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docs/v3/core/v3.0.rst

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@@ -55,35 +55,34 @@ Introduction
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This specification defines a format for multidimensional array data. This
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type of data is common in scientific and numerical computing
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applications. Many domains are facing computational challenges as
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applications. Many domains face computational challenges as
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increasingly large volumes of data are being generated, for example,
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via high resolution microscopy, remote sensing imagery, genome
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sequencing or numerical simulation. The primary motivation for the
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development of Zarr has been to help address this challenge by
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development of Zarr is to address this challenge by
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enabling the storage of large multidimensional arrays in a way that is
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compatible with parallel and/or distributed computing applications.
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This specification is intended to supersede the `Zarr storage
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This specification supersedes the `Zarr storage
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specification version 2
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<https://zarr.readthedocs.io/en/stable/spec/v2.html>`_ (Zarr v2). The
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Zarr v2 specification has been implemented in several programming
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languages and has been used successfully to store and analyse large
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scientific datasets from a variety of domains. However, as experience
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has been gained, it has become clear that there are several
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opportunities for modest but useful improvements to be made in the
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format, and for establishing a foundation that allows for greater
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interoperability, whilst also enabling a variety of more advanced and
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specialised features to be explored and developed.
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Zarr v2 specification is implemented in several programming
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languages and is used to store and analyse large
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scientific datasets from a variety of domains. However, it has become
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clear that there are several opportunities for modest but useful
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improvements to be made in the format, and for establishing a foundation
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that allows for greater interoperability, whilst also enabling a variety
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of more advanced and specialised features to be explored and developed.
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This specification also draws heavily on the `N5 API and
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file-system specification <https://github.com/saalfeldlab/n5>`_, which
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was developed in parallel to Zarr v2 and has many of the same design
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was developed in parallel to Zarr v2 with similar
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goals and features. This specification defines a core set of features
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at the intersection of both Zarr v2 and N5, and so aims to provide a
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common target that can be fully implemented across multiple
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programming environments and serve a wide range of applications.
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In particular, we highlight the following areas motivating the
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We highlight the following areas motivating the
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development of this specification.
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Extensibility
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This core specification adheres to a ``MAJOR.MINOR`` version
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number format. When incrementing the minor version, only additional features
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can be added. Breaking changes require to increment the major version.
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can be added. Breaking changes require incrementing the major version.
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A zarr implementation that provides the read and write API by
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implementing a specification ``X.Y`` can be considered compatible with all
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example, if an array_ has 2 dimensions_, where the length of the
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first dimension_ is 100 and the length of the second dimension_ is
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20, then the shape of the array_ is (100, 20). A shape can be the empty
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tuple in the case of zero-dimension arrays (scalar)
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tuple in the case of zero-dimension arrays (scalars).
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.. _element:
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.. _elements:
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*Element*
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An array_ contains zero or more elements. Each element can be
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An array_ contains zero or more elements. Each element is
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identified by a tuple of integer coordinates, one for each
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dimension_ of the array_. If all dimensions_ of an array_ have
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finite length, then the number of elements in the array_ is given
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within the chunk) is the product of its interval lengths.
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The chunk shape elements are non-zero when the corresponding dimensions of
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the arrays are of non-zero length.
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the arrays have non-zero length.
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.. _grid:
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.. _grids:
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.. note::
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Currently only fixed size elements are supported as a core data type.
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There are many request for variable length element encoding. There are many
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There are many requests for variable length element encoding. There are many
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ways to encode variable length and we want to keep flexibility. While we seem
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to agree that for random access the most likely contender is to have two
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arrays, one with the actual variable length data and one with fixed size
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Storage transformers
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====================
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A Zarr storage transformer allows changing the zarr-compatible data before storing it.
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A Zarr storage transformer modifies a request to read or write data before passing
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that request to the following transformer or store.
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The stored transformed data is restored to its original state whenever data is requested
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by the Array. Storage transformers can be configured per array via the
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`storage_transformers <storage_transformers_>`_ name in the `array metadata`_. Storage transformers which do
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Resizing
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--------
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In general, arrays can be resized for writable (and if necessary deletable)
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stores. In the most basic case, two scenarios can be considered, shrinking along
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In general, arrays can be resized for writable (and, if necessary, deletable)
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stores. In the most basic case, two scenarios can be considered: shrinking along
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an array dimension, or increasing its size.
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When shrinking, implementations can consider whether to delete chunks if the

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