle, *[, ...])	Internal-only common initializer steps.
exists(uri[, context, tiledb_timestamp])	Finds whether an object of this type exists at the given URI.
create(uri, *, type, shape[, ...])	Creates a SOMA NDArray at the given URI.
open(uri[, mode, tiledb_timestamp, context, ...])	Opens this specific type of SOMA object.
reopen(mode[, tiledb_timestamp])	Return a new copy of the SOMAObject with the given mode at the current Unix timestamp.
close()	Release any resources held while the object is open.
read([coords, result_order, partitions, ...])	Reads a user-defined dense slice of the array and return as an Arrow Tensor.
write(coords, values, *[, platform_config])	Writes a subarray, defined by coords and values.
verify_open_for_writing()	Raises an error if the object is not open for writing.
non_empty_domain()	Retrieves the non-empty domain for each dimension, namely the smallest and largest indices in each dimension for which the array/dataframe has data occupied.
resize(newshape[, check_only])	Increases the shape of the array as specfied.
config_options_from_schema()	Returns metadata about the array that is not encompassed within the Arrow Schema, in the form of a PlatformConfig (deprecated).

Attributes

uri	Accessor for the object's storage URI.
soma_type	A string describing the SOMA type of this object.
schema	Returns data schema, in the form of an Arrow Schema.
is_sparse	True if the array is sparse, False if it is dense.
ndim	The number of dimensions in this array.
shape	Returns capacity of each dimension, always a list of length ndim.
maxshape	Returns the maximum resizable capacity of each dimension, always a list of length ndim.
tiledbsoma_has_upgraded_shape	Returns true if the array has the upgraded resizeable shape feature from TileDB-SOMA 1.15: the array was created with this support, or it has had .tiledbsoma_upgrade_shape applied to it.
mode	The mode this object was opened in, either r or w.
closed	True if the object has been closed.
context	A value storing implementation-specific configuration information.
tiledb_timestamp	The time that this object was opened in UTC.
tiledb_timestamp_ms	The time this object was opened, as millis since the Unix epoch.
metadata	The metadata of this SOMA object.