Range reads M0/M1 (indexed lookups, Storage trait), ZFP, in-place editing #17

Merged
osobh merged 52 commits from feat/p3-range-zfp-edit into main 2026-09-26 20:42:22 +00:00
4 changed files with 38 additions and 10 deletions
Showing only changes of commit 2b7065998a - Show all commits
+24
View File
@@ -2,6 +2,30 @@
## Unreleased
### ZFP (2026-09-26)
- **ZFP (filter 32013, H5Z-ZFP) reads, in pure Rust.** It was the last
filter in the conformance corpus that failed with `UnsupportedFilter`.
New feature `zfp` (`clawhdf5-format` and `clawhdf5`, included in
`plugin-filters`, no dependencies) ports the zfp 1.0.1 decoder and the
decompression half of H5Z-ZFP 1.1.1: every mode (fixed rate, fixed
precision, fixed accuracy, reversible, expert), int32, int64, float and
double, 1-4-D fields with partial blocks, and headers written by
big-endian machines (values byte-swapped as H5Z-ZFP does). Read only:
there is no ZFP encoder. The decoder is deterministic, so lossy modes have
one right answer, and clawhdf5 returns exactly libzfp's values.
- Tests: `crates/clawhdf5/tests/zfp_interop.rs` has h5py + hdf5plugin 7.1
(H5Z-ZFP 1.1.1, zfp 1.0.1) write 2205 datasets over 16 mode settings
(including expert parameters at their edges) x the four types x 1-4-D
shapes with partial edge chunks, partial blocks and unit chunk
dimensions x smooth, noisy, wide-range, zero and inf/NaN data; each must
read byte for byte as h5py reads it. `tests/zfp_alloc_bounds.rs` fuzzes
headers and streams under a counting allocator: no panics, and the output
is allocated only when it matches the chunk's size and the stream holds at
least a bit per block. A stream that ends before the decoder is done is an
error (libzfp reads past its buffer).
- Conformance on tank (2026-09-26, `conformance/run.sh --no-fetch`): 600 of
697 files ok (599 before); `h5ex_d_zfp.h5` now reads.
### Chunked full reads (2026-09-26)
- **Chunks are decoded straight into the output, into reused buffers.** A
full read of a chunked dataset faulted in about three times its size in
+1 -1
View File
@@ -11,7 +11,7 @@ Cargo workspace with 18 crates under `crates/` (plus `libaec-sys`, an internal F
|-------|------|
| `clawhdf5-format` | HDF5 binary spec parser (superblock, B-tree, heap) — also holds shared type definitions and physical constants |
| `clawhdf5-io` | Read/write implementation |
| `clawhdf5-filters` | Deflate backends (zlib-rs, zlib-ng, Apple Compression); the HDF5 filter pipeline, the filter registry (`clawhdf5_format::filter_registry`) and the other codecs (LZ4, Zstd, SZIP, N-Bit, scale-offset, pcodec, and the pure-Rust plugin filters LZF, bitshuffle, bzip2, Blosc 1, and Blosc2 read-only) live in `clawhdf5-format`. No ZFP. |
| `clawhdf5-filters` | Deflate backends (zlib-rs, zlib-ng, Apple Compression); the HDF5 filter pipeline, the filter registry (`clawhdf5_format::filter_registry`) and the other codecs (LZ4, Zstd, SZIP, N-Bit, scale-offset, pcodec, and the pure-Rust plugin filters LZF, bitshuffle, bzip2, Blosc 1, and Blosc2 and ZFP read-only) live in `clawhdf5-format`. |
| `clawhdf5-derive` | Proc-macro derive for HDF5-serializable structs |
| `clawhdf5` | Main facade crate |
| `clawhdf5-netcdf4` | NetCDF-4 compatibility layer |
+5 -5
View File
@@ -780,14 +780,14 @@ stores keep their setting. Opt out with `float16 = false` or
| `bzip2` | no | bzip2 filter (id 307): read and write. Pure Rust (the `bzip2` crate's libbz2-rs-sys backend compiles no C) |
| `blosc` | no | Blosc 1 filter (id 32001): reads BloscLZ, LZ4/LZ4HC, Snappy, Zlib and Zstandard frames with byte or bit shuffle; writes LZ4, Snappy, Zlib or Zstandard (not BloscLZ). Pure Rust |
| `blosc2` | no | Blosc2 filter (id 32026), read only: hdf5plugin's frames and B2ND (n-D) chunks, BloscLZ, LZ4/LZ4HC, Zlib and Zstandard, with shuffle, bit shuffle, delta or truncated precision. Pure Rust |
| `plugin-filters` | no | All five above |
| `zfp` | no | ZFP filter (id 32013, H5Z-ZFP), read only: every mode (rate, precision, accuracy, reversible, expert) for int32, int64, float and double, 1-4-D, returning exactly libzfp's values. Pure Rust, no dependencies |
| `plugin-filters` | no | All six above |
ZFP (32013) is not implemented: reading it fails with `UnsupportedFilter`,
whose message names the filter. clawhdf5 cannot write Blosc2. Any other
clawhdf5 cannot write Blosc2 or ZFP. Any other
filter can be supplied at run time with `filter_registry::register_filter` (a
decoder closure, or a `FilterCodec` that also encodes). The facade
(`clawhdf5`) forwards `lzf`, `bitshuffle`, `bzip2`, `blosc`, `blosc2` and
`plugin-filters`. Write
(`clawhdf5`) forwards `lzf`, `bitshuffle`, `bzip2`, `blosc`, `blosc2`, `zfp`
and `plugin-filters`. Write
with `DatasetBuilder::with_lzf()`, `with_bitshuffle(..)`, `with_bzip2(..)`
and `with_blosc(..)`; h5py + hdf5plugin read the result (tested both ways in
`crates/clawhdf5/tests/plugin_filters_interop.rs`). The pure-Rust Zstandard
+8 -4
View File
@@ -293,10 +293,14 @@ fill-value item that did is fixed).
697 ok, tank, `conformance/run.sh --no-fetch`). Blosc2 frames using
dictionaries, lazy chunks, variable-length blocks, user-defined codecs or
registered filters (e.g. bytedelta) are refused with an error.
**Still open:** ZFP (32013) fails with an `UnsupportedFilter` error that
names the filter, and can be plugged in with
`filter_registry::register_filter` (32023, Granular BitRound, too, since
2026-09-26 even with the `pcodec` feature). clawhdf5 cannot write Blosc2.
**Fixed 2026-09-26** for ZFP (32013, `zfp` feature, also in
`plugin-filters`), read only: every H5Z-ZFP mode and type, bit-exact
against h5py + hdf5plugin 7.1 (`crates/clawhdf5/tests/zfp_interop.rs`);
h5ex_d_zfp now reads (conformance 600 of 697 ok, tank,
`conformance/run.sh --no-fetch`). **Still open:** clawhdf5 cannot write
Blosc2 or ZFP. Other filters (32023, Granular BitRound, too, since
2026-09-26 even with the `pcodec` feature) can be plugged in with
`filter_registry::register_filter`.
- **Wrong data: a chunk whose filters decode to fewer bytes than the chunk
read with zeros for the missing bytes** (any filter; found reviewing the plugin
filters). **Fixed 2026-09-26:** it is an error naming the chunk. A corrupt