N5

A (mostly pure) rust implementation of the N5 "Not HDF5" n-dimensional tensor file system storage format created by the Saalfeld lab at Janelia Research Campus.

Compatible with Java N5 Version 2.0.2.

Differences from Java N5

• Dataset paths are relative. The root path in a dataset is "", not "/".
• Dataset paths are more strict. Calling methods with paths outside the dataset, e.g., "..", will return a Result::Err.

Quick start

toml [dependencies] n5 = "0.2"

```rust extern crate n5;

use n5::{ DatasetAttributes, DataBlock, DataType, N5Reader, N5Writer, VecDataBlock }; use n5::compression::CompressionType; use n5::filesystem::N5Filesystem;

fn n5roundtrip(rootpath: &str) -> std::io::Result<()> { let n = N5Filesystem::openorcreate(root_path)?;

let block_size = vec![44i32, 33, 22];
let data_attrs = DatasetAttributes::new(
    vec![100, 200, 300],
    block_size.clone(),
    DataType::INT16,
    CompressionType::default(),
);
let numel = block_size.iter().product::<i32>() as usize;
let block_data: Vec<i16> = vec![0i16; numel];

let block_in = VecDataBlock::new(
    block_size,
    vec![0, 0, 0],
    block_data.clone());

let path_name = "test/dataset/group";

n.create_dataset(path_name, &data_attrs)?;
n.write_block(path_name, &data_attrs, &block_in)?;

let block_out = n.read_block::<i16>(path_name, &data_attrs, vec![0, 0, 0])?
    .expect("Block is empty");
assert_eq!(block_out.get_data(), &block_data);

Ok(())

}

fn main() { n5_roundtrip("tmp.n5").expect("N5 roundtrip failed!"); } ```

Major TODOs

• Easy import prelude
• Kludge DefaultBlock type
• Generally, direct translation from Java is unidiomatic and a mess of boxes

License

Licensed under either of

• Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.