https://github.com/zarr-developers/zarr-java
Java implementation of the Zarr Specification
https://github.com/zarr-developers/zarr-java
Last synced: 21 days ago
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Java implementation of the Zarr Specification
- Host: GitHub
- URL: https://github.com/zarr-developers/zarr-java
- Owner: zarr-developers
- License: mit
- Created: 2023-03-21T11:51:02.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-04-18T11:28:20.000Z (about 1 month ago)
- Last Synced: 2025-04-19T00:52:47.432Z (about 1 month ago)
- Language: Java
- Size: 25.1 MB
- Stars: 9
- Watchers: 14
- Forks: 12
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Early preview of `zarr-java`
This repository contains an early preview of a Java implementation of the Zarr specification.
It is intended for collecting feedback from the community and not for use. The API is subject to changes.
Refer to [JZarr](https://github.com/zarr-developers/jzarr) for a stable implementation of Zarr version 2.
## Usage
```java
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` installed.
Also, you need to set up a venv for zarrita at the root of the project:
`python3.11 -m venv venv_zarrita`.
Then install zarrita there with `venv_zarrita/Scripts/pip install zarrita`
for Windows and `venv_zarrita/bin/pip install zarrita` for Linux.
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
`