SOMA Dense Nd-Array

SOMADenseNDArray is a dense, N-dimensional array of a primitive type, with offset (zero-based) int64 integer indexing on each dimension with domain [0, maxInt64). The SOMADenseNDArray has a user-defined schema, which includes:

• type: a primitive type, expressed as an Arrow type (e.g., int64, float32, etc), indicating the type of data contained within the array.

• shape: the shape of the array, i.e., number and length of each dimension. This is a soft limit which can be increased using $resize() up to the maxshape.

• maxshape: the hard limit up to which shape may be increased using $resize().

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

The default “fill” value for SOMADenseNDArray is the zero or null value of the array type (e.g., arrow::float32() defaults to 0.0).

Super classes

tiledbsoma::SOMAObject -> tiledbsoma::SOMAArrayBase -> tiledbsoma::SOMANDArrayBase -> SOMADenseNDArray

Methods

Public methods

• SOMADenseNDArray$read_arrow_table()

• SOMADenseNDArray$read_dense_matrix()

• SOMADenseNDArray$write()

• SOMADenseNDArray$clone()

Inherited methods

• tiledbsoma::SOMAObject$class()
• tiledbsoma::SOMAObject$exists()
• tiledbsoma::SOMAObject$get_metadata()
• tiledbsoma::SOMAObject$initialize()
• tiledbsoma::SOMAObject$is_open()
• tiledbsoma::SOMAObject$mode()
• tiledbsoma::SOMAObject$reopen()
• tiledbsoma::SOMAObject$set_metadata()
• tiledbsoma::SOMAArrayBase$allows_duplicates()
• tiledbsoma::SOMAArrayBase$attributes()
• tiledbsoma::SOMAArrayBase$attrnames()
• tiledbsoma::SOMAArrayBase$close()
• tiledbsoma::SOMAArrayBase$colnames()
• tiledbsoma::SOMAArrayBase$dimensions()
• tiledbsoma::SOMAArrayBase$dimnames()
• tiledbsoma::SOMAArrayBase$index_column_names()
• tiledbsoma::SOMAArrayBase$is_sparse()
• tiledbsoma::SOMAArrayBase$maxshape()
• tiledbsoma::SOMAArrayBase$ndim()
• tiledbsoma::SOMAArrayBase$non_empty_domain()
• tiledbsoma::SOMAArrayBase$open()
• tiledbsoma::SOMAArrayBase$print()
• tiledbsoma::SOMAArrayBase$schema()
• tiledbsoma::SOMAArrayBase$shape()
• tiledbsoma::SOMANDArrayBase$create()
• tiledbsoma::SOMANDArrayBase$resize()
• tiledbsoma::SOMANDArrayBase$set_data_type()
• tiledbsoma::SOMANDArrayBase$tiledbsoma_has_upgraded_shape()
• tiledbsoma::SOMANDArrayBase$tiledbsoma_upgrade_shape()

---

Method read_arrow_table()

Read as an Arrow table (lifecycle: maturing).

Usage

SOMADenseNDArray$read_arrow_table(
  coords = NULL,
  result_order = "auto",
  log_level = "auto"
)

Arguments

coords

Optional list of integer vectors, one for each dimension, with a length equal to the number of values to read. If NULL, all values are read. List elements can be named when specifying a subset of dimensions.

result_order

Optional order of read results. This can be one of either "ROW_MAJOR, "COL_MAJOR", or "auto"` (default).

log_level

Optional logging level with default value of “warn”.

Returns

An Arrow table.

---

Method read_dense_matrix()

Read as a dense matrix (lifecycle: maturing).

Usage

SOMADenseNDArray$read_dense_matrix(
  coords = NULL,
  result_order = "ROW_MAJOR",
  log_level = "warn"
)

Arguments

coords

Optional list of integer vectors, one for each dimension, with a length equal to the number of values to read. If NULL, all values are read. List elements can be named when specifying a subset of dimensions.

result_order

Optional order of read results. This can be one of either "ROW_MAJOR, "COL_MAJOR", or "auto"` (default).

log_level

Optional logging level with default value of “warn”.

Returns

A matrix.

---

Method write()

Write matrix data to the array (lifecycle: maturing).

Note: The $write() method is currently limited to writing from two-dimensional matrices (lifecycle: maturing).

Usage

SOMADenseNDArray$write(values, coords = NULL)

Arguments

values

A matrix. Character dimension names are ignored because SOMANDArrays use integer indexing.

coords

A list of integer vectors, one for each dimension, with a length equal to the number of values to write. If NULL, the default, the values are taken from the row and column names of values.

Returns

Invisibly returns self.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SOMADenseNDArray$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

uri <- withr::local_tempfile(pattern = "soma-dense-array")
mat <- matrix(stats::rnorm(100L ^ 2L), nrow = 100L, ncol = 100L)
mat[1:3, 1:5]
#>            [,1]       [,2]        [,3]       [,4]        [,5]
#> [1,]  1.1796642  0.5143278  0.90426912  1.3364468 -1.54103029
#> [2,] -0.2569212 -1.7513751  0.07964921 -0.8603562 -0.31031012
#> [3,] -1.0563361  0.8935975 -1.25882722  0.6665378 -0.02010818

(arr <- SOMADenseNDArrayCreate(uri, arrow::float64(), shape = dim(mat)))
#> <SOMADenseNDArray>
#>   uri: /tmp/RtmpgbdEWv/soma-dense-array276a45f244e6
#>   dimensions: soma_dim_0, soma_dim_1 
#>   attributes: soma_data 
arr$write(mat)
arr$close()

(arr <- SOMADenseNDArrayOpen(uri))
#> <SOMADenseNDArray>
#>   uri: /tmp/RtmpgbdEWv/soma-dense-array276a45f244e6
#>   dimensions: soma_dim_0, soma_dim_1 
#>   attributes: soma_data 
arr$read_arrow_table()
#> Table
#> 10000 rows x 1 columns
#> $soma_data <double not null>