clawhdf5/crates/clawhdf5-format

clawhdf5-format

The HDF5 file format in pure Rust: parsers and writers for every on-disk structure, the filter pipeline and its codecs, and the shared type definitions the other crates use. Most users want the clawhdf5 facade, which wraps this crate in an h5py-like API; use this one directly for low-level access or in no_std code.

Not on crates.io yet; depend on it from git:

[dependencies]
clawhdf5-format = { git = "https://git.redclaw.dev/quantumclaw/clawhdf5" }

What is in it

• Parsing: superblock v0–v3 (superblock, with the superblock extension and metadata cache images, superblock_ext), object headers v1 and v2 (object_header), every header message the readers use (datatype, dataspace, data_layout v1–v4 including virtual datasets, fill_value, attribute, link_message, shared_message, ...), groups old and new (group_v1 symbol tables with local heaps, group_v2 with fractal heaps and v2 B-trees), and every chunk index (v1 B-tree, single chunk, implicit, fixed array, extensible array, v2 B-tree).
• Reading data: data_read (contiguous, compact, chunked), partial_read and selection (hyperslabs and points), vl_data (variable-length strings and sequences through the global heap), chunk_cache.
• Storage: the storage::Storage trait (read_at, read_ranges, len, hint) that every read path goes through, so a file can be read from memory, a file handle or a remote backend (clawhdf5-remote).
• Writing: file_writer::FileWriter and the builders in type_builders (datasets, groups, attributes, compound and enum types, links, virtual datasets, creation-order tracking); chunk indexes and dense-storage B-trees of any size (chunked_write, btree_v2_write, ea_writer, and the version-1 chunk B-tree of btree_v1_write). Output is read by h5py and h5dump; FileWriter::libver_bounds (libver) picks the format: HDF5 1.10 by default, or one HDF5 1.8 reads.
• Filters: filter_pipeline and filter_registry (look up by ID; other IDs can be registered at run time with register_filter). Built in: deflate, shuffle, Fletcher-32, N-Bit, scale-offset; behind features LZ4, Zstd, SZIP (decode), pcodec, and the plugin filters LZF, bitshuffle, bzip2, Blosc 1 (read and write), Blosc2 and ZFP (read only).
• Shared pieces: float16 (the one IEEE half-precision conversion the workspace uses), provenance (SHA-256 dataset hashes), checksum (Jenkins lookup3 for v2+ structures).

Example

use clawhdf5_format::file_writer::{AttrValue, FileWriter};
use clawhdf5_format::{group_v2, object_header, signature, superblock};

// Write a file to memory
let mut fw = FileWriter::new();
fw.create_dataset("data")
    .with_f64_data(&[1.0, 2.0, 3.0])
    .with_shape(&[3])
    .set_attr("unit", AttrValue::String("m/s".into()));
let bytes = fw.finish().unwrap();

// Parse it back: superblock -> path -> object header
let (_user_block, file) = signature::split_user_block(&bytes).unwrap();
let sb = superblock::Superblock::parse(file, 0).unwrap();
let addr = group_v2::resolve_path_any(file, &sb, "data").unwrap();
let hdr = object_header::ObjectHeader::parse(file, addr as usize, sb.offset_size, sb.length_size)
    .unwrap();
assert!(!hdr.messages.is_empty());

Features

Feature	Default	What	Builds C
std	yes	standard library; without it the crate is no_std + alloc (CI builds it for thumbv7em-none-eabihf)	no
checksum	yes	verify Jenkins lookup3 checksums	no
deflate	yes	deflate through flate2	no
zlib-rs	yes	flate2's pure-Rust zlib-rs backend, with runtime_detection (without it zlib-rs loses SIMD and inflates 3.5x slower)	no
system-zlib-decompress	yes	macOS only: inflate with the system libz first, falling back to flate2; no effect elsewhere	no (links the system libz on macOS)
provenance	yes	SHA-256 provenance hashes	no
lzf	yes	LZF (32000)	no
parallel	no	rayon-parallel chunk decoding	no
fast-checksum	no	hardware CRC32 through crc32fast	no
lz4	no	LZ4 (32004)	no
pcodec	no	pcodec	no
bitshuffle, bzip2, blosc	no	32008, 307, 32001, read and write	no
blosc2, zfp	no	32026, 32013, read only	no
plugin-filters	no	all six plugin filters above	no
lookup-stats	no	counters for name-lookup benchmarks	no
zstd	no	Zstandard (32015)	yes (libzstd)
szip	no	SZIP (4) decoding	links the system libaec (libaec-dev)
fast-deflate	no	zlib-ng	yes (cmake)
system-zlib	no	the system zlib	yes (libz-sys)
blake3_hash	no	provenance::blake3_hash	yes (cc)

Robustness

Every parser is meant to return an error, never panic, on hostile input: nine cargo-fuzz targets live in fuzz/, the conformance sweep includes the HDF Group's CVE corpus (CONFORMANCE.md), and header checks follow libhdf5's. Open gaps are in docs/known-issues.md.

License

MIT