Chunk management

This class implements the regular chunk grid for Zarr arrays. It manages reading from and writing to Zarr stores, using the codecs for data transformation.

Super classes

zarr_extension -> chunking -> chunk_grid_regular

Active bindings

codecs

The list of codecs used by the chunking scheme. These are set by the array when starting to use chunking for file I/O. Upon reading, the list of registered codecs.

Methods

Public methods

• chunk_grid_regular$new()

• chunk_grid_regular$print()

• chunk_grid_regular$metadata_fragment()

• chunk_grid_regular$read()

• chunk_grid_regular$write()

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chunk_grid_regular$new()

Initialize a new chunking scheme for an array.

Usage

chunk_grid_regular$new(array_shape, chunk_shape)

Arguments

array_shape

Integer vector of the array dimensions. This may be NA for a scalar array.

chunk_shape

Integer vector of the dimensions of each chunk. Ignored for a scalar array.

Returns

An instance of chunk_grid_regular.

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chunk_grid_regular$print()

Print a short description of this chunking scheme to the console.

Usage

chunk_grid_regular$print()

Returns

Self, invisibly.

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chunk_grid_regular$metadata_fragment()

Return the metadata fragment that describes this chunking scheme.

Usage

chunk_grid_regular$metadata_fragment()

Returns

A list with the metadata of this chunking scheme.

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chunk_grid_regular$read()

Read data from the Zarr array into an R object. The read can span multiple chunks. Reads will be parallelised if future::plan(multisession) is set; by default the reading is sequential.

Usage

chunk_grid_regular$read(start, stop)

Arguments

start, stop

Integer vectors of the same length as the dimensionality of the Zarr array, indicating the starting and ending (inclusive) indices of the data along each axis. These are ignored if the Zarr array is a scalar.

Returns

A vector, matrix or array of data.

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chunk_grid_regular$write()

Write data to the array. Writing data always uses a sequential plan.

Usage

chunk_grid_regular$write(data, start, stop)

Arguments

data

An R object with the same dimensionality as the Zarr array.

start, stop

Integer vectors of the same length as the dimensionality of the Zarr array, indicating the starting and ending (inclusive) indices of the data along each axis.

Returns

Self, invisibly.