Array Initialisation

Opening an Existing Array

An existing array can be opened with Array::open (or async_open):

let array_path = "/group/array";
let array = Array::open(store.clone(), array_path)?;
// let array = Array::async_open(store.clone(), array_path).await?;

Note

These methods will open a Zarr V2 or Zarr V3 array. If you only want to open a specific Zarr version, see open_opt and MetadataRetrieveVersion.

Creating a Zarr V3 Array with the ArrayBuilder

Note

The ArrayBuilder only supports Zarr V3 groups.

let array_path = "/group/array";
let array = ArrayBuilder::new(
    vec![8, 8], // array shape
    vec![4, 4], // regular chunk shape
    DataType::Float32,
    f32::NAN,
)
// .bytes_to_bytes_codecs(vec![]) // uncompressed
.bytes_to_bytes_codecs(vec![
    Arc::new(GzipCodec::new(5)?),
])
.dimension_names(["y", "x"].into())
// .attributes(...)
// .storage_transformers(vec![].into())
.build(store.clone(), array_path)?;
array.store_metadata()?;
// array.async_store_metadata().await?;

ArrayBuilder::new supports more advanced initialisation from metadata, explicit extensions, etc. Consult the documentation.

Tip

The Group Initialisation Chapter has tips for creating attributes.

Remember to Store Metadata!

Array metadata must always be stored explicitly, otherwise an array cannot be opened.

Tip

Consider deferring storage of array metadata until after chunks operations are complete. The presence of valid metadata can act as a signal that the data is ready.

Creating a Zarr V3 Sharded Array

The ShardingCodecBuilder is useful for creating an array that uses the sharding_indexed codec.

let mut sharding_codec_builder = ShardingCodecBuilder::new(
    vec![4, 4].try_into()? // inner chunk shape
);
sharding_codec_builder.bytes_to_bytes_codecs(vec![
    Arc::new(codec::GzipCodec::new(5)?),
]);

let array = ArrayBuilder::new(
    ...
)
.array_to_bytes_codec(sharding_codec_builder.build_arc())
.build(store.clone(), array_path)?;
array.store_metadata()?;
// array.async_store_metadata().await?;

Creating a Zarr V3 Array from Metadata

An array can be created from ArrayMetadata instead of an ArrayBuilder if needed.

let json: &str = r#"{
    "zarr_format": 3,
    "node_type": "array",
    ...
}#";

let json: &str = r#"{
    "zarr_format": 3,
    "node_type": "array",
    "shape": [
        10000,
        1000
    ],
    "data_type": "float64",
    "chunk_grid": {
        "name": "regular",
        "configuration": {
        "chunk_shape": [
            1000,
            100
        ]
        }
    },
    "chunk_key_encoding": {
        "name": "default",
        "configuration": {
        "separator": "/"
        }
    },
    "fill_value": "NaN",
    "codecs": [
        {
        "name": "bytes",
        "configuration": {
            "endian": "little"
        }
        },
        {
        "name": "gzip",
        "configuration": {
            "level": 1
        }
        }
    ],
    "attributes": {
        "foo": 42,
        "bar": "apples",
        "baz": [
        1,
        2,
        3,
        4
        ]
    },
    "dimension_names": [
        "rows",
        "columns"
    ]
}"#;

/// Parse the JSON metadata
let array_metadata: ArrayMetadata = serde_json::from_str(json)?;

/// Create the array
let array = Array::new_with_metadata(
    store.clone(),
    "/group/array",
    array_metadata.into(),
)?;
array.store_metadata()?;
// array.async_store_metadata().await?;

Alternatively, ArrayMetadataV3 can be constructed with ArrayMetadataV3::new() and subsequent with_ methods:

/// Specify the array metadata
let array_metadata: ArrayMetadata = ArrayMetadataV3::new(
    serde_json::from_str("[10, 10]"),
    serde_json::from_str(r#"{"name": "regular", "configuration":{"chunk_shape": [5, 5]}}"#)?,
    serde_json::from_str(r#""float32""#)?,
    serde_json::from_str("0.0")?,
    serde_json::from_str(r#"[ { "name": "blosc", "configuration": { "cname": "blosclz", "clevel": 9, "shuffle": "bitshuffle", "typesize": 2, "blocksize": 0 } } ]"#)?,
).with_chunk_key_encoding(
    serde_json::from_str(r#"{"name": "default", "configuration": {"separator": "/"}}"#)?,
).with_attributes(
    serde_json::from_str(r#"{"foo": 42, "bar": "apples", "baz": [1, 2, 3, 4]}"#)?,
).with_dimension_names(
    Some(serde_json::from_str(r#"["y", "x"]"#)?),
)
.into();

/// Create the array
let array = Array::new_with_metadata(
    store.clone(),
    "/group/array",
    array_metadata,
)?;
array.store_metadata()?;
// array.async_store_metadata().await?;

Creating a Zarr V2 Array

The ArrayBuilder does not support Zarr V2 arrays. Instead, they must be built from ArrayMetadataV2.

/// Specify the array metadata
let array_metadata: ArrayMetadata = ArrayMetadataV2::new(
    vec![10, 10], // array shape
    vec![5, 5].try_into()?, // regular chunk shape
    ">f4".into(), // big endian float32
    FillValueMetadataV2::NaN, // fill value
    None, // compressor
    None, // filters
)
.with_dimension_separator(ChunkKeySeparator::Slash)
.with_order(ArrayMetadataV2Order::F)
.with_attributes(attributes.clone())
.into();

/// Create the array
let array = Array::new_with_metadata(
    store.clone(),
    "/group/array",
    array_metadata,
)?;
array.store_metadata()?;
// array.async_store_metadata().await?;

Warning

Array::new_with_metadata can fail if Zarr V2 metadata is unsupported by zarrs.

Mutating Array Metadata

The shape, dimension names, attributes, and additional fields of an array are mutable.

• Array::set_shape
• Array::set_dimension_names
• Array::attributes_mut
• Array::additional_fields_mut

Don’t forget to write the metadata after mutating array metadata!

The next chapters detail the reading and writing of array data.