Skip to contents

ZarrArray Class

Source: R/zarr-array.R
ZarrArray.Rd

Instantiate an array from an initialized store.

Format

R6::R6Class

Details

The Zarr Array class.

Methods

Public methods

ZarrArray$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.

ZarrArray$get_store()

get store from array.

Usage

ZarrArray$get_store()

Returns

Store.

ZarrArray$get_path()

get array path

Usage

ZarrArray$get_path()

Returns

character(1) or NA.

ZarrArray$get_name()

get full array name

Usage

ZarrArray$get_name()

Returns

character(1) or NA.

ZarrArray$get_basename()

get the basename of an array

Usage

ZarrArray$get_basename()

Returns

character(1) or NA.

ZarrArray$get_read_only()

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

Usage

ZarrArray$get_read_only()

Returns

logical(1).

ZarrArray$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).

ZarrArray$get_chunk_store()

get the chunk store for an array

Usage

ZarrArray$get_chunk_store()

Returns

Store.

ZarrArray$get_shape()

get the shape of an array

Usage

ZarrArray$get_shape()

Returns

integer().

ZarrArray$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).

ZarrArray$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).

ZarrArray$get_chunks()

get the chunk metadata of an array

Usage

ZarrArray$get_chunks()

Returns

integer().

ZarrArray$get_dtype()

get the Dtype of an array

Usage

ZarrArray$get_dtype()

Returns

Dtype.

ZarrArray$get_compressor()

get the compressor of an array

Usage

ZarrArray$get_compressor()

Returns

Codec or NA.

ZarrArray$get_fill_value()

get the fill value of an array

Usage

ZarrArray$get_fill_value()

Returns

Scalar fill value.

ZarrArray$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).

ZarrArray$set_dimension_names()

Set dimension names of the array (V3 only).

Usage

ZarrArray$set_dimension_names(names)

Arguments

names

Character vector of length equal to the number of array dimensions, or NULL to clear.

Returns

NULL (called for side effects).

ZarrArray$get_order()

get the storage order metadata of an array.

Usage

ZarrArray$get_order()

Returns

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

ZarrArray$get_filters()

get the filters metadata of an array

Usage

ZarrArray$get_filters()

Returns

list() of Codec objects or NA.

ZarrArray$get_synchronizer()

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

Usage

ZarrArray$get_synchronizer()

Returns

Synchronizer object or NA.

ZarrArray$get_attrs()

get attributes of array

Usage

ZarrArray$get_attrs()

Returns

Attributes.

ZarrArray$get_ndim()

get number of dimensions of array

Usage

ZarrArray$get_ndim()

Returns

integer(1).

ZarrArray$get_dimension_names()

Get dimension names of the array (V3 only).

Usage

ZarrArray$get_dimension_names()

Returns

Character vector or NULL.

ZarrArray$get_size()

Get the total number of elements in the array.

Usage

ZarrArray$get_size()

Returns

numeric(1).

ZarrArray$get_itemsize()

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

Usage

ZarrArray$get_itemsize()

Returns

integer(1).

ZarrArray$get_nbytes()

get number of bytes of an array

Usage

ZarrArray$get_nbytes()

Returns

numeric(1).

ZarrArray$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).

ZarrArray$get_cdata_shape()

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

Usage

ZarrArray$get_cdata_shape()

Returns

numeric().

ZarrArray$get_nchunks()

Get the total number of chunks in the array.

Usage

ZarrArray$get_nchunks()

Returns

integer(1).

ZarrArray$get_nchunks_initialized()

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

Usage

ZarrArray$get_nchunks_initialized()

Returns

integer(1).

ZarrArray$get_is_view()

get is_view metadata of array

Usage

ZarrArray$get_is_view()

Returns

logical(1).

ZarrArray$get_oindex()

get orthogonal index of array

Usage

ZarrArray$get_oindex()

Returns

OIndex.

ZarrArray$get_vindex()

get vectorized index of array

Usage

ZarrArray$get_vindex()

Returns

VIndex.

ZarrArray$get_write_empty_chunks()

get write empty chunks setting of array

Usage

ZarrArray$get_write_empty_chunks()

Returns

logical(1).

ZarrArray$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).

ZarrArray$print()

Print a human-readable summary of the array.

Usage

ZarrArray$print(...)

Arguments

...

Ignored.

Returns

self (invisibly).

ZarrArray$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.

ZarrArray$length()

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

Usage

ZarrArray$length()

Returns

integer(1).

ZarrArray$get_item()

Subset the array.

Usage

ZarrArray$get_item(selection)

Arguments

selection

Selection specifying the subset to retrieve.

Returns

NestedArray.

ZarrArray$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.

ZarrArray$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.

ZarrArray$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.

ZarrArray$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.

ZarrArray$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).

ZarrArray$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).

ZarrArray$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).

ZarrArray$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).

ZarrArray$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).

ZarrArray$get_info()

Get array diagnostic info. Not yet implemented.

Usage

ZarrArray$get_info()

Returns

character(1).

ZarrArray$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).

ZarrArray$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).

ZarrArray$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).

ZarrArray$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.

ZarrArray$astype()

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

Usage

ZarrArray$astype(dtype)

Arguments

dtype

Not yet implemented.

Returns

ZarrArray.

ZarrArray$get_dimension_separator()

Get the dimension separator used in chunk keys.

Usage

ZarrArray$get_dimension_separator()

Returns

character(1).

ZarrArray$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.

ZarrArray$clone()

The objects of this class are cloneable with this method.

Usage

ZarrArray$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.