GitHub - zarr-developers/zarr-java: Java implementation of the Zarr Specification

This repository contains a Java implementation of Zarr version 2 and 3.

Documentation

For comprehensive documentation, see the User Guide, which includes:

Installation instructions
Quick start examples
Core concepts and API reference
Working with arrays and groups
Storage backends (Filesystem, HTTP, S3, ZIP, Memory)
Compression and codecs
Best practices
Troubleshooting

Quick Usage Example

import dev.zarr.zarrjava.store.FilesystemStore;
import dev.zarr.zarrjava.store.HttpStore;
import dev.zarr.zarrjava.v3.Array;
import dev.zarr.zarrjava.v3.DataType;
import dev.zarr.zarrjava.v3.Group;

Group hierarchy = Group.open(
        new HttpStore("https://static.webknossos.org/data/zarr_v3")
                .resolve("l4_sample")
);
Group color = (Group) hierarchy.get("color");
Array array = (Array) color.get("1");
ucar.ma2.Array outArray = array.read(
        new long[]{0, 3073, 3073, 513}, // offset
        new int[]{1, 64, 64, 64} // shape
);

Array array = Array.create(
        new FilesystemStore("/path/to/zarr").resolve("array"),
        Array.metadataBuilder()
                .withShape(1, 4096, 4096, 1536)
                .withDataType(DataType.UINT32)
                .withChunkShape(1, 1024, 1024, 1024)
                .withFillValue(0)
                .withCodecs(c -> c.withSharding(new int[]{1, 32, 32, 32}, c1 -> c1.withBlosc()))
                .build()
);
ucar.ma2.Array data = ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{1, 1024, 1024, 1024});
array.

write(
    new long[] {
    0, 0, 0, 0
}, // offset
data
);

Development Start-Guide

Run Tests Locally

To be able to run the tests locally, make sure to have python3.11 and uv installed.

Furthermore, you will need the l4_sample test data:

curl https://static.webknossos.org/data/zarr_v3/l4_sample.zip -o testdata/l4_sample.zip && cd testdata && unzip l4_sample.zip

Code Style & Formatting

This project uses IntelliJ IDEA default Java formatting

Before submitting changes, please run:

IntelliJ: Reformat Code and Optimize Imports