ZarrArray Class

Instantiate an array from an initialized store.

Value

A subset of the array, as a NestedArray instance.

Details

The Zarr Array class.

Methods

Public methods

• ZarrArray$new()

• ZarrArray$get_store()

• ZarrArray$get_path()

• ZarrArray$get_name()

• ZarrArray$get_basename()

• ZarrArray$get_read_only()

• ZarrArray$set_read_only()

• ZarrArray$get_chunk_store()

• ZarrArray$get_shape()

• ZarrArray$set_shape()

• ZarrArray$resize()

• ZarrArray$get_chunks()

• ZarrArray$get_dtype()

• ZarrArray$get_compressor()

• ZarrArray$get_fill_value()

• ZarrArray$set_fill_value()

• ZarrArray$get_order()

• ZarrArray$get_filters()

• ZarrArray$get_synchronizer()

• ZarrArray$get_attrs()

• ZarrArray$get_ndim()

• ZarrArray$get_size()

• ZarrArray$get_itemsize()

• ZarrArray$get_nbytes()

• ZarrArray$get_nbytes_stored()

• ZarrArray$get_cdata_shape()

• ZarrArray$get_nchunks()

• ZarrArray$get_nchunks_initialized()

• ZarrArray$get_is_view()

• ZarrArray$get_oindex()

• ZarrArray$get_vindex()

• ZarrArray$get_write_empty_chunks()

• ZarrArray$equals()

• ZarrArray$islice()

• ZarrArray$length()

• ZarrArray$get_item()

• ZarrArray$get_basic_selection()

• ZarrArray$get_orthogonal_selection()

• ZarrArray$get_coordinate_selection()

• ZarrArray$get_mask_selection()

• ZarrArray$set_item()

• ZarrArray$set_basic_selection()

• ZarrArray$set_orthogonal_selection()

• ZarrArray$set_coordinate_selection()

• ZarrArray$set_mask_selection()

• ZarrArray$get_info()

• ZarrArray$get_digest()

• ZarrArray$get_hexdigest()

• ZarrArray$append()

• ZarrArray$view()

• ZarrArray$astype()

• ZarrArray$get_dimension_separator()

• ZarrArray$[()

• ZarrArray$[<-()

• ZarrArray$as.array()

• ZarrArray$clone()

---

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

Array store already initialized.

path

character path

read_only

logical read only?

chunk_store

TODO

synchronizer

TODO

cache_metadata

logical cache metadata?

cache_attrs

logical cache attributes?

write_empty_chunks

logical write empty chunks?

Returns

An Array instance.

---

Method get_store()

get store from array.

Usage

ZarrArray$get_store()

---

Method get_path()

get array path

Usage

ZarrArray$get_path()

---

Method get_name()

get full array name

Usage

ZarrArray$get_name()

---

Method get_basename()

get the basename of an array

Usage

ZarrArray$get_basename()

---

Method get_read_only()

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

Usage

ZarrArray$get_read_only()

---

Method set_read_only()

set the read only property of an array

Usage

ZarrArray$set_read_only(val)

Arguments

val

value to set

---

Method get_chunk_store()

get the chunk store for an array

Usage

ZarrArray$get_chunk_store()

---

Method get_shape()

get the shape of an array

Usage

ZarrArray$get_shape()

---

Method set_shape()

set or reset the size of an array

Usage

ZarrArray$set_shape(value)

Arguments

value

numeric size to set

---

Method resize()

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

Usage

ZarrArray$resize(...)

Arguments

...

arguments for do.call

---

Method get_chunks()

get the chunk metadata of an array

Usage

ZarrArray$get_chunks()

---

Method get_dtype()

get the Dtype of an array

Usage

ZarrArray$get_dtype()

---

Method get_compressor()

get the compressor of an array

Usage

ZarrArray$get_compressor()

---

Method get_fill_value()

get the fill value of an array

Usage

ZarrArray$get_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

---

Method get_order()

get the storage order metadata of an array.

Usage

ZarrArray$get_order()

---

Method get_filters()

get the filters metadata of an array

Usage

ZarrArray$get_filters()

---

Method get_synchronizer()

get the synchronizer of an array TODO: not implemented

Usage

ZarrArray$get_synchronizer()

---

Method get_attrs()

get attributes of array

Usage

ZarrArray$get_attrs()

---

Method get_ndim()

get number of dimensions of array

Usage

ZarrArray$get_ndim()

---

Method get_size()

get size of an array TODO: not implemented

Usage

ZarrArray$get_size()

---

Method get_itemsize()

TODO: not implemented

Usage

ZarrArray$get_itemsize()

---

Method get_nbytes()

get number of bytes of an array

Usage

ZarrArray$get_nbytes()

---

Method get_nbytes_stored()

TODO

Usage

ZarrArray$get_nbytes_stored()

---

Method get_cdata_shape()

TODO

Usage

ZarrArray$get_cdata_shape()

---

Method get_nchunks()

TODO

Usage

ZarrArray$get_nchunks()

---

Method get_nchunks_initialized()

TODO

Usage

ZarrArray$get_nchunks_initialized()

---

Method get_is_view()

get is_view metadata of array

Usage

ZarrArray$get_is_view()

---

Method get_oindex()

get orthogonal index of array

Usage

ZarrArray$get_oindex()

---

Method get_vindex()

get vectorized index of array

Usage

ZarrArray$get_vindex()

---

Method get_write_empty_chunks()

get write empty chunks setting of array

Usage

ZarrArray$get_write_empty_chunks()

---

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

---

Method islice()

TODO

Usage

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

Arguments

start

start of slice

end

end of slice

---

Method length()

TODO

Usage

ZarrArray$length()

---

Method get_item()

Subset the array.

Usage

ZarrArray$get_item(selection)

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

---

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

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

out

TODO

fields

TODO

---

Method get_orthogonal_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

out

TODO

fields

TODO

---

Method get_coordinate_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

out

TODO

fields

TODO

---

Method get_mask_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

out

TODO

fields

TODO

---

Method set_item()

Set a subset of the array.

Usage

ZarrArray$set_item(selection, value)

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

value

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

---

Method set_basic_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

value

TODO

fields

TODO

---

Method set_orthogonal_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

value

TODO

fields

TODO

---

Method set_coordinate_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

value

TODO

fields

TODO

---

Method set_mask_selection()

TODO

Usage

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

Arguments

selection

Selections are lists containing either scalars, strings, or Slice objects. Two character literals are supported: "..." selects all remaining array dimensions and ":" selects all of a specific array dimension.

value

TODO

fields

TODO

---

Method get_info()

TODO

Usage

ZarrArray$get_info()

---

Method get_digest()

TODO

Usage

ZarrArray$get_digest(hashname = "sha1")

Arguments

hashname

name of hash

---

Method get_hexdigest()

TODO

Usage

ZarrArray$get_hexdigest(hashname = "sha1")

Arguments

hashname

name of hash

---

Method append()

TODO

Usage

ZarrArray$append(data, axis = 0)

Arguments

data

data to append

axis

axis to append

---

Method view()

TODO

Usage

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

Arguments

shape

TODO

chunks

TODO

dtype

TODO

fill_value

TODO

filters

TODO

read_only

TODO

synchronizer

TODO

---

Method astype()

TODO

Usage

ZarrArray$astype(dtype)

Arguments

dtype

TODO

---

Method get_dimension_separator()

TODO

Usage

ZarrArray$get_dimension_separator()

---

Method [()

Set values for a selection using bracket notation (for S3 method).

Usage

ZarrArray$[(...)

Arguments

...

Contains the slicing parameters, one for each dimension. Use empty space to get whole dimension e.g. [1:5,,]

Returns

Sliced Zarr object

---

Method [<-()

Assign values for a selection using bracket notation (for S3 method).

Usage

ZarrArray$[<-(...)

Arguments

...

Contains the slicing parameters, one for each dimension. Use empty space to get whole dimension e.g. [1:5,,]

---

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

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.