Zarr object

This class implements a Zarr object. A Zarr object is a set of objects that make up an instance of a Zarr data set, irrespective of where it is located. The Zarr object manages the hierarchy as well as the underlying store.

A Zarr object may contain multiple Zarr arrays in a hierarchy. The main class for managing Zarr arrays is zarr_array. The hierarchy is made up of zarr_group instances. Each zarr_array is located in a zarr_group.

Value

A zarr object.

Active bindings

version

(read-only) The version of the Zarr object.

root

(read-only) The root node of the Zarr object, usually a zarr_group instance but it could also be a zarr_array instance.

store

(read-only) The store of the Zarr object.

groups

(read-only) Retrieve the paths to the groups of the Zarr object, starting from the root group, as a character vector.

arrays

(read-only) Retrieve the paths to the arrays of the Zarr object, starting from the root group, as a character vector.

Methods

Public methods

• zarr$new()

• zarr$print()

• zarr$hierarchy()

• zarr$get_node()

• zarr$add_group()

• zarr$add_array()

• zarr$delete_group()

• zarr$delete_array()

• zarr$clone()

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Method new()

Create a new Zarr instance. The Zarr instance manages the groups and arrays in the Zarr store that it refers to. This instance provides access to all objects in the Zarr store.

Usage

zarr$new(store)

Arguments

store

An instance of a zarr_store descendant class where the Zarr objects are located.

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Method print()

Print a summary of the Zarr object to the console.

Usage

zarr$print()

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Method hierarchy()

Print the Zarr hierarchy to the console.

Usage

zarr$hierarchy()

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Method get_node()

Retrieve the group or array represented by the node located at the path.

Usage

zarr$get_node(path)

Arguments

path

The path to the node to retrieve. Must start with a forward-slash "/".

Returns

The zarr_group or zarr_array instance located at path, or NULL if the path was not found.

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Method add_group()

Add a group below a given path.

Usage

zarr$add_group(path, name)

Arguments

path

The path to the parent group of the new group, a single character string.

name

The name for the new group, a single character string.

Returns

The newly created zarr_group, or NULL if the group could not be created.

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Method add_array()

Add an array in a group with a given path.

Usage

zarr$add_array(path, name, metadata)

Arguments

path

The path to the group of the new array, a single character string.

name

The name for the new array, a single character string.

metadata

A list with the metadata for the new array.

Returns

The newly created zarr_array, or NULL if the array could not be created.

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Method delete_group()

Delete a group from the Zarr object. This will also delete the group from the Zarr store. The root group cannot be deleted but it can be specified through path = "/" in which case the root group loses any specific group metadata (with only the basic parameters remaining), as well as any arrays and sub-groups if recursive = TRUE. Warning: this operation is irreversible for many stores!

Usage

zarr$delete_group(path, recursive = FALSE)

Arguments

path

The path to the group.

recursive

Logical, default FALSE. If FALSE, the operation will fail if the group has any arrays or sub-groups. If TRUE, the group and all Zarr objects contained by it will be deleted.

Returns

Self, invisible.

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Method delete_array()

Delete an array from the Zarr object. If the array is the root of the Zarr object, it will be converted into a regular Zarr object with a root group. Warning: this operation is irreversible for many stores!

Usage

zarr$delete_array(path)

Arguments

path

The path to the array.

Returns

Self, invisible.

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Method clone()

The objects of this class are cloneable with this method.

Usage

zarr$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.