Type: Package
Title: Slice into 'Zarr' Arrays
Version: 0.1.0
Description: An implementation of chunked, compressed, N-dimensional arrays for R following the 'Zarr' specification. Provides array and group creation, reading and writing with configurable chunk shapes, compression codecs, and storage backends including in-memory, local directory, and HTTP stores. Supports both 'Zarr' spec V2 (2024) <doi:10.5281/zenodo.11320255> and V3, enabling interoperable access to large array data commonly used in scientific computing and geospatial applications.
Language: en-US
License: MIT + file LICENSE
BugReports: https://github.com/zarr-developers/pizzarr/issues
URL: https://zarr.dev/pizzarr/
Depends: R (≥ 4.1.0)
Imports: jsonlite, stats, R6, qs2, stringr, memoise, utils
Encoding: UTF-8
RoxygenNote: 7.3.3
Suggests: testthat, knitr, covr, bslib, pkgdown, rmarkdown, crul, blosc, vcr (≥ 0.6.0), pbapply, parallel, future, future.apply, bench, bit64, withr
Config/testthat/parallel: false
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-03-20 15:09:07 UTC; dblodgett
Author: David Blodgett ORCID iD [cre, aut], Mark Keller ORCID iD [aut], Artür Manukyan ORCID iD [aut], zarr-developers [cph]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Repository: CRAN
Date/Publication: 2026-03-24 10:40:08 UTC

Attributes Class

Description

Class providing access to user attributes on an array or group.

Format

R6::R6Class

Details

The Zarr Attributes class.

Public fields

store

Attributes store, already initialized.

key

The key under which the attributes will be stored.

read_only

If True, attributes cannot be modified.

cache

If True (default), attributes will be cached locally.

synchronizer

Only necessary if attributes may be modified from multiple threads or processes.

Methods

Public methods

Method new()

Create a new Attributes instance.

Usage
Attributes$new(
  store,
  key = NA,
  read_only = FALSE,
  cache = TRUE,
  synchronizer = NA,
  zarr_format = NULL
)
Arguments
store

(Store)
Attributes store, already initialized.

key

(character(1))
Key to use for attributes (.zattrs is default).

read_only

(logical(1))
Whether the attributes are read-only.

cache

(logical(1))
Whether to cache attributes.

synchronizer

(ANY or NA)
Synchronizer object.

zarr_format

(integer(1) or NULL)
Zarr format version: 2L for V2 (.zattrs), 3L for V3 (zarr.json).

Returns

An Attributes instance.

Method to_list()

convert attributes to list

Usage
Attributes$to_list()
Returns

list().

Method refresh()

refresh attributes

Usage
Attributes$refresh()
Returns

NULL (called for side effects).

Method contains()

check if object contains item

Usage
Attributes$contains(x)
Arguments
x

Object to test.

Returns

logical(1).

Method get_item()

get attribute

Usage
Attributes$get_item(item)
Arguments
item

Character attribute name.

Returns

The attribute value.

Method set_item()

set attribute

Usage
Attributes$set_item(item, value)
Arguments
item

Character attribute name.

value

Value to add or update.

Returns

NULL (called for side effects).

Method del_item()

delete attribute

Usage
Attributes$del_item(item)
Arguments
item

Character attribute name.

Returns

NULL (called for side effects).

Method set_cached_v3_attrs()

Set cached attributes from V3 embedded metadata. In V3, attributes are part of zarr.json rather than a separate .zattrs file. This method pre-populates the cache so the normal .zattrs read path is skipped.

Usage
Attributes$set_cached_v3_attrs(attrs_list)
Arguments
attrs_list

A named list of attributes from V3 zarr.json.

Returns

NULL (modifies cache in place).

Method clone()

The objects of this class are cloneable with this method.

Usage
Attributes$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

BasicIndexer Class

Description

An indexer class to normalize a selection of an array and provide an iterator of indexes over the dimensions of an array.

Details

The Zarr BasicIndexer class.

Super class

pizzarr::Indexer -> BasicIndexer

Public fields

dim_indexers

List of per-dimension indexers (IntDimIndexer or SliceDimIndexer).

Methods

Public methods

Method new()

Create a new BasicIndexer instance.

Usage
BasicIndexer$new(selection, array)
Arguments
selection

Selection as with ZarrArray: scalar, string, or Slice.

array

ZarrArray object that will be indexed.

Returns

A BasicIndexer instance.

Method iter()

An iterator over the dimensions of an array

Usage
BasicIndexer$iter()
Returns

A list of ChunkProjection objects

Method clone()

The objects of this class are cloneable with this method.

Usage
BasicIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

BloscCodec Class

Description

Class representing a Blosc compressor

Format

R6::R6Class inheriting from Codec.

Details

Blosc compressor for Zarr

Super class

pizzarr::Codec -> BloscCodec

Public fields

cname

(character(1))
The compression algorithm to use.

clevel

(integer(1))
The compression level.

shuffle

(logical(1) | integer(1))
The shuffle filter to use.

blocksize

(integer(1) | NA)
The block size.

Methods

Public methods

Method new()

Create a new Blosc compressor.

Usage
BloscCodec$new(cname = "lz4", clevel = 5, shuffle = TRUE, blocksize = NA, ...)
Arguments
cname

(character(1))
The compression algorithm to use.

clevel

(integer(1))
The compression level.

shuffle

(logical(1) | integer(1))
The shuffle filter to use.

blocksize

(integer(1) | NA)
The block size.

...

Not used.

Returns

A new BloscCodec object.

Method encode()

Compress data.

Usage
BloscCodec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
BloscCodec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
BloscCodec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
BloscCodec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: Bz2Codec, Codec, GzipCodec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZlibCodec, ZstdCodec

BoolArrayDimIndexer Class

Description

Indexer for a boolean array selection along one dimension, selecting elements where the mask is TRUE.

Details

The Zarr BoolArrayDimIndexer class.

Super class

pizzarr::DimIndexer -> BoolArrayDimIndexer

Public fields

dim_sel

Selection on dimension.

dim_len

Dimension length.

dim_chunk_len

Dimension chunk length.

num_chunks

Number of chunks.

chunk_nitems

Number of items per chunk.

chunk_nitems_cumsum

Offsets into the output array.

dim_chunk_ixs

Chunks that should be visited.

dim_out_sel

Output array indices for the selected elements.

Methods

Public methods

Method new()

Create a new BoolArrayDimIndexer instance.

Usage
BoolArrayDimIndexer$new(dim_sel, dim_len, dim_chunk_len)
Arguments
dim_sel

Integer dimension selection.

dim_len

Integer dimension length.

dim_chunk_len

Integer dimension chunk length.

Returns

A BoolArrayDimIndexer instance.

Method iter()

An iterator over the dimensions of an array

Usage
BoolArrayDimIndexer$iter()
Returns

A list of ChunkProjection objects

Method clone()

The objects of this class are cloneable with this method.

Usage
BoolArrayDimIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Bz2Codec Class

Description

Class representing a bz2 compressor

Format

R6::R6Class inheriting from Codec.

Details

Bz2 compressor for Zarr

Super class

pizzarr::Codec -> Bz2Codec

Public fields

level

The compression level.

Methods

Public methods

Method new()

Create a new Bz2 compressor.

Usage
Bz2Codec$new(level = 6, ...)
Arguments
level

The compression level, between 1 and 22.

...

Not used.

Returns

A new Bz2Codec object.

Method encode()

Compress data.

Usage
Bz2Codec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
Bz2Codec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
Bz2Codec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
Bz2Codec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Codec, GzipCodec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZlibCodec, ZstdCodec

Chunk Dimension Projection

Description

A mapping from chunk to output array for a single dimension. Used internally to track which items within a single chunk dimension correspond to which items in the target output array.

Format

R6::R6Class object.

Public fields

dim_chunk_index

(integer(1))
Index of chunk.

dim_chunk_sel

(integer() | list())
Selection of items from chunk array.

dim_out_sel

(integer() | list())
Selection of items in target (output) array.

Methods

Public methods

Method new()

Creates a new instance of this R6 class.

Usage
ChunkDimProjection$new(dim_chunk_index, dim_chunk_sel, dim_out_sel)
Arguments
dim_chunk_index

(integer(1))
Index of chunk.

dim_chunk_sel

(integer() | list())
Selection of items from chunk array.

dim_out_sel

(integer() | list())
Selection of items in target (output) array.

Method clone()

The objects of this class are cloneable with this method.

Usage
ChunkDimProjection$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Indexing classes: ChunkProjection, DimIndexer, Indexer

Chunk Projection

Description

A mapping of items from chunk to output array. Can be used to extract items from the chunk array for loading into an output array. Can also be used to extract items from a value array for setting/updating in a chunk array.

Format

R6::R6Class object.

Public fields

chunk_coords

(integer())
Indices of chunk.

chunk_sel

(list())
Selection of items from chunk array.

out_sel

(list())
Selection of items in target (output) array.

Methods

Public methods

Method new()

Creates a new instance of this R6 class.

Usage
ChunkProjection$new(chunk_coords, chunk_sel, out_sel)
Arguments
chunk_coords

(integer())
Indices of chunk.

chunk_sel

(list())
Selection of items from chunk array.

out_sel

(list())
Selection of items in target (output) array.

Method clone()

The objects of this class are cloneable with this method.

Usage
ChunkProjection$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Indexing classes: ChunkDimProjection, DimIndexer, Indexer

Codec Class

Description

Abstract class representing a compressor.

Format

R6::R6Class

Details

Abstract compressor for Zarr

Methods

Public methods

Method encode()

Compress data.

Usage
Codec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
Codec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
Codec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
Codec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, GzipCodec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZlibCodec, ZstdCodec

Dimension Indexer

Description

Abstract base class for per-dimension chunk indexers. A dimension indexer maps a selection on a single array dimension to a sequence of ChunkDimProjection objects. Concrete subclasses include IntDimIndexer, SliceDimIndexer, IntArrayDimIndexer, and BoolArrayDimIndexer.

Format

R6::R6Class object.

Public fields

num_items

(integer(1))
Number of items in the selection.

Methods

Public methods

Method iter()

Iterate over ChunkDimProjection objects for this dimension.

Usage
DimIndexer$iter()
Returns

list() of ChunkDimProjection objects.

Method clone()

The objects of this class are cloneable with this method.

Usage
DimIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Indexing classes: ChunkDimProjection, ChunkProjection, Indexer

DirectoryStore Class

Description

Store class using directories and files on a standard file system.

Format

R6::R6Class inheriting from Store.

Details

DirectoryStore for Zarr

Super class

pizzarr::Store -> DirectoryStore

Public fields

root

The path to the root of the store.

Methods

Public methods

Inherited methods

Method new()

Create a new file system store.

Usage
DirectoryStore$new(root)
Arguments
root

The path to the root of the store.

Returns

A new DirectoryStore object.

Method get_item()

Get an item from the store.

Usage
DirectoryStore$get_item(key)
Arguments
key

The item key.

Returns

The item data in a vector of type raw.

Method set_item()

Set an item in the store.

Usage
DirectoryStore$set_item(key, value)
Arguments
key

The item key.

value

The item value as a vector of type raw.

Returns

NULL (called for side effects).

Method contains_item()

Determine whether the store contains an item.

Usage
DirectoryStore$contains_item(key)
Arguments
key

The item key.

Returns

A boolean value.

Method delete_item()

Delete an item from the store.

Usage
DirectoryStore$delete_item(key)
Arguments
key

The item key.

Returns

NULL (called for side effects).

Method rmdir()

Remove a path within a Store.

Usage
DirectoryStore$rmdir(path = NA)
Arguments
path

Character path.

Returns

NULL (called for side effects).

Method listdir()

List the store directory.

Usage
DirectoryStore$listdir(key = NA)
Arguments
key

Character key.

Returns

character() vector of entries.

Method print()

Print a human-readable summary of the store.

Usage
DirectoryStore$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method clone()

The objects of this class are cloneable with this method.

Usage
DirectoryStore$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Store classes: HttpStore, MemoryStore, Store

Dtype Class

Description

A data type object (an instance of Dtype class) describes how the bytes in the fixed-size block of memory corresponding to an array item should be interpreted.

Format

R6::R6Class

Details

The Zarr Dtype class.

Public fields

dtype

The original dtype string, like "<f4".

byte_order

The byte order of the dtype, either "little", "big", or "nr".

basic_type

The basic type of the dtype, like "f".

num_bytes

The number of bytes of the dtype.

num_items

The number of items of the dtype.

is_signed

Whether the dtype is signed. Logical/boolean.

is_structured

Whether the dtype is structured. Logical/boolean.

is_object

Whether the dtype is an object. Logical/boolean.

object_codec

The object codec instance.

Methods

Public methods

Method new()

Create a new Dtype instance.

Usage
Dtype$new(dtype, object_codec = NA)
Arguments
dtype

The original dtype string, like "<f4".

object_codec

The object codec instance.

Returns

A Dtype instance.

Method get_asrtype()

Get the R coercion function name for this dtype.

Usage
Dtype$get_asrtype()
Returns

Character string (e.g., "as.double").

Method get_rtype()

Get the R base type for this dtype.

Usage
Dtype$get_rtype()
Returns

An R prototype value (e.g., integer(), double(), or bit64::integer64()).

Method get_typed_array_ctr()

Get a constructor function for typed arrays of this dtype.

Usage
Dtype$get_typed_array_ctr()
Returns

A function that takes dim and returns an array.

Method clone()

The objects of this class are cloneable with this method.

Usage
Dtype$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

References

https://numpy.org/doc/stable/reference/arrays.dtypes.html

GzipCodec Class

Description

Class representing a gzip compressor.

Gzip encoding uses temporary files because R's memCompress() produces zlib framing rather than gzip framing. This makes GzipCodec slower than ZstdCodec for writes. Prefer ZstdCodec when performance matters.

Format

R6::R6Class inheriting from Codec.

Details

Gzip compressor for Zarr

Super class

pizzarr::Codec -> GzipCodec

Public fields

level

The compression level.

Methods

Public methods

Method new()

Create a new Gzip compressor.

Usage
GzipCodec$new(level = 6, ...)
Arguments
level

The compression level, between 1 and 22.

...

Not used.

Returns

A new GzipCodec object.

Method encode()

Compress data.

Usage
GzipCodec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
GzipCodec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
GzipCodec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
GzipCodec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZlibCodec, ZstdCodec

HttpStore Class

Description

Store class that uses HTTP requests. Read-only. Depends on the crul package.

Format

R6::R6Class inheriting from Store.

Details

For parallel operation, set the "pizzarr.parallel_backend" option to one of:

Set the option "pizzarr.progress_bar" to TRUE to get a progress bar for long running reads.

For more, see ⁠vignette("parallel").⁠

Super class

pizzarr::Store -> HttpStore

Methods

Public methods

Inherited methods

Method new()

Create a HttpStore object

Usage
HttpStore$new(url, options = NA, headers = NA)
Arguments
url

(character(1))
URL of the store.

options

(list() or NA)
Options passed to crul.

headers

(list() or NA)
Headers passed to crul.

Returns

A new HttpStore object.

Method get_item()

Get an item from the store.

Usage
HttpStore$get_item(item)
Arguments
item

The item key.

Returns

The item data in a vector of type raw.

Method contains_item()

Determine whether the store contains an item.

Usage
HttpStore$contains_item(item)
Arguments
item

The item key.

Returns

A boolean value.

Method listdir()

Fetches .zmetadata from the store evaluates its names

Usage
HttpStore$listdir()
Returns

Character vector of unique keys that do not start with a ..

Method get_cache_time_seconds()

Get cache time of http requests.

Usage
HttpStore$get_cache_time_seconds()
Returns

numeric(1).

Method set_cache_time_seconds()

Set cache time of http requests.

Usage
HttpStore$set_cache_time_seconds(seconds)
Arguments
seconds

Number of seconds until cache is invalid – 0 for no cache.

Returns

NULL (called for side effects).

Method print()

Print a human-readable summary of the store.

Usage
HttpStore$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method clone()

The objects of this class are cloneable with this method.

Usage
HttpStore$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Store classes: DirectoryStore, MemoryStore, Store

Indexer

Description

Abstract base class for chunk indexers. An indexer maps a user-level array selection to a sequence of ChunkProjection objects, each describing which items to read or write within a single chunk. Concrete subclasses include BasicIndexer and OrthogonalIndexer.

Format

R6::R6Class object.

Public fields

shape

(integer())
Shape of the selection.

drop_axes

(integer() | NULL)
Axes to drop from the result.

Methods

Public methods

Method iter()

Iterate over ChunkProjection objects for the selection.

Usage
Indexer$iter()
Returns

list() of ChunkProjection objects.

Method clone()

The objects of this class are cloneable with this method.

Usage
Indexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Indexing classes: ChunkDimProjection, ChunkProjection, DimIndexer

IntArrayDimIndexer Class

Description

Indexer for an integer array selection along one dimension, supporting fancy/advanced indexing.

Details

The Zarr IntArrayDimIndexer class.

Super class

pizzarr::DimIndexer -> IntArrayDimIndexer

Public fields

dim_len

Dimension length.

dim_chunk_len

Dimension chunk length.

num_chunks

Number of chunks.

dim_sel

Selection on dimension.

dim_out_sel

Output array indices corresponding to each selected element, reordered when selection is not increasing.

order

Memory order.

chunk_nitems

Number of items per chunk.

dim_chunk_ixs

Chunks that should be visited.

chunk_nitems_cumsum

Offsets into the output array.

Methods

Public methods

Method new()

Create a new IntArrayDimIndexer instance.

Usage
IntArrayDimIndexer$new(
  dim_sel,
  dim_len,
  dim_chunk_len,
  sel_order = Order$public_fields$UNKNOWN
)
Arguments
dim_sel

Integer dimension selection.

dim_len

Integer dimension length.

dim_chunk_len

Integer dimension chunk length.

sel_order

order

Returns

A IntArrayDimIndexer instance.

Method iter()

An iterator over the dimensions of an array

Usage
IntArrayDimIndexer$iter()
Returns

A list of ChunkProjection objects

Method clone()

The objects of this class are cloneable with this method.

Usage
IntArrayDimIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

IntDimIndexer Class

Description

Indexer for a single integer selection along one dimension.

Details

The Zarr IntDimIndexer class.

Super class

pizzarr::DimIndexer -> IntDimIndexer

Public fields

dim_sel

Normalized integer index for this dimension.

dim_len

Length of the array along this dimension.

dim_chunk_len

Length of a chunk along this dimension.

Methods

Public methods

Method new()

Create a new IntDimIndexer instance.

Usage
IntDimIndexer$new(dim_sel, dim_len, dim_chunk_len)
Arguments
dim_sel

Integer dimension selection.

dim_len

Integer dimension length.

dim_chunk_len

Integer dimension chunk length.

Returns

A IntDimIndexer instance.

Method iter()

Compute the chunk dimension projection for the single selected index.

Usage
IntDimIndexer$iter()
Returns

a ChunkDimProjection instance

Method clone()

The objects of this class are cloneable with this method.

Usage
IntDimIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Lz4Codec Class

Description

Class representing a LZ4 compressor

Format

R6::R6Class inheriting from Codec.

Details

LZ4 compressor for Zarr

Deprecation Notice

This codec is deprecated because the underlying qs package was archived on CRAN. For LZ4 compression, use BloscCodec$new(cname = "lz4") instead. This class will be removed in a future version.

Super class

pizzarr::Codec -> Lz4Codec

Public fields

acceleration

The compression level.

Methods

Public methods

Method new()

Create a new LZ4 compressor.

Usage
Lz4Codec$new(acceleration = 1, ...)
Arguments
acceleration

The compression level.

...

Not used.

Returns

A new Lz4Codec object.

Method encode()

Compress data.

Usage
Lz4Codec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
Lz4Codec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
Lz4Codec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
Lz4Codec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, GzipCodec, LzmaCodec, VLenUtf8Codec, ZlibCodec, ZstdCodec

LzmaCodec Class

Description

Class representing a lzma compressor

Format

R6::R6Class inheriting from Codec.

Details

Lzma compressor for Zarr

Super class

pizzarr::Codec -> LzmaCodec

Public fields

level

The compression level.

format

The compression format.

Methods

Public methods

Method new()

Create a new lzma compressor.

Usage
LzmaCodec$new(level = 9, format = 1, ...)
Arguments
level

The compression level, between 1 and 22.

format

(integer(1))
Only 1 is supported.

...

Not used.

Returns

A new LzmaCodec object.

Method encode()

Compress data.

Usage
LzmaCodec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
LzmaCodec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
LzmaCodec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
LzmaCodec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, GzipCodec, Lz4Codec, VLenUtf8Codec, ZlibCodec, ZstdCodec

MemoryStore Class

Description

Store class that uses a hierarchy of list objects, thus all data will be held in main memory.

Format

R6::R6Class inheriting from Store.

Details

MemoryStore for Zarr

Super class

pizzarr::Store -> MemoryStore

Public fields

root

The root list for the store.

Methods

Public methods

Inherited methods

Method new()

Create a new memory store.

Usage
MemoryStore$new()
Returns

A new MemoryStore object.

Method get_parent()

Get the parent of an item.

Usage
MemoryStore$get_parent(item)
Arguments
item

The item key.

Returns

A list with the keys parent and key.

Method get_item()

Get an item from the store.

Usage
MemoryStore$get_item(item = NA)
Arguments
item

The item key.

Returns

The item data in a vector of type raw.

Method set_item()

Set an item in the store.

Usage
MemoryStore$set_item(item, value)
Arguments
item

The item key.

value

The item value as a vector of type raw.

Returns

NULL (called for side effects).

Method contains_item()

Determine whether the store contains an item.

Usage
MemoryStore$contains_item(item)
Arguments
item

The item key.

Returns

A boolean value.

Method listdir()

List the store directory.

Usage
MemoryStore$listdir(key = NA)
Arguments
key

Character key.

Returns

character() vector of entries.

Method delete_item()

Delete an item from the store.

Usage
MemoryStore$delete_item(key)
Arguments
key

The item key.

Returns

NULL (called for side effects).

Method rmdir()

Remove a path within a Store.

Usage
MemoryStore$rmdir(item)
Arguments
item

Character item.

Returns

NULL (called for side effects).

Method print()

Print a human-readable summary of the store.

Usage
MemoryStore$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method clone()

The objects of this class are cloneable with this method.

Usage
MemoryStore$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Store classes: DirectoryStore, HttpStore, Store

Zarr V2 Metadata Codec

Description

Handles encoding and decoding of Zarr V2 metadata. Provides methods to parse raw JSON bytes into R lists and to serialize metadata back to JSON bytes, for both array and group nodes. Array metadata includes shape, chunks, dtype, compressor, fill_value, order, and filters. Group metadata contains only the zarr_format field.

Format

R6::R6Class object.

Methods

Public methods

Method decode_metadata()

Parse metadata from raw bytes or return as-is if already a list.

Usage
Metadata2$decode_metadata(s, auto_unbox = FALSE)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes, a pre-parsed list, or NULL.

auto_unbox

(logical(1))
Passed to jsonlite::toJSON(). Default FALSE.

Returns

list() or NULL.

Method encode_metadata()

Encode metadata list to raw JSON bytes.

Usage
Metadata2$encode_metadata(meta, auto_unbox = FALSE)
Arguments
meta

(list())
Metadata to encode.

auto_unbox

(logical(1))
Passed to jsonlite::toJSON(). Default FALSE.

Returns

raw().

Method decode_array_metadata()

Decode and validate V2 array metadata.

Usage
Metadata2$decode_array_metadata(s)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes or pre-parsed list.

Returns

list() or NULL.

Method decode_group_metadata()

Decode and validate V2 group metadata.

Usage
Metadata2$decode_group_metadata(s)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes or pre-parsed list.

Returns

list() or NULL.

Method encode_array_metadata()

Encode array metadata to raw JSON bytes, setting zarr_format to 2.

Usage
Metadata2$encode_array_metadata(meta)
Arguments
meta

(list())
Array metadata list.

Returns

raw().

Method encode_group_metadata()

Encode group metadata to raw JSON bytes, setting zarr_format to 2.

Usage
Metadata2$encode_group_metadata(meta = NA)
Arguments
meta

(list() | NA)
Ignored; a fresh group metadata list is created.

Returns

raw().

Method clone()

The objects of this class are cloneable with this method.

Usage
Metadata2$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Metadata classes: Metadata3

Zarr V3 Metadata Codec

Description

Handles decoding of Zarr V3 metadata. In V3, each node has a single zarr.json file containing zarr_format, node_type, and all metadata (shape, data_type, codecs, chunk_grid, chunk_key_encoding, fill_value, attributes, etc.). This class is read-only; no encode methods are provided.

Format

R6::R6Class object.

Methods

Public methods

Method decode_metadata()

Parse metadata from raw bytes or return as-is if already a list.

Usage
Metadata3$decode_metadata(s)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes, a pre-parsed list, or NULL.

Returns

list() or NULL.

Method decode_array_metadata()

Decode and validate V3 array metadata from zarr.json. V3 arrays have node_type = "array" and contain shape, data_type, chunk_grid, chunk_key_encoding, codecs, fill_value, and attributes.

Usage
Metadata3$decode_array_metadata(s)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes or pre-parsed list.

Returns

list() or NULL.

Method decode_group_metadata()

Decode and validate V3 group metadata from zarr.json. V3 groups have node_type = "group" and may contain attributes.

Usage
Metadata3$decode_group_metadata(s)
Arguments
s

(raw() | list() | NULL)
Raw JSON bytes or pre-parsed list.

Returns

list() or NULL.

Method encode_array_metadata()

Encode V3 array metadata to raw JSON bytes. Expects a list built by create_v3_array_meta() with all scalars already wrapped in jsonlite::unbox().

Usage
Metadata3$encode_array_metadata(meta)
Arguments
meta

(list())
V3 array metadata list.

Returns

raw().

Method encode_group_metadata()

Encode V3 group metadata to raw JSON bytes. Produces ⁠{"zarr_format":3,"node_type":"group","attributes":{}}⁠.

Usage
Metadata3$encode_group_metadata(meta = NA, attributes = NULL)
Arguments
meta

(list() | NA)
Ignored; a fresh group metadata list is created.

attributes

(list())
Attributes to embed in zarr.json. Default empty.

Returns

raw().

Method clone()

The objects of this class are cloneable with this method.

Usage
Metadata3$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Metadata classes: Metadata2

NestedArray Class

Description

Represents a multi-dimensional array that can be accessed and subsetted via list of Slice instances.

Format

R6::R6Class

Details

The Zarr NestedArray class.

Public fields

shape

The shape of the array.

dtype

The Zarr dtype of the array, as a string like ">f8".

dtype_obj

The Zarr dtype of the array, as a Dtype instance.

data

The array contents as a base R array.

Methods

Public methods

Method new()

Create a new NestedArray instance.

Usage
NestedArray$new(data, shape = NA, dtype = NA, order = NA)
Arguments
data

The data to initialize the array with. Either NULL, base R array, base R vector (numeric/logical), scalar, or raw vector.

shape

The shape of the array.

dtype

The Zarr dtype of the array, as a string like ">f8".

order

The order of the array, either "C" or "F". Only used when data is a raw vector. Optional.

Returns

A NestedArray instance.

Method get()

Subset the array.

Usage
NestedArray$get(selection)
Arguments
selection

A list of slices.

Returns

A new NestedArray (potentially a subset) representing the selection.

Method set()

Set a subset of the array.

Usage
NestedArray$set(selection, value)
Arguments
selection

A list of slices.

value

A NestedArray or a base R array.

Returns

NULL (called for side effects, modifies self$data in place).

Method flatten()

Flatten the array contents.

Usage
NestedArray$flatten(order = NA)
Arguments
order

Either "C", "F", or NA.

Returns

The data as a flat vector.

Method flatten_to_raw()

Flatten the array contents and convert to a raw vector.

Usage
NestedArray$flatten_to_raw(order = NA)
Arguments
order

Either "C", "F", or NA.

Returns

The data as a flat raw() vector (or plain vector for object dtypes).

Method as.array()

Convert NestedArray to a base R array.

Usage
NestedArray$as.array()
Returns

array().

Method clone()

The objects of this class are cloneable with this method.

Usage
NestedArray$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

OIndex Class

Description

Orthogonal index class

Details

The Zarr OIndex class.

Public fields

array

The array instance.

Methods

Public methods

Method new()

Create a new OIndex instance.

Usage
OIndex$new(array)
Arguments
array

The array instance.

Returns

An OIndex instance.

Method get_item()

get method for the Oindex instance

Usage
OIndex$get_item(selection)
Arguments
selection

Selection to apply.

Returns

An OIndex instance.

Method clone()

The objects of this class are cloneable with this method.

Usage
OIndex$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Order Class

Description

Determines the sort order of an integer array selection (increasing, decreasing, or unordered).

Details

The Order class.

Public fields

UNKNOWN

UNKNOWN

INCREASING

INCREASING

DECREASING

DECREASING

UNORDERED

UNORDERED

Methods

Public methods

Method check()

checking order of numbers

Usage
Order$check(a)
Arguments
a

Vector of numbers.

Method clone()

The objects of this class are cloneable with this method.

Usage
Order$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

OrthogonalIndexer Class

Description

An indexer class to normalize a selection of an array and provide an iterator of indexes over the dimensions of an array.

Details

The Zarr OrthogonalIndexer class.

Super class

pizzarr::Indexer -> OrthogonalIndexer

Public fields

dim_indexers

List of per-dimension indexers (IntDimIndexer, SliceDimIndexer, IntArrayDimIndexer, or BoolArrayDimIndexer).

Methods

Public methods

Method new()

Create a new OrthogonalIndexer instance.

Usage
OrthogonalIndexer$new(selection, array)
Arguments
selection

Selection as with ZarrArray: scalar, string, or Slice.

array

ZarrArray object that will be indexed.

Returns

An OrthogonalIndexer instance.

Method iter()

An iterator over the dimensions of an array

Usage
OrthogonalIndexer$iter()
Returns

A list of ChunkProjection objects

Method clone()

The objects of this class are cloneable with this method.

Usage
OrthogonalIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

RawArray Class

Description

TODO: Add export annotation / remove keywords internal annotation once implemented.

Details

The Zarr RawArray class.

Methods

Public methods

Method new()

Create a new RawArray instance.

Usage
RawArray$new()
Returns

A RawArray instance.

Method clone()

The objects of this class are cloneable with this method.

Usage
RawArray$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SliceDimIndexer Class

Description

Indexer for a slice selection along one dimension.

Details

The Zarr SliceDimIndexer class.

Super class

pizzarr::DimIndexer -> SliceDimIndexer

Public fields

dim_len

Dimension length.

dim_chunk_len

Dimension chunk length.

num_chunks

Number of chunks.

start

Start index.

stop

Stop index.

step

Step size.

Methods

Public methods

Method new()

Create a new SliceDimIndexer instance.

Usage
SliceDimIndexer$new(dim_sel, dim_len, dim_chunk_len)
Arguments
dim_sel

Integer dimension selection.

dim_len

Integer dimension length.

dim_chunk_len

Integer dimension chunk length.

Returns

A SliceDimIndexer instance.

Method iter()

Iterate over chunks that overlap the slice, yielding a ChunkDimProjection for each.

Usage
SliceDimIndexer$iter()
Returns

A list of ChunkDimProjection objects.

Method clone()

The objects of this class are cloneable with this method.

Usage
SliceDimIndexer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Store Class

Description

Class representing an abstract store

Format

R6::R6Class

Details

Abstract store for Zarr

Public fields

metadata_class

The metadata encoder/decoder for this store.

Methods

Public methods

Method new()

Create a Store object

Usage
Store$new()

Method is_readable()

Test if Store is readable.

Usage
Store$is_readable()
Returns

Logical.

Method is_writeable()

Test if Store is writeable.

Usage
Store$is_writeable()
Returns

Logical.

Method is_erasable()

Test if Store is eraseable.

Usage
Store$is_erasable()
Returns

Logical.

Method is_listable()

Test if Store is listable.

Usage
Store$is_listable()
Returns

Logical.

Method close()

Close the store.

Usage
Store$close()
Returns

NULL.

Method listdir()

List the store directory.

Usage
Store$listdir(path = NA)
Arguments
path

character path.

Returns

Character vector of keys.

Method rename()

Rename a Store path.

Usage
Store$rename(src_path, dst_path)
Arguments
src_path

character source path.

dst_path

character destination path.

Returns

NULL (called for side effects).

Method rmdir()

Remove a path within a Store.

Usage
Store$rmdir(path)
Arguments
path

character path.

Returns

NULL (called for side effects).

Method get_item()

Get an item from the store.

Usage
Store$get_item(key)
Arguments
key

The item key.

Returns

The item data in a vector of type raw.

Method set_item()

Set an item in the store.

Usage
Store$set_item(key, value)
Arguments
key

The item key.

value

The item value as a vector of type raw.

Returns

NULL (called for side effects).

Method contains_item()

Determine whether the store contains an item.

Usage
Store$contains_item(key)
Arguments
key

The item key.

Returns

A boolean value.

Method delete_item()

Delete an item from the store.

Usage
Store$delete_item(key)
Arguments
key

The item key.

Returns

NULL (called for side effects).

Method get_consolidated_metadata()

Get consolidated metadata if it exists.

Usage
Store$get_consolidated_metadata()
Returns

A list or NULL.

Method print()

Print a human-readable summary of the store.

Usage
Store$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method clone()

The objects of this class are cloneable with this method.

Usage
Store$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Store classes: DirectoryStore, HttpStore, MemoryStore

VIndex Class

Description

Vectorized index class

Details

The Zarr VIndex class.

Public fields

array

The array instance.

Methods

Public methods

Method new()

Create a new VIndex instance.

Usage
VIndex$new(array)
Arguments
array

The array instance.

Returns

A VIndex instance.

Method clone()

The objects of this class are cloneable with this method.

Usage
VIndex$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

VLenUtf8Codec Class

Description

Class representing a VLenUtf8 compressor

Format

R6::R6Class inheriting from Codec.

Details

Variable-length UTF-8 codec for Zarr

Super class

pizzarr::Codec -> VLenUtf8Codec

Methods

Public methods

Method encode()

Compress data.

Usage
VLenUtf8Codec$encode(buf, zarr_arr)
Arguments
buf

(character())
The un-compressed data (character vector).

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
VLenUtf8Codec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
VLenUtf8Codec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
VLenUtf8Codec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, GzipCodec, Lz4Codec, LzmaCodec, ZlibCodec, ZstdCodec

ZarrArray Class

Description

Instantiate an array from an initialized store.

Format

R6::R6Class

Details

The Zarr Array class.

Methods

Public methods

Method new()

Create a new ZarrArray instance.

Usage
ZarrArray$new(
  store,
  path = NA,
  read_only = FALSE,
  chunk_store = NA,
  synchronizer = NA,
  cache_metadata = TRUE,
  cache_attrs = TRUE,
  write_empty_chunks = TRUE
)
Arguments
store

(Store)
Array store, already initialized.

path

(character(1))
Storage path.

read_only

(logical(1))
Whether the array is read-only.

chunk_store

(Store or NA)
Separate storage for chunks. If not provided, store will be used for both chunks and metadata.

synchronizer

(ANY or NA)
Object used to synchronize write access to the array.

cache_metadata

(logical(1))
Whether to cache metadata.

cache_attrs

(logical(1))
Whether to cache attributes.

write_empty_chunks

(logical(1))
Whether to write empty chunks.

Returns

A ZarrArray instance.

Method get_store()

get store from array.

Usage
ZarrArray$get_store()
Returns

Store.

Method get_path()

get array path

Usage
ZarrArray$get_path()
Returns

character(1) or NA.

Method get_name()

get full array name

Usage
ZarrArray$get_name()
Returns

character(1) or NA.

Method get_basename()

get the basename of an array

Usage
ZarrArray$get_basename()
Returns

character(1) or NA.

Method get_read_only()

get the read only property of an array (TRUE/FALSE)

Usage
ZarrArray$get_read_only()
Returns

logical(1).

Method set_read_only()

set the read only property of an array

Usage
ZarrArray$set_read_only(val)
Arguments
val

(logical(1))
Value to set.

Returns

NULL (called for side effects).

Method get_chunk_store()

get the chunk store for an array

Usage
ZarrArray$get_chunk_store()
Returns

Store.

Method get_shape()

get the shape of an array

Usage
ZarrArray$get_shape()
Returns

integer().

Method set_shape()

set or reset the size of an array

Usage
ZarrArray$set_shape(value)
Arguments
value

(integer())
Numeric size to set.

Returns

NULL (called for side effects).

Method resize()

Change the shape of the array by growing or shrinking one or more dimensions.

Usage
ZarrArray$resize(...)
Arguments
...

Arguments for do.call.

Returns

NULL (called for side effects).

Method get_chunks()

get the chunk metadata of an array

Usage
ZarrArray$get_chunks()
Returns

integer().

Method get_dtype()

get the Dtype of an array

Usage
ZarrArray$get_dtype()
Returns

Dtype.

Method get_compressor()

get the compressor of an array

Usage
ZarrArray$get_compressor()
Returns

Codec or NA.

Method get_fill_value()

get the fill value of an array

Usage
ZarrArray$get_fill_value()
Returns

Scalar fill value.

Method set_fill_value()

set the fill value of an array

Usage
ZarrArray$set_fill_value(val)
Arguments
val

Fill value to use.

Returns

NULL (called for side effects).

Method get_order()

get the storage order metadata of an array.

Usage
ZarrArray$get_order()
Returns

character(1), "C" or "F".

Method get_filters()

get the filters metadata of an array

Usage
ZarrArray$get_filters()
Returns

list() of Codec objects or NA.

Method get_synchronizer()

Get the synchronizer used to coordinate write access to the array.

Usage
ZarrArray$get_synchronizer()
Returns

Synchronizer object or NA.

Method get_attrs()

get attributes of array

Usage
ZarrArray$get_attrs()
Returns

Attributes.

Method get_ndim()

get number of dimensions of array

Usage
ZarrArray$get_ndim()
Returns

integer(1).

Method get_size()

Get the total number of elements in the array.

Usage
ZarrArray$get_size()
Returns

numeric(1).

Method get_itemsize()

Get the size in bytes of each item in the array.

Usage
ZarrArray$get_itemsize()
Returns

integer(1).

Method get_nbytes()

get number of bytes of an array

Usage
ZarrArray$get_nbytes()
Returns

numeric(1).

Method get_nbytes_stored()

Get the total number of stored bytes for the array, including metadata and compressed chunk data.

Usage
ZarrArray$get_nbytes_stored()
Returns

numeric(1).

Method get_cdata_shape()

Get the number of chunks along each dimension of the array.

Usage
ZarrArray$get_cdata_shape()
Returns

numeric().

Method get_nchunks()

Get the total number of chunks in the array.

Usage
ZarrArray$get_nchunks()
Returns

integer(1).

Method get_nchunks_initialized()

Get the number of chunks that have been initialized with data.

Usage
ZarrArray$get_nchunks_initialized()
Returns

integer(1).

Method get_is_view()

get is_view metadata of array

Usage
ZarrArray$get_is_view()
Returns

logical(1).

Method get_oindex()

get orthogonal index of array

Usage
ZarrArray$get_oindex()
Returns

OIndex.

Method get_vindex()

get vectorized index of array

Usage
ZarrArray$get_vindex()
Returns

VIndex.

Method get_write_empty_chunks()

get write empty chunks setting of array

Usage
ZarrArray$get_write_empty_chunks()
Returns

logical(1).

Method equals()

check if another object refers to the same array. does not check array data

Usage
ZarrArray$equals(other)
Arguments
other

Other object to check.

Returns

logical(1).

Method print()

Print a human-readable summary of the array.

Usage
ZarrArray$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method islice()

Iterate over the array or a range of it, yielding successive slices along the first dimension. Uses chunk caching for efficient sequential access.

Usage
ZarrArray$islice(start = NA, end = NA)
Arguments
start

Start index of the iteration range (1-based, inclusive).

end

End index of the iteration range (1-based, inclusive).

Returns

list() of NestedArray slices.

Method length()

Return the length of the first dimension. Raises an error for zero-dimensional arrays.

Usage
ZarrArray$length()
Returns

integer(1).

Method get_item()

Subset the array.

Usage
ZarrArray$get_item(selection)
Arguments
selection

Selection specifying the subset to retrieve.

Returns

NestedArray.

Method get_basic_selection()

Get a selection of an array based on a "basic" list of slices.

Usage
ZarrArray$get_basic_selection(selection = NA, out = NA, fields = NA)
Arguments
selection

Selection specifying the subset to retrieve.

out

Not yet implemented.

fields

Not yet implemented.

Returns

NestedArray.

Method get_orthogonal_selection()

Retrieve data using orthogonal (outer) indexing.

Usage
ZarrArray$get_orthogonal_selection(selection = NA, out = NA, fields = NA)
Arguments
selection

Selection specifying the subset to retrieve.

out

Not yet implemented.

fields

Not yet implemented.

Returns

NestedArray.

Method get_coordinate_selection()

Retrieve data using coordinate (point) indexing. Not yet implemented.

Usage
ZarrArray$get_coordinate_selection(selection = NA, out = NA, fields = NA)
Arguments
selection

Selection specifying the subset to retrieve.

out

Not yet implemented.

fields

Not yet implemented.

Returns

NestedArray.

Method get_mask_selection()

Retrieve data using a boolean mask. Not yet implemented.

Usage
ZarrArray$get_mask_selection(selection = NA, out = NA, fields = NA)
Arguments
selection

Selection specifying the subset to retrieve.

out

Not yet implemented.

fields

Not yet implemented.

Returns

NestedArray.

Method set_item()

Set a subset of the array.

Usage
ZarrArray$set_item(selection, value)
Arguments
selection

Selection specifying the subset to set.

value

The value to set, as an R array() or a Zarr NestedArray instance.

Returns

NULL (called for side effects).

Method set_basic_selection()

Set a selection of the array using basic (integer/slice) indexing.

Usage
ZarrArray$set_basic_selection(selection, value, fields = NA)
Arguments
selection

Selection specifying the subset to set.

value

The value to set.

fields

Not yet implemented.

Returns

NULL (called for side effects).

Method set_orthogonal_selection()

Set data using orthogonal (outer) indexing. Not yet implemented.

Usage
ZarrArray$set_orthogonal_selection(selection, value, fields = NA)
Arguments
selection

Selection specifying the subset to set.

value

Not yet implemented.

fields

Not yet implemented.

Returns

NULL (called for side effects).

Method set_coordinate_selection()

Set data using coordinate (point) indexing. Not yet implemented.

Usage
ZarrArray$set_coordinate_selection(selection, value, fields = NA)
Arguments
selection

Selection specifying the subset to set.

value

Not yet implemented.

fields

Not yet implemented.

Returns

NULL (called for side effects).

Method set_mask_selection()

Set data using a boolean mask. Not yet implemented.

Usage
ZarrArray$set_mask_selection(selection, value, fields = NA)
Arguments
selection

Selection specifying the subset to set.

value

Not yet implemented.

fields

Not yet implemented.

Returns

NULL (called for side effects).

Method get_info()

Get array diagnostic info. Not yet implemented.

Usage
ZarrArray$get_info()
Returns

character(1).

Method get_digest()

Compute a checksum digest of the array data. Not yet implemented.

Usage
ZarrArray$get_digest(hashname = "sha1")
Arguments
hashname

Name of hash.

Returns

character(1).

Method get_hexdigest()

Compute a hex-string checksum digest. Not yet implemented.

Usage
ZarrArray$get_hexdigest(hashname = "sha1")
Arguments
hashname

Name of hash.

Returns

character(1).

Method append()

Append data to the array along the specified axis.

Usage
ZarrArray$append(data, axis = 1)
Arguments
data

Data to append. Will be coerced to array if needed.

axis

Axis to append along (1-indexed, R convention). Default 1.

Returns

NULL (called for side effects).

Method view()

Return a view on the array with modified interpretation. Not yet implemented.

Usage
ZarrArray$view(
  shape = NA,
  chunks = NA,
  dtype = NA,
  fill_value = NA,
  filters = NA,
  read_only = NA,
  synchronizer = NA
)
Arguments
shape

Not yet implemented.

chunks

Not yet implemented.

dtype

Not yet implemented.

fill_value

Not yet implemented.

filters

Not yet implemented.

read_only

Not yet implemented.

synchronizer

Not yet implemented.

Returns

ZarrArray.

Method astype()

Return a view with a different dtype. Not yet implemented.

Usage
ZarrArray$astype(dtype)
Arguments
dtype

Not yet implemented.

Returns

ZarrArray.

Method get_dimension_separator()

Get the dimension separator used in chunk keys.

Usage
ZarrArray$get_dimension_separator()
Returns

character(1).

Method as.array()

Convert Zarr object to R array (for S3 method). Note that this loads all data into memory.

Usage
ZarrArray$as.array()
Returns

An R array.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZarrArray$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ZarrGroup Class

Description

Instantiate a group from an initialized store.

Format

R6::R6Class

Details

The Zarr Group class.

Methods

Public methods

Method new()

Create a new ZarrGroup instance.

Usage
ZarrGroup$new(
  store,
  path = NA,
  read_only = FALSE,
  chunk_store = NA,
  cache_attrs = TRUE,
  synchronizer = NA
)
Arguments
store

(Store)
Group store, already initialized.

path

(character(1))
Storage path.

read_only

(logical(1))
Whether the group is read-only.

chunk_store

(Store or NA)
Separate storage for chunks.

cache_attrs

(logical(1))
Whether to cache attributes.

synchronizer

(ANY or NA)
Object used to synchronize write access.

Returns

A ZarrGroup instance.

Method get_store()

Get group store

Usage
ZarrGroup$get_store()
Returns

Store.

Method get_path()

Get group path

Usage
ZarrGroup$get_path()
Returns

character(1).

Method get_meta()

Get group metadata

Usage
ZarrGroup$get_meta()
Returns

list() or NULL.

Method get_name()

Get group name

Usage
ZarrGroup$get_name()
Returns

character(1).

Method get_read_only()

Is store read only?

Usage
ZarrGroup$get_read_only()
Returns

logical(1).

Method get_chunk_store()

Get group chunk store

Usage
ZarrGroup$get_chunk_store()
Returns

Store.

Method get_synchronizer()

Get group synchronizer

Usage
ZarrGroup$get_synchronizer()
Returns

Synchronizer object or NA.

Method get_attrs()

Get group attributes

Usage
ZarrGroup$get_attrs()
Returns

Attributes.

Method contains_item()

Test for group membership.

Usage
ZarrGroup$contains_item(item)
Arguments
item

Character item to test for.

Returns

logical(1).

Method get_item()

Obtain a group member.

Usage
ZarrGroup$get_item(item)
Arguments
item

Character item to retrieve.

Returns

ZarrArray or ZarrGroup.

Method create_group()

create a group

Usage
ZarrGroup$create_group(name, overwrite = FALSE)
Arguments
name

Character group name.

overwrite

Logical overwrite.

Returns

ZarrGroup.

Method create_dataset()

Create a dataset (array) within this group.

Usage
ZarrGroup$create_dataset(name, data = NA, ...)
Arguments
name

Character dataset name.

data

Data to add to group.

...

Extra arguments to pass to zarr_create() or array().

Returns

ZarrArray.

Method print()

Print a human-readable summary of the group.

Usage
ZarrGroup$print(...)
Arguments
...

Ignored.

Returns

self (invisibly).

Method tree()

Print an ASCII tree showing the group hierarchy.

Usage
ZarrGroup$tree(level = NA)
Arguments
level

Maximum depth to display. NA (default) shows all levels.

Returns

self (invisibly).

Method clone()

The objects of this class are cloneable with this method.

Usage
ZarrGroup$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

ZlibCodec Class

Description

Class representing a zlib compressor

Format

R6::R6Class inheriting from Codec.

Details

Zlib compressor for Zarr

Super class

pizzarr::Codec -> ZlibCodec

Public fields

level

The compression level.

Methods

Public methods

Method new()

Create a new Zlib compressor.

Usage
ZlibCodec$new(level = 6, ...)
Arguments
level

The compression level, between 1 and 22.

...

Not used.

Returns

A new ZlibCodec object.

Method encode()

Compress data.

Usage
ZlibCodec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
ZlibCodec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
ZlibCodec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZlibCodec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, GzipCodec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZstdCodec

ZstdCodec Class

Description

Class representing a ZSTD compressor

Format

R6::R6Class inheriting from Codec.

Details

ZSTD compressor for Zarr

Super class

pizzarr::Codec -> ZstdCodec

Public fields

level

The compression level.

Methods

Public methods

Method new()

Create a new ZSTD compressor.

Usage
ZstdCodec$new(level = 1, ...)
Arguments
level

The compression level, between 1 and 22.

...

Not used.

Returns

A new ZstdCodec object.

Method encode()

Compress data.

Usage
ZstdCodec$encode(buf, zarr_arr)
Arguments
buf

(raw())
The un-compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Compressed data.

Method decode()

Decompress data.

Usage
ZstdCodec$decode(buf, zarr_arr)
Arguments
buf

(raw())
The compressed data.

zarr_arr

(ZarrArray)
The ZarrArray instance.

Returns

Un-compressed data.

Method get_config()

Get codec configuration as a list.

Usage
ZstdCodec$get_config()
Returns

A named list.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZstdCodec$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Codec classes: BloscCodec, Bz2Codec, Codec, GzipCodec, Lz4Codec, LzmaCodec, VLenUtf8Codec, ZlibCodec

S3 method for custom bracket assignment

Description

S3 method for custom bracket assignment

Usage

## S3 replacement method for class 'ZarrArray'
obj[...] <- value

Arguments

obj

Object.

...

Dots.

value

Array or ZarrArray.

S3 method for custom bracket subsetting

Description

S3 method for custom bracket subsetting

Usage

## S3 method for class 'ZarrArray'
obj[...]

Arguments

obj

Object.

...

Dots.

S3 method for as.array

Description

S3 method for as.array

Usage

## S3 method for class 'NestedArray'
as.array(x, ...)

Arguments

x

Object.

...

Not used.

S3 method for as.array

Description

S3 method for as.array

Usage

## S3 method for class 'ZarrArray'
as.array(x, ...)

Arguments

x

Object.

...

Not used.

Convert a value to a scalar to opt-out of R default vector casting behavior. This uses the jsonlite::unbox function to "tag" the value as a scalar.

Description

Convert a value to a scalar to opt-out of R default vector casting behavior. This uses the jsonlite::unbox function to "tag" the value as a scalar.

Usage

as_scalar(obj)

Arguments

obj

The value to convert.

Value

The value wrapped as a scalar.

Fill in an R array with a single scalar value.

Description

Fill in an R array with a single scalar value.

Usage

chunk_fill(chunk, value)

Arguments

chunk

The R array to fill.

value

The scalar value (after is_scalar() check).

Compute Size

Description

Compute Size

Usage

compute_size(shape)

Arguments

shape

A shape vector

Value

The product of shape elements.

Create a V3 array metadata list. Parallel to create_zarray_meta() for V2. Builds the zarr.json metadata for a V3 array node. All scalar values are wrapped with jsonlite::unbox() so the result can be encoded with toJSON(auto_unbox = FALSE).

Description

Create a V3 array metadata list. Parallel to create_zarray_meta() for V2. Builds the zarr.json metadata for a V3 array node. All scalar values are wrapped with jsonlite::unbox() so the result can be encoded with toJSON(auto_unbox = FALSE).

Usage

create_v3_array_meta(
  shape,
  chunks,
  dtype,
  compressor,
  fill_value,
  order,
  filters,
  chunk_key_encoding = NULL,
  attributes = NULL,
  dimension_names = NULL
)

Arguments

shape

Integer vector. Array shape.

chunks

Integer vector. Chunk shape.

dtype

Character. V2-style dtype string (e.g., "<f8", "|b1").

compressor

Codec object or NA.

fill_value

Fill value (numeric, logical, or NA).

order

Character. "C" or "F" (unused in V3 codec pipeline but stored).

filters

List of Codec objects or NA.

chunk_key_encoding

List or NULL. If NULL, defaults to default "/" encoding.

attributes

List or NULL. Embedded attributes. Default empty.

dimension_names

Character vector or NULL. Omitted from zarr.json if NULL.

Value

A list ready for jsonlite::toJSON encoding.

Create a list of zarray metadata.

Description

Create a list of zarray metadata.

Usage

create_zarray_meta(
  shape = NA,
  chunks = NA,
  dtype = NA,
  compressor = NA,
  fill_value = NA,
  order = NA,
  filters = NA,
  dimension_separator = NA
)

Arguments

shape

: int or tuple of ints Array shape.

chunks

: int or tuple of ints, optional Chunk shape. If True, will be guessed from shape and dtype. If False, will be set to shape, i.e., single chunk for the whole array. If an int, the chunk size in each dimension will be given by the value of chunks. Default is True.

dtype

: string or dtype, optional NumPy dtype.

compressor

: Codec, optional Primary compressor.

fill_value

: object Default value to use for uninitialized portions of the array.

order

: 'C', 'F', optional Memory layout to be used within each chunk.

filters

: sequence, optional Sequence of filters to use to encode chunk data prior to compression.

dimension_separator

: '.', '/', optional Separator placed between the dimensions of a chunk.

Value

A list.

Encode a fill_value for V3 zarr.json. V3 requires special float values as JSON strings: NaN, Infinity, -Infinity. Normal numeric values are returned as unboxed scalars.

Description

Encode a fill_value for V3 zarr.json. V3 requires special float values as JSON strings: NaN, Infinity, -Infinity. Normal numeric values are returned as unboxed scalars.

Usage

decode_fill_value_v3(fill_value)

Arguments

fill_value

The fill value to encode.

Value

A value suitable for inclusion in a jsonlite::toJSON call.

Ensure that scalars and lists of integers are converted to an R vector of integers.

Description

Ensure that scalars and lists of integers are converted to an R vector of integers.

Usage

ensure_integer_vec(selection)

Ensure that scalars, single slices, and R integer vectors are converted to a list containing either R integer vectors or slice instances as values.

Description

Ensure that scalars, single slices, and R integer vectors are converted to a list containing either R integer vectors or slice instances as values.

Usage

ensure_list(selection)

Get a codec instance from the registry.

Description

Get a codec instance from the registry.

Usage

get_codec(config)

Arguments

config

A codec config as a named list.

Value

The instance of the codec.

Get the default compressor.

Description

Get the default compressor.

Usage

get_default_compressor()

Value

A Zstd compressor instance.

Generate a product of lists.

Description

Generate a product of lists.

Usage

get_list_product(dim_indexer_iterables)

Arguments

dim_indexer_iterables

A list of lists.

Value

A list of lists.

get parallel settings

Description

given information about user preferences and environment conditions, returns a function and cluster object.

Usage

get_parallel_settings(
  on_windows = (.Platform$OS.type == "windows"),
  parallel_option = getOption("pizzarr.parallel_backend", NA),
  progress = getOption("pizzarr.progress_bar", FALSE)
)

Arguments

on_windows

Logical indicating if windows restrictions should apply.

parallel_option

Integer, or "future" to control how parallelization occurs.

progress

Logical to control whether pbapply is used such that progress is printed.

Value

list containing the function to use in parallel operations, a cluster object to be used in parallel operations, and whether or not the cluster object needs to be closed.

Check if the bit64 package is available

Description

Check if the bit64 package is available

Usage

has_bit64()

Value

Logical.

Initialize an array store with the given configuration. Note that this is a low-level function and there should be no need to call this directly from user code.

Description

Initialize an array store with the given configuration. Note that this is a low-level function and there should be no need to call this directly from user code.

Usage

init_array(
  store,
  shape,
  chunks = TRUE,
  dtype = NA,
  compressor = NA,
  fill_value = NA,
  order = NA,
  overwrite = FALSE,
  path = NA,
  chunk_store = NA,
  filters = NA,
  object_codec = NA,
  dimension_separator = NA,
  zarr_format = 2L
)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

shape

: int or tuple of ints Array shape.

chunks

: bool, int or tuple of ints, optional Chunk shape. If True, will be guessed from shape and dtype. If False, will be set to shape, i.e., single chunk for the whole array.

dtype

: string or dtype, optional NumPy dtype.

compressor

: Codec, optional Primary compressor.

fill_value

: object Default value to use for uninitialized portions of the array.

order

: 'C', 'F', optional Memory layout to be used within each chunk.

overwrite

: bool, optional If True, erase all data in store prior to initialisation.

path

: string, bytes, optional Path under which array is stored.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

filters

: sequence, optional Sequence of filters to use to encode chunk data prior to compression.

object_codec

: Codec, optional A codec to encode object arrays, only needed if dtype=object.

dimension_separator

: '.', '/', optional Separator placed between the dimensions of a chunk.

Initialize a group store. Note that this is a low-level function and there should be no need to call this directly from user code.

Description

Initialize a group store. Note that this is a low-level function and there should be no need to call this directly from user code.

Usage

init_group(
  store,
  overwrite = FALSE,
  path = NA,
  chunk_store = NA,
  zarr_format = 2L
)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

overwrite

: bool, optional If True, erase all data in store prior to initialisation.

path

: string, bytes, optional Path under which array is stored.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

Convenience function for the internal Int class constructor.

Description

Convenience function for the internal Int class constructor.

Usage

int(index, zero_based = FALSE)

Arguments

index

The integer index.

zero_based

The index of the dimension. By default, FALSE for R-like behavior.

Value

A Int instance with the specified parameters.

Convert integer64 vector to raw bytes

Description

Convert integer64 vector to raw bytes

Usage

integer64_to_raw(x, endian = "little")

Arguments

x

A bit64::integer64 vector.

endian

"little" or "big".

Value

A raw vector.

Check that a value is boolean with length 1

Description

Check that a value is boolean with length 1

Usage

is_bool(s)

Check that a value is a list of one or more boolean

Description

Check that a value is a list of one or more boolean

Usage

is_bool_list(s)

Check that a value is a vector of one or more boolean

Description

Check that a value is a vector of one or more boolean

Usage

is_bool_vec(s)

Check if a dtype represents a 64-bit integer type

Description

Check if a dtype represents a 64-bit integer type

Usage

is_int64_dtype(dtype_obj)

Arguments

dtype_obj

A Dtype instance.

Value

Logical.

Check if a value is an integer R vector or scalar.

Description

Check if a value is an integer R vector or scalar.

Usage

is_integer(s)

Check that a value is a list of one or more integers.

Description

Check that a value is a list of one or more integers.

Usage

is_integer_list(s)

Check if a value is both a scalar (tagged by as_scalar) and an integer.

Description

Check if a value is both a scalar (tagged by as_scalar) and an integer.

Usage

is_integer_scalar(s)

Check that a value is a vector of one or more integers and has not been explicitly tagged as a scalar.

Description

Check that a value is a vector of one or more integers and has not been explicitly tagged as a scalar.

Usage

is_integer_vec(s)

Check if an error is a KeyError.

Description

Check if an error is a KeyError.

Usage

is_key_error(e)

Arguments

e

The error to check.

Value

TRUE if the error is a KeyError, FALSE otherwise.

Check if a value, potentially a vector, is NA

Description

Check if a value, potentially a vector, is NA

Usage

is_na(val)

Arguments

val

The value to check

Value

Whether the value is NA

Check if a value is a scalar (i.e., a one-element vector that was converted with as_scalar).

Description

Check if a value is a scalar (i.e., a one-element vector that was converted with as_scalar).

Usage

is_scalar(s)

Arguments

s

The value to check.

Value

TRUE if the value is a scalar, FALSE otherwise.

Check if a value is a Slice instance.

Description

Check if a value is a Slice instance.

Usage

is_slice(s)

Arguments

s

The value to check.

Value

TRUE if the value is a Slice instance, FALSE otherwise.

Create an empty named list

Description

A helper function to construct an empty list which converts to a JSON object rather than a JSON array.

Usage

obj_list(...)

Arguments

...

A variable number of list entries.

Value

A named list.

Examples

default_window <- obj_list(
  min = 0,
  max = 255
)

pizzarr_option_defaults

Description

Usage

pizzarr_option_defaults

Format

An object of class list of length 4.

pizzarr demo data

Description

pizzarr demo data

Usage

pizzarr_sample(
  dataset = NULL,
  outdir = file.path(tools::R_user_dir("pizzarr"), "pizzarr_sample")
)

Arguments

dataset

character defining which demo dataset is desired, If NULL, all are returned

outdir

character directory path to store sample zarr stores

Details

For directory stores, unzips the store to a temporary directory and returns the resulting path.

Value

path to ready to use zarr store

Examples



sample_dir <- tools::R_user_dir("pizzarr")

clean <- !dir.exists(sample_dir)

zarr_samples <- pizzarr_sample(outdir = sample_dir)

#printing without system path for example
gsub(sample_dir, "...", zarr_samples, fixed = TRUE)

# clean up if you don't want to keep them for next time
if(clean) unlink(sample_dir, recursive = TRUE)

Convert raw bytes to double from int64 (fallback when bit64 unavailable)

Description

Convert raw bytes to double from int64 (fallback when bit64 unavailable)

Usage

raw_to_double_from_int64(buf, n, endian = "little", signed = TRUE)

Arguments

buf

Raw vector of 8-byte integers.

n

Number of elements to read.

endian

"little" or "big".

signed

Logical; if TRUE, treat as signed int64.

Value

A double vector (precision loss possible for values > 2^53).

Convert raw bytes to integer64 vector

Description

Convert raw bytes to integer64 vector

Usage

raw_to_integer64(buf, n, endian = "little")

Arguments

buf

Raw vector of 8-byte little-endian integers.

n

Number of elements to read.

endian

"little" or "big".

Value

A bit64::integer64 vector.

Convert user selections, potentially containing "...", to a list of slices that can be used internally.

Description

Convert user selections, potentially containing "...", to a list of slices that can be used internally.

Usage

replace_ellipsis(selection, shape)

Arguments

selection

The user-provided selection list.

shape

The shape of the array, to be used to fill in ellipsis values.

Value

A list of selections with ellipsis values converted to NA.

Convenience function for the internal Slice R6 class constructor.

Description

Convenience function for the internal Slice R6 class constructor.

Usage

slice(start, stop = NA, step = NA, zero_based = FALSE)

Arguments

start

The start index.

stop

The stop index.

step

The step size. Negative values reverse the direction of the slice, matching Python/NumPy semantics (e.g., step = -1 iterates backward from start toward stop).

zero_based

The index of the dimension. By default, FALSE for R-like behavior.

Value

A Slice instance with the specified parameters.

Examples

g <- zarr_volcano()
v <- g$get_item("volcano")

# Reverse the first 5 columns of row 1 (zero-based: 5:0:-1)
v$get_orthogonal_selection(list(zb_slice(0, 1), zb_slice(5, 0, -1)))

# Full reverse of row 1 (zero-based: -1::-1)
v$get_orthogonal_selection(list(zb_slice(0, 1), zb_slice(-1, NA, -1)))

Convert a string into a character vector.

Description

Convert a string into a character vector.

Usage

str_to_vec(s)

Arguments

s

The string.

Value

A vector where each element is an individual character.

Create an empty array

Description

Create an empty array

Usage

zarr_create(
  shape,
  chunks = TRUE,
  dtype = NA,
  compressor = NA,
  fill_value = NA,
  order = NA,
  store = NA,
  synchronizer = NA,
  overwrite = FALSE,
  path = NA,
  chunk_store = NA,
  filters = NA,
  cache_metadata = TRUE,
  cache_attrs = TRUE,
  read_only = FALSE,
  object_codec = NA,
  dimension_separator = NA,
  write_empty_chunks = TRUE,
  zarr_format = 2L
)

Arguments

shape

: int or tuple of ints Array shape.

chunks

: int or tuple of ints, optional Chunk shape. If True, will be guessed from shape and dtype. If False, will be set to shape, i.e., single chunk for the whole array. If an int, the chunk size in each dimension will be given by the value of chunks. Default is True.

dtype

: string or dtype, optional NumPy dtype.

compressor

: Codec, optional Primary compressor.

fill_value

: object Default value to use for uninitialized portions of the array.

order

: 'C', 'F', optional Memory layout to be used within each chunk.

store

: Store A mapping that supports string keys and bytes-like values.

synchronizer

: object, optional Array synchronizer.

overwrite

: bool, optional If True, erase all data in store prior to initialisation.

path

: string, bytes, optional Path under which array is stored.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

filters

: sequence, optional Sequence of filters to use to encode chunk data prior to compression.

cache_metadata

: bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded prior to all data access and modification operations (may incur overhead depending on storage and data access pattern).

cache_attrs

: bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.

read_only

: bool, optional True if array should be protected against modification.

object_codec

: Codec, optional A codec to encode object arrays, only needed if dtype=object.

dimension_separator

: '.', '/', optional Separator placed between the dimensions of a chunk.

write_empty_chunks

: bool, optional If True (default), all chunks will be stored regardless of their contents. If False, each chunk is compared to the array's fill value prior to storing. If a chunk is uniformly equal to the fill value, then that chunk is not be stored, and the store entry for that chunk's key is deleted. This setting enables sparser storage, as only chunks with non-fill-value data are stored, at the expense of overhead associated with checking the data of each chunk.

zarr_format

: int, optional Zarr format version. Use 2L (default) for Zarr V2 or 3L for Zarr V3.

Value

ZarrArray

Create an array initialized with data.

Description

Create an array initialized with data.

Usage

zarr_create_array(data, ...)

Arguments

data

A base R array() or pizzarr NestedArray instance.

...

The params of zarr_create()

Value

ZarrArray

Create an array filled with NAs.

Description

Create an array filled with NAs.

Usage

zarr_create_empty(shape, ...)

Arguments

shape

: int or tuple of ints Array shape.

...

The params of zarr_create()

Value

ZarrArray

Create a group.

Description

Create a group.

Usage

zarr_create_group(
  store = NA,
  overwrite = FALSE,
  chunk_store = NA,
  cache_attrs = TRUE,
  synchronizer = NA,
  path = NA,
  zarr_format = 2L
)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

overwrite

: bool, optional If True, erase all data in store prior to initialisation.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

cache_attrs

: bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.

synchronizer

: object, optional Array synchronizer.

path

: string, bytes, optional Path under which array is stored.

zarr_format

: int, optional Zarr format version. Use 2L (default) for Zarr V2 or 3L for Zarr V3.

Value

ZarrGroup

Create an array filled with zeros.

Description

Create an array filled with zeros.

Usage

zarr_create_zeros(shape, ...)

Arguments

shape

: int or tuple of ints Array shape.

...

The params of zarr_create()

Value

ZarrArray

Convenience function to open a group or array using file-mode-like semantics.

Description

Convenience function to open a group or array using file-mode-like semantics.

Usage

zarr_open(store = NA, mode = NA, path = NA, ...)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

mode

: 'r', 'r+', 'a', 'w', 'w-', optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't exist); 'w' means create (overwrite if exists); 'w-' means create (fail if exists).

path

: string, bytes, optional Path under which array is stored.

...

Additional arguments to pass to zarr_open_array or zarr_open_group.

Value

ZarrArray or ZarrGroup

Open an array using file-mode-like semantics.

Description

Open an array using file-mode-like semantics.

Usage

zarr_open_array(
  store = NA,
  storage_options = NA,
  mode = NA,
  shape = NA,
  chunks = TRUE,
  dtype = NA,
  compressor = NA,
  fill_value = NA,
  order = NA,
  synchronizer = NA,
  overwrite = FALSE,
  path = NA,
  chunk_store = NA,
  filters = NA,
  cache_metadata = TRUE,
  cache_attrs = TRUE,
  object_codec = NA,
  dimension_separator = NA,
  write_empty_chunks = TRUE,
  zarr_format = 2L
)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

storage_options

: dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise.

mode

: 'r', 'r+', 'a', 'w', 'w-', optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't exist); 'w' means create (overwrite if exists); 'w-' means create (fail if exists).

shape

: int or tuple of ints Array shape.

chunks

: bool, int or tuple of ints, optional Chunk shape. If True, will be guessed from shape and dtype. If False, will be set to shape, i.e., single chunk for the whole array.

dtype

: string or dtype, optional NumPy dtype.

compressor

: Codec, optional Primary compressor.

fill_value

: object Default value to use for uninitialized portions of the array.

order

: 'C', 'F', optional Memory layout to be used within each chunk.

synchronizer

: object, optional Array synchronizer.

overwrite

: bool, optional If True, erase all data in store prior to initialisation.

path

: string, bytes, optional Path under which array is stored.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

filters

: sequence, optional Sequence of filters to use to encode chunk data prior to compression.

cache_metadata

: bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded prior to all data access and modification operations (may incur overhead depending on storage and data access pattern).

cache_attrs

: bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.

object_codec

: Codec, optional A codec to encode object arrays, only needed if dtype=object.

dimension_separator

: '.', '/', optional Separator placed between the dimensions of a chunk.

write_empty_chunks

: bool, optional If True (default), all chunks will be stored regardless of their contents. If False, each chunk is compared to the array's fill value prior to storing. If a chunk is uniformly equal to the fill value, then that chunk is not be stored, and the store entry for that chunk's key is deleted. This setting enables sparser storage, as only chunks with non-fill-value data are stored, at the expense of overhead associated with checking the data of each chunk.

zarr_format

: int, optional Zarr format version. Use 2L (default) for Zarr V2 or 3L for Zarr V3.

Value

ZarrArray

Open a group using file-mode-like semantics.

Description

Open a group using file-mode-like semantics.

Usage

zarr_open_group(
  store = NA,
  mode = NA,
  cache_attrs = TRUE,
  synchronizer = NA,
  path = NA,
  chunk_store = NA,
  storage_options = NA,
  zarr_format = 2L
)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

mode

: 'r', 'r+', 'a', 'w', 'w-', optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't exist); 'w' means create (overwrite if exists); 'w-' means create (fail if exists).

cache_attrs

: bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior to all attribute read operations.

synchronizer

: object, optional Array synchronizer.

path

: string, bytes, optional Path under which array is stored.

chunk_store

: Store, optional Separate storage for chunks. If not provided, store will be used for storage of both chunks and metadata.

storage_options

: dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise.

zarr_format

: int, optional Zarr format version. Use 2L (default) for Zarr V2 or 3L for Zarr V3.

Value

ZarrGroup

Convenience function to save a ZarrArray to the local file system.

Description

Convenience function to save a ZarrArray to the local file system.

Usage

zarr_save_array(store, arr, ...)

Arguments

store

: Store A mapping that supports string keys and bytes-like values.

arr

: ZarrArray The array with data to save.

...

Additional arguments to pass to zarr_create_array().

Create a demo Zarr group containing R's volcano dataset

Description

Writes the volcano matrix into a temporary DirectoryStore as a Zarr array named "volcano" and returns the opened group.

Usage

zarr_volcano()

Value

A ZarrGroup containing a single array called "volcano".

Examples

g <- zarr_volcano()
v <- g$get_item("volcano")
image(v$get_item("...")$data, main = "Maunga Whau Volcano")

Convenience function for the internal Int class constructor with zero-based indexing

Description

Convenience function for the internal Int class constructor with zero-based indexing

Usage

zb_int(index)

Arguments

index

integer index

Convenience function for the internal Slice R6 class constructor with zero-based indexing and exclusive stop index.

Description

Convenience function for the internal Slice R6 class constructor with zero-based indexing and exclusive stop index.

Usage

zb_slice(start, stop = NA, step = NA)

Arguments

start

The start index.

stop

The stop index.

step

The step size. Negative values reverse the direction of the slice, matching Python/NumPy semantics (e.g., step = -1 iterates backward from start toward stop).

Value

A Slice instance with the specified parameters.

Examples

# Equivalent to Python's arr[5:0:-1]
zb_slice(5, 0, -1)

# Equivalent to Python's arr[-1::-1] (full reverse)
zb_slice(-1, NA, -1)

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