Crate hidefix

HIDEFIX

A fast and concurrent reader for HDF5 and NetCDF (v4) files.

Currently requires Rust nightly.

This library allows a HDF5 file to be read in a multi-threaded and concurrent way. The chunks of a dataset need to be indexed in advance, this can be time-consuming, but efficient serialization and partially zero-copy deserialization through serde is implemented. In particular by storing the indexes in a fast database, like sled allows speedy access.

This allows multiple datasets (variables) to be read at the same time, or even different domains of the same dataset to be read at the same time.

The library is meant to be used in conjunction with the bindings to the official HDF5 library.

Usage

Create an index, then read the values:

use hidefix::idx::Index;
use hidefix::reader::Reader;

let indx = Index::index("tests/data/coads_climatology.nc4").unwrap();
let mut r = indx.reader("SST").unwrap();

let values = r.values::<f32>(None, None).unwrap();
println!("SST: {:?}", values);

It is also possible to stream the values. The streamer is currently optimized for streaming bytes.

Fast indexing

The indexing can be sped up considerably (about 200x) by adding a new interface to iterating over chunks in HDF5. The fast-index feature flag currently requires a patched version of hdf5-rust and hdf5. See this upstream pull-request. You therefore have to use patch to point the hdf5 and hdf5-sys dependencies to the patched versions for now.

Re-exports

pub use idx::IntoIndex;

Modules

filters
idx
reader