package zarr

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An Ocaml implementation of the Zarr V3 specification

Install 

dune-project
 Dependency

github.com Readme Edit opam file Versions (1)

Authors

  1. Z
    Zolisa Bleki

Maintainers

  1. Z
    Zolisa Bleki

Sources

v0.1.0.tar.gz
md5=df6bb0048a4479632c2867d5259c9b27
sha512=341b9db6910a90bb3663c36ae75afb84324c52980b7c6866809424f40cdcc4490eb1f606f5d2a3b1cc91e54671bb09cfc9feae3d9bb55474a66762658d26860c

doc/zarr/Zarr/index.html

Module ZarrSource

zarr Provides an Ocaml implementation of the Zarr version 3 storage format specification. It supports creation of arrays and groups as well as chunking arrays along any dimension. One can store a Zarr hierarchy in memory or on disk. Zarr also supports reading zarr hierarchies created using other implementations, as long as they are spec-compliant.

Consult the examples and limitations for more info.

References

Node

Sourcemodule Node : sig ... end

This module provides functionality for manipulating Zarr nodes.

Metadata

Sourcemodule Metadata : sig ... end

This module provides functionality for manipulating a Zarr node's metadata JSON document.

Storage

module Storage : sig ... end

A Zarr store is a system that can be used to store and retrieve data from a Zarr hierarchy. For a store to be compatible with this specification, it must support a set of operations defined in the Abstract store interface STORE. The store interface can be implemented using a variety of underlying storage technologies.

module Memory : sig ... end
Sourcemodule Types : sig ... end

Codecs

module Codecs : sig ... end

An array has an associated list of codecs. Each codec specifies a bidirectional transform (an encode transform and a decode transform). This module contains building blocks for creating and working with a chain of codecs.

Indexing

Sourcemodule Indexing = Ndarray.Indexing

Utils

Sourcemodule Util : sig ... end

Ndarray

Sourcemodule Ndarray : sig ... end

Examples

Create, read & write array.

Here we show how the library's asynchronous API using Lwt's concurrency monad can be used.

open Zarr.Metadata
open Zarr.Node
open Zarr.Codecs
open Zarr_lwt.Storage
open FilesystemStore.Deferred.Syntax

let _ =
  Lwt_main.run begin
    let store = FilesystemStore.create "testdata.zarr" in
    let group_node = GroupNode.of_path "/some/group" in
    let* () = FilesystemStore.create_group store group_node in
    let array_node = ArrayNode.(group_node / "name") in
    let* () = FilesystemStore.create_array
      ~codecs:[`Bytes BE] ~shape:[|100; 100; 50|] ~chunks:[|10; 15; 20|]
      Bigarray.Float32 Float.neg_infinity array_node store in
    let slice = Owl_types.[|R [0; 20]; I 10; R []|] in
    let* x = FilesystemStore.read_array store array_node slice Bigarray.Float32 in
    let x' = Owl.Dense.Ndarray.Generic.map (fun _ -> Owl_stats_dist.uniform_rvs 0. 10.) x
    in FilesystemStore.write_array store array_node slice x'
  end

Extension Points

This library also provides custom extensions not defined in the version 3 specification. These are tabulated below:

Extension Point

Details

Data Types

char, complex32, int (63-bit integer), nativeint

Limitations

Although this implementation tries to be spec compliant, it does come with a few limitations:

  • Ocaml does not have support for unsigned integers as array data types and thus this library cannot support reading values of datatypes uint32, uint64 and complex128.