tiledbsoma.SparseNDArray¶

SparseNDArray is a sparse, N-dimensional array, with offset (zero-based) integer indexing on each dimension.

SparseNDArray 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. Implicitly stored elements (i.e., those not explicitly stored in the array) are assumed to have a value of zero.

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
>>> import scipy.sparse
>>> with tiledbsoma.SparseNDArray.create(
...     "./test_sparse_ndarray", type=pa.float32(), shape=(1000, 100)
... ) as arr:
...     data = pa.SparseCOOTensor.from_scipy(
...         scipy.sparse.random(1000, 100, format="coo", dtype=np.float32)
...     )
...     arr.write(data)
... with tiledbsoma.SparseNDArray.open("./test_sparse_ndarray") as arr:
...     print(arr.schema)
...     print('---')
...     print(arr.read().coos().concat())
...
soma_dim_0: int64
soma_dim_1: int64
soma_data: float
---
<pyarrow.SparseCOOTensor>
type: float
shape: (1000, 100)

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, *, uri, context[, ...])	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 `SparseNDArray` 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, batch_size, ...])	Reads a user-defined slice of the `SparseNDArray`.
`write`(values, *[, platform_config])	Writes an Arrow object to the SparseNDArray.
`delete_cells`(coords, *[, platform_config])	Deletes cells at the specified coordinates in a `SparseNDArray`.
`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.
`tiledbsoma_upgrade_shape`(newshape[, check_only])	Allows the array to have a resizeable shape as described in the TileDB-SOMA 1.15 release notes.
`resize`(newshape[, check_only])	Increases the shape of the array as specfied.

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`
`ndim`	The number of dimensions in this array.
`nnz`	The number of stored values in the array, including explicitly stored zeros.
`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`, `w`, or `d`.
`closed`	True if the object has been closed.
`context`
`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`