feat(format): Blosc filter (32001), read and write, pure Rust

hdf5plugin's Blosc (hdf5-blosc) failed with UnsupportedFilter(32001). The
new `blosc` feature decodes the Blosc 1 frame c-blosc 1.x writes: the
16-byte header, raw ("memcpyed") frames, the block table, blocks split
into one stream per byte plane (and the "do not split" flag), streams
stored raw, the byte shuffle and bit shuffle (whole 8-element groups, the
rest copied) - and every codec hdf5plugin offers: BloscLZ (implemented
here from c-blosc 1.21's blosclz_decompress, including its rejection of
malformed and truncated streams), LZ4/LZ4HC (lz4_flex), Snappy (snap),
Zlib (flate2) and Zstandard (ruzstd). Every stream must decode to exactly
its size and the frame to at most the chunk size; a frame of another
format version (Blosc 2) is a clear error.

It also encodes (DatasetBuilder::with_blosc(codec, level, shuffle)):
LZ4, Snappy, Zlib or Zstandard, with c-blosc's split rule, raw streams
where compression does not pay, and a stored frame for level 0 or
incompressible data. It cannot write BloscLZ (asking for it is an
error). `plugin-filters` enables LZF, bitshuffle, bzip2 and Blosc.

Interop: hdf5plugin writes all six codecs x {no, byte, bit} shuffle at
levels 5/9/1, plus level 0, over the 12-case matrix, read byte for byte;
our four codecs x four shuffle/level settings read back through
hdf5plugin. Both fail with the decoder removed. `cargo tree` with
`plugin-filters` has no -sys crate other than libbz2-rs-sys (pure Rust),
no cc and no cmake.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
This commit is contained in:
osobh
2026-09-26 00:10:05 -05:00
co-authored by Claude Opus 5.5
parent 6dfd239011
commit 1f71f3bcbc
9 changed files with 758 additions and 6 deletions
+5
View File
@@ -28,6 +28,7 @@ ruzstd = { version = "0.9", optional = true }
# bzip2 with its default backend, libbz2-rs-sys: a pure-Rust port of # bzip2 with its default backend, libbz2-rs-sys: a pure-Rust port of
# libbzip2 (no C is compiled, despite the -sys name). # libbzip2 (no C is compiled, despite the -sys name).
bzip2 = { version = "0.6", optional = true } bzip2 = { version = "0.6", optional = true }
snap = { version = "1", optional = true }
[dev-dependencies] [dev-dependencies]
half = { workspace = true } half = { workspace = true }
@@ -69,6 +70,10 @@ lzf = []
bitshuffle = ["lz4_flex", "ruzstd"] bitshuffle = ["lz4_flex", "ruzstd"]
# bzip2 (307). # bzip2 (307).
bzip2 = ["dep:bzip2", "std"] bzip2 = ["dep:bzip2", "std"]
# Blosc 1 (32001) with its BloscLZ, LZ4, Snappy, Zlib and Zstandard codecs.
blosc = ["lz4_flex", "ruzstd", "snap", "deflate", "std"]
# Every plugin filter above.
plugin-filters = ["lzf", "bitshuffle", "bzip2", "blosc"]
[[bench]] [[bench]]
name = "parallel_decompress_bench" name = "parallel_decompress_bench"
+67 -2
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@@ -12,8 +12,8 @@ use crate::chunk_grid::ChunkGrid;
use crate::ea_writer; use crate::ea_writer;
use crate::error::FormatError; use crate::error::FormatError;
use crate::filter_pipeline::{ use crate::filter_pipeline::{
FILTER_BITSHUFFLE, FILTER_BZIP2, FILTER_DEFLATE, FILTER_FLETCHER32, FILTER_LZ4, FILTER_LZF, FILTER_BITSHUFFLE, FILTER_BLOSC, FILTER_BZIP2, FILTER_DEFLATE, FILTER_FLETCHER32, FILTER_LZ4,
FILTER_PCODEC, FILTER_PCODEC_NAME, FILTER_SHUFFLE, FILTER_ZSTD, FilterDescription, FILTER_LZF, FILTER_PCODEC, FILTER_PCODEC_NAME, FILTER_SHUFFLE, FILTER_ZSTD, FilterDescription,
FilterPipeline, FilterPipeline,
}; };
use crate::filters::compress_chunk; use crate::filters::compress_chunk;
@@ -77,6 +77,41 @@ pub enum PluginFilter {
/// Block size 1-9 (9 = hdf5plugin's default). /// Block size 1-9 (9 = hdf5plugin's default).
level: u32, level: u32,
}, },
/// Blosc 1 (filter 32001): `codec` at `level` (0-9; 0 stores), after
/// `shuffle`. Needs the `blosc` feature.
Blosc {
/// The codec inside the Blosc frame.
codec: BloscCodec,
/// Compression level 0-9 (0 stores the data uncompressed).
level: u32,
/// The shuffle Blosc applies first.
shuffle: BloscShuffle,
},
}
/// The codec inside a Blosc frame that clawhdf5 can write. (It reads
/// BloscLZ too, but cannot write it.)
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum BloscCodec {
/// LZ4.
Lz4,
/// Snappy.
Snappy,
/// Zlib, at the Blosc level.
Zlib,
/// Zstandard (clawhdf5's pure-Rust encoder has one level, about zstd 1).
Zstd,
}
/// The shuffle Blosc applies before compressing.
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum BloscShuffle {
/// None.
None,
/// Byte shuffle (Blosc's default).
Byte,
/// Bit shuffle.
Bit,
} }
/// What bitshuffle compresses its blocks with. /// What bitshuffle compresses its blocks with.
@@ -102,6 +137,7 @@ impl PluginFilter {
PluginFilter::Lzf => false, PluginFilter::Lzf => false,
PluginFilter::Bitshuffle { .. } => true, PluginFilter::Bitshuffle { .. } => true,
PluginFilter::Bzip2 { .. } => false, PluginFilter::Bzip2 { .. } => false,
PluginFilter::Blosc { .. } => true,
} }
} }
@@ -120,6 +156,35 @@ impl PluginFilter {
}, },
// bshuf_h5_set_local: version 0.4, element size, block size, // bshuf_h5_set_local: version 0.4, element size, block size,
// compression (0 none, 2 LZ4, 3 Zstandard), Zstandard level. // compression (0 none, 2 LZ4, 3 Zstandard), Zstandard level.
// hdf5-blosc's blosc_set_local: filter revision 2, Blosc format
// 2, type size, chunk size, then level, shuffle, compressor.
PluginFilter::Blosc {
codec,
level,
shuffle,
} => FilterDescription {
filter_id: FILTER_BLOSC,
name: Some("blosc".into()),
flags: 1,
client_data: vec![
2,
2,
element_size,
chunk_bytes,
(*level).min(9),
match shuffle {
BloscShuffle::None => 0,
BloscShuffle::Byte => 1,
BloscShuffle::Bit => 2,
},
match codec {
BloscCodec::Lz4 => 1,
BloscCodec::Snappy => 3,
BloscCodec::Zlib => 4,
BloscCodec::Zstd => 5,
},
],
},
PluginFilter::Bzip2 { level } => FilterDescription { PluginFilter::Bzip2 { level } => FilterDescription {
filter_id: FILTER_BZIP2, filter_id: FILTER_BZIP2,
name: Some("bzip2".into()), name: Some("bzip2".into()),
+7
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@@ -206,6 +206,13 @@ pub(crate) static BUILTIN_FILTERS: &[BuiltinFilter] = &[
decode: crate::filters_lzf::lzf_decode, decode: crate::filters_lzf::lzf_decode,
encode: Some(crate::filters_lzf::lzf_encode), encode: Some(crate::filters_lzf::lzf_encode),
}, },
#[cfg(feature = "blosc")]
BuiltinFilter {
id: crate::filter_pipeline::FILTER_BLOSC,
name: "blosc",
decode: crate::filters_blosc::blosc_decode,
encode: Some(crate::filters_blosc::blosc_encode),
},
#[cfg(feature = "lz4")] #[cfg(feature = "lz4")]
BuiltinFilter { BuiltinFilter {
id: FILTER_LZ4, id: FILTER_LZ4,
@@ -218,7 +218,7 @@ pub(crate) fn bitshuffle_decode(
} }
/// Decode Zstandard frames into exactly `dst`, failing if they hold more. /// Decode Zstandard frames into exactly `dst`, failing if they hold more.
#[cfg(feature = "bitshuffle")] #[cfg(any(feature = "bitshuffle", feature = "blosc"))]
pub(crate) fn zstd_decode_into( pub(crate) fn zstd_decode_into(
decoder: &mut ruzstd::decoding::FrameDecoder, decoder: &mut ruzstd::decoding::FrameDecoder,
frames: &[u8], frames: &[u8],
@@ -231,7 +231,7 @@ pub(crate) fn zstd_decode_into(
/// Compress with ruzstd. It implements one level (roughly zstd's level 1), /// Compress with ruzstd. It implements one level (roughly zstd's level 1),
/// so the requested level only matters to other encoders. /// so the requested level only matters to other encoders.
#[cfg(feature = "bitshuffle")] #[cfg(any(feature = "bitshuffle", feature = "blosc"))]
pub(crate) fn zstd_encode(data: &[u8]) -> Vec<u8> { pub(crate) fn zstd_encode(data: &[u8]) -> Vec<u8> {
ruzstd::encoding::compress_to_vec(data, ruzstd::encoding::CompressionLevel::Fastest) ruzstd::encoding::compress_to_vec(data, ruzstd::encoding::CompressionLevel::Fastest)
} }
+604
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@@ -0,0 +1,604 @@
//! Blosc 1 (HDF5 filter 32001, `hdf5-blosc`, hdf5plugin's `Blosc`), in pure
//! Rust: the Blosc 1 frame, its byte shuffle and bit shuffle, and the
//! BloscLZ, LZ4/LZ4HC, Snappy, Zlib and Zstandard codecs inside it.
//!
//! **Frame** (c-blosc 1.x, format version 2). A 16-byte header — version
//! (2), codec format version (1), flags, type size, then little-endian `u32`
//! decoded size, block size and frame size. Flags: bit 0 byte shuffle, bit
//! 1 stored raw ("memcpyed": the data follows the header), bit 2 bit
//! shuffle, bit 4 "do not split", bits 5-7 the codec (0 BloscLZ, 1 LZ4 and
//! LZ4HC, 2 Snappy, 3 Zlib, 4 Zstandard). Unless stored raw, a table of
//! `u32` block offsets follows, one per block of `block size` bytes (the
//! last one may be shorter). A block is one stream, or — when the "do not
//! split" flag is clear, the type size is at most 16, the block holds at
//! least 128 elements, and it is not the short last block — `type size`
//! streams, one per byte plane. Each stream is a `u32` length and the
//! codec's output; a length equal to the stream's decoded size means the
//! bytes are stored raw. The decoded block is then unshuffled (byte shuffle
//! for type size > 1; bit shuffle when the block holds a multiple of 8
//! elements, the trailing partial element copied as is).
//!
//! **Filter** (`blosc_filter.c`) `cd_values`: `[0]` filter revision, `[1]`
//! Blosc format version, `[2]` type size, `[3]` chunk size in bytes, `[4]`
//! compression level, `[5]` shuffle (0 none, 1 byte, 2 bit), `[6]`
//! compressor (0 blosclz, 1 lz4, 2 lz4hc, 3 snappy, 4 zlib, 5 zstd). The
//! decoder needs only the frame.
use crate::error::FormatError;
use crate::filter_registry::FilterContext;
use crate::filters_bitshuffle::{bitshuffle_block, bitunshuffle_block};
const HEADER: usize = 16;
const FLAG_SHUFFLE: u8 = 0x01;
const FLAG_MEMCPYED: u8 = 0x02;
const FLAG_BITSHUFFLE: u8 = 0x04;
const FLAG_FUTURE: u8 = 0x08;
const FLAG_DONT_SPLIT: u8 = 0x10;
const MAX_SPLITS: usize = 16;
const MIN_BUFFERSIZE: usize = 128;
fn err(msg: &str) -> FormatError {
FormatError::DecompressionError(format!("blosc: {msg}"))
}
fn le32(b: &[u8], at: usize) -> Result<usize, FormatError> {
b.get(at..at + 4)
.map(|s| u32::from_le_bytes(s.try_into().unwrap()) as usize)
.ok_or_else(|| err("truncated frame"))
}
/// The codec inside a Blosc frame (flags bits 5-7).
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
enum Codec {
BloscLz,
Lz4,
Snappy,
Zlib,
Zstd,
}
impl Codec {
fn from_flags(flags: u8) -> Result<Codec, FormatError> {
match flags >> 5 {
0 => Ok(Codec::BloscLz),
1 => Ok(Codec::Lz4),
2 => Ok(Codec::Snappy),
3 => Ok(Codec::Zlib),
4 => Ok(Codec::Zstd),
other => Err(err(&format!("unknown codec {other}"))),
}
}
}
/// Decode one codec stream into exactly `dst`.
fn decode_stream(
codec: Codec,
src: &[u8],
dst: &mut [u8],
zstd: &mut Option<ruzstd::decoding::FrameDecoder>,
) -> Result<(), FormatError> {
let n = match codec {
Codec::BloscLz => blosclz_decompress(src, dst),
Codec::Lz4 => {
lz4_flex::block::decompress_into(src, dst).map_err(|e| err(&format!("lz4: {e}")))?
}
Codec::Snappy => {
let len = snap::raw::decompress_len(src).map_err(|e| err(&format!("snappy: {e}")))?;
if len != dst.len() {
return Err(err("snappy stream has the wrong size"));
}
snap::raw::Decoder::new()
.decompress(src, dst)
.map_err(|e| err(&format!("snappy: {e}")))?
}
Codec::Zlib => {
let out = crate::filters::inflate_bounded(src, dst.len(), dst.len())
.map_err(|e| err(&format!("zlib: {e}")))?;
let n = out.len();
if n == dst.len() {
dst.copy_from_slice(&out);
}
n
}
Codec::Zstd => crate::filters_bitshuffle::zstd_decode_into(
zstd.get_or_insert_with(ruzstd::decoding::FrameDecoder::new),
src,
dst,
)?,
};
if n != dst.len() {
return Err(err("stream decoded to the wrong size"));
}
Ok(())
}
/// Decode a Blosc-filtered chunk: one Blosc 1 frame.
pub(crate) fn blosc_decode(input: &[u8], ctx: &FilterContext<'_>) -> Result<Vec<u8>, FormatError> {
blosc_decompress(input, ctx.output_limit())
}
/// Decompress a Blosc 1 frame, refusing more than `limit` bytes of output.
pub fn blosc_decompress(input: &[u8], limit: usize) -> Result<Vec<u8>, FormatError> {
if input.len() < HEADER {
return Err(err("truncated header"));
}
let version = input[0];
let codec_version = input[1];
let flags = input[2];
let typesize = input[3] as usize;
let nbytes = le32(input, 4)?;
let blocksize = le32(input, 8)?;
let cbytes = le32(input, 12)?;
if version != 1 && version != 2 {
return Err(err(&format!(
"frame format version {version} is not Blosc 1 (a Blosc 2 chunk?)"
)));
}
if flags & FLAG_FUTURE != 0 {
return Err(err("unknown header flags"));
}
if nbytes > limit {
return Err(err("decoded size exceeds the chunk size"));
}
if cbytes > input.len() {
return Err(err("frame is longer than the chunk"));
}
let src = &input[..cbytes];
if nbytes == 0 {
return Ok(Vec::new());
}
if blocksize == 0 || typesize == 0 {
return Err(err("bad block or type size"));
}
let mut out = vec![0u8; nbytes];
if flags & FLAG_MEMCPYED != 0 {
if cbytes != nbytes + HEADER {
return Err(err("stored frame has the wrong size"));
}
out.copy_from_slice(&src[HEADER..]);
return Ok(out);
}
let codec = Codec::from_flags(flags)?;
if codec_version != 1 {
return Err(err(&format!(
"unsupported {codec:?} format version {codec_version}"
)));
}
let nblocks = nbytes.div_ceil(blocksize);
let leftover = nbytes % blocksize;
if nblocks > (cbytes - HEADER) / 4 {
return Err(err("block table is truncated"));
}
let block_len = blocksize.min(nbytes);
let mut tmp = vec![0u8; block_len];
let mut zstd = None;
let dont_split = flags & FLAG_DONT_SPLIT != 0;
for j in 0..nblocks {
let is_leftover = j == nblocks - 1 && leftover > 0;
let bsize = if is_leftover { leftover } else { blocksize };
let nsplits = if !dont_split
&& typesize <= MAX_SPLITS
&& bsize / typesize >= MIN_BUFFERSIZE
&& !is_leftover
{
typesize
} else {
1
};
let neblock = bsize / nsplits;
let mut pos = le32(src, HEADER + 4 * j)?;
let tmp = &mut tmp[..bsize];
for s in 0..nsplits {
if pos + 4 > src.len() {
return Err(err("block offset out of range"));
}
let clen = le32(src, pos)?;
pos += 4;
let stream = src
.get(pos..pos.saturating_add(clen))
.ok_or_else(|| err("stream runs past the frame"))?;
let dst = &mut tmp[s * neblock..(s + 1) * neblock];
if clen == neblock {
dst.copy_from_slice(stream);
} else {
decode_stream(codec, stream, dst, &mut zstd)?;
}
pos += clen;
}
// `bsize` is a whole number of splits by construction (`nsplits` > 1
// only for full blocks, and c-blosc sizes those in whole elements).
if nsplits * neblock != bsize {
return Err(err("block is not a whole number of streams"));
}
let dest = &mut out[j * blocksize..j * blocksize + bsize];
unshuffle_block(flags, typesize, tmp, dest);
}
Ok(out)
}
/// Undo the frame's shuffle on one decoded block.
fn unshuffle_block(flags: u8, typesize: usize, src: &[u8], dest: &mut [u8]) {
let bsize = src.len();
if flags & FLAG_SHUFFLE != 0 && typesize > 1 {
let n = bsize / typesize;
for i in 0..n {
for b in 0..typesize {
dest[i * typesize + b] = src[b * n + i];
}
}
dest[n * typesize..].copy_from_slice(&src[n * typesize..]);
} else if flags & FLAG_BITSHUFFLE != 0 && bsize >= typesize {
let n = bsize / typesize;
if n.is_multiple_of(8) {
let body = n * typesize;
bitunshuffle_block(&src[..body], &mut dest[..body], n, typesize);
dest[body..].copy_from_slice(&src[body..]);
} else {
dest.copy_from_slice(src);
}
} else {
dest.copy_from_slice(src);
}
}
/// BloscLZ decompression (c-blosc 1.21 `blosclz_decompress`): returns the
/// number of bytes written, or 0 on malformed input — exactly as the C
/// decoder, including stopping before a match that ends the stream, so a
/// stream libblosc rejects is rejected here too.
///
/// Instructions: a control byte `ctrl`. Below 32, a literal run of
/// `ctrl + 1` bytes. Otherwise a match: length `(ctrl >> 5) + 2`, extended
/// by following bytes while they are 255 when the top three bits are all
/// set; distance `((ctrl & 31) << 8) + next byte + 1`, or — when that byte
/// is 255 and the high bits are 31 — a 16-bit big-endian distance plus 8192.
/// The first instruction is always a literal.
pub(crate) fn blosclz_decompress(input: &[u8], out: &mut [u8]) -> usize {
const MAX_DISTANCE: usize = 8191;
let limit = input.len();
if limit == 0 {
return 0;
}
let mut ip = 1usize;
let mut op = 0usize;
let mut ctrl = (input[0] & 31) as usize;
loop {
if ctrl >= 32 {
let mut len = (ctrl >> 5) - 1;
let ofs = (ctrl & 31) << 8;
if len == 6 {
loop {
if ip + 1 >= limit {
return 0;
}
let code = input[ip] as usize;
ip += 1;
len += code;
if code != 255 {
break;
}
}
} else if ip + 1 >= limit {
return 0;
}
let code = input[ip] as usize;
ip += 1;
len += 3;
// The copy source is `distance` bytes back.
let mut distance = ofs + code + 1;
if code == 255 && ofs == 31 << 8 {
if ip + 1 >= limit {
return 0;
}
let far = ((input[ip] as usize) << 8) + input[ip + 1] as usize;
ip += 2;
distance = far + MAX_DISTANCE + 1;
}
if op + len > out.len() {
return 0;
}
if distance > op {
return 0;
}
if ip >= limit {
break;
}
ctrl = input[ip] as usize;
ip += 1;
let start = op - distance;
if distance >= len {
out.copy_within(start..start + len, op);
} else {
for k in 0..len {
out[op + k] = out[start + k];
}
}
op += len;
} else {
let run = ctrl + 1;
if op + run > out.len() || ip + run > limit {
return 0;
}
out[op..op + run].copy_from_slice(&input[ip..ip + run]);
op += run;
ip += run;
if ip >= limit {
break;
}
ctrl = input[ip] as usize;
ip += 1;
}
}
op
}
/// The codec our encoder puts inside the frame.
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub(crate) enum EncodeCodec {
Lz4,
Snappy,
Zlib,
Zstd,
}
impl EncodeCodec {
/// From the filter's `cd_values[6]` compressor code.
fn from_cd(code: u32) -> Result<EncodeCodec, FormatError> {
match code {
1 | 2 => Ok(EncodeCodec::Lz4),
3 => Ok(EncodeCodec::Snappy),
4 => Ok(EncodeCodec::Zlib),
5 => Ok(EncodeCodec::Zstd),
0 => Err(FormatError::CompressionError(
"blosc: clawhdf5 cannot write BloscLZ; choose lz4, snappy, zlib or zstd".into(),
)),
other => Err(FormatError::CompressionError(format!(
"blosc: unknown compressor {other}"
))),
}
}
fn flags(self) -> u8 {
(match self {
EncodeCodec::Lz4 => 1,
EncodeCodec::Snappy => 2,
EncodeCodec::Zlib => 3,
EncodeCodec::Zstd => 4,
}) << 5
}
fn encode(self, data: &[u8], level: u32) -> Result<Vec<u8>, FormatError> {
match self {
EncodeCodec::Lz4 => Ok(lz4_flex::block::compress(data)),
EncodeCodec::Snappy => snap::raw::Encoder::new()
.compress_vec(data)
.map_err(|e| FormatError::CompressionError(format!("blosc: snappy: {e}"))),
EncodeCodec::Zlib => crate::filters::deflate_bounded(data, level.min(9))
.map_err(|e| FormatError::CompressionError(format!("blosc: zlib: {e}"))),
EncodeCodec::Zstd => Ok(crate::filters_bitshuffle::zstd_encode(data)),
}
}
}
/// Block size our encoder uses: at most 256 KiB, a whole number of
/// elements (and, for bit shuffle, of 8-element groups).
fn encode_block_size(nbytes: usize, typesize: usize, bitshuffle: bool) -> usize {
let unit = if bitshuffle { 8 * typesize } else { typesize };
let target = (256 * 1024).min(nbytes);
if target < unit {
return nbytes.max(1);
}
target / unit * unit
}
/// Encode a chunk as one Blosc 1 frame. `cd_values` as hdf5-blosc:
/// `[2]` type size, `[4]` level (0 = store), `[5]` shuffle, `[6]` codec.
pub(crate) fn blosc_encode(input: &[u8], ctx: &FilterContext<'_>) -> Result<Vec<u8>, FormatError> {
let cd = ctx.client_data();
let cerr = |m: &str| FormatError::CompressionError(format!("blosc: {m}"));
let typesize = match cd.get(2) {
Some(&t) if t != 0 => t as usize,
_ => ctx.element_size.max(1),
};
// Blosc records the type size in one byte; c-blosc treats larger types
// as bytes.
let typesize = if typesize > 255 { 1 } else { typesize };
let level = cd.get(4).copied().unwrap_or(5);
let shuffle = cd.get(5).copied().unwrap_or(1);
let codec = EncodeCodec::from_cd(cd.get(6).copied().unwrap_or(1))?;
let nbytes = input.len();
if nbytes > i32::MAX as usize - HEADER {
return Err(cerr("chunk too large for a Blosc frame"));
}
let mut flags = codec.flags();
match shuffle {
0 => {}
1 => flags |= FLAG_SHUFFLE,
2 => flags |= FLAG_BITSHUFFLE,
other => return Err(cerr(&format!("unknown shuffle mode {other}"))),
}
let blocksize = encode_block_size(nbytes, typesize, shuffle == 2);
let header = |flags: u8, blocksize: usize, cbytes: usize| {
let mut h = Vec::with_capacity(HEADER);
h.extend_from_slice(&[2, 1, flags, typesize as u8]);
h.extend_from_slice(&(nbytes as u32).to_le_bytes());
h.extend_from_slice(&(blocksize as u32).to_le_bytes());
h.extend_from_slice(&(cbytes as u32).to_le_bytes());
h
};
let stored = || {
let mut out = header(
FLAG_MEMCPYED | (flags & !(FLAG_SHUFFLE | FLAG_BITSHUFFLE)),
blocksize,
nbytes + HEADER,
);
out.extend_from_slice(input);
out
};
if level == 0 || nbytes == 0 {
return Ok(stored());
}
let nblocks = nbytes.div_ceil(blocksize);
let leftover = nbytes % blocksize;
let mut body = Vec::with_capacity(nbytes / 2);
let mut starts = Vec::with_capacity(nblocks);
let table_end = HEADER + 4 * nblocks;
let mut shuffled = vec![0u8; blocksize];
for j in 0..nblocks {
let is_leftover = j == nblocks - 1 && leftover > 0;
let bsize = if is_leftover { leftover } else { blocksize };
let block = &input[j * blocksize..j * blocksize + bsize];
let sh = &mut shuffled[..bsize];
shuffle_block(flags, typesize, block, sh);
starts.push(table_end + body.len());
let nsplits = if typesize <= MAX_SPLITS
&& bsize / typesize >= MIN_BUFFERSIZE
&& !is_leftover
&& bsize.is_multiple_of(typesize)
{
typesize
} else {
1
};
let neblock = bsize / nsplits;
for s in 0..nsplits {
let part = &sh[s * neblock..(s + 1) * neblock];
let comp = codec.encode(part, level)?;
if comp.len() < neblock {
body.extend_from_slice(&(comp.len() as u32).to_le_bytes());
body.extend_from_slice(&comp);
} else {
body.extend_from_slice(&(neblock as u32).to_le_bytes());
body.extend_from_slice(part);
}
}
if table_end + body.len() >= nbytes + HEADER {
// Incompressible: store instead, as c-blosc does.
return Ok(stored());
}
}
// A split block must decode as split: the decoder infers splitting from
// the same rule, which requires a whole number of elements per block.
let cbytes = table_end + body.len();
let mut out = header(flags, blocksize, cbytes);
for s in starts {
out.extend_from_slice(&(s as u32).to_le_bytes());
}
out.extend_from_slice(&body);
Ok(out)
}
/// Apply the frame's shuffle to one block (the inverse of
/// [`unshuffle_block`]).
fn shuffle_block(flags: u8, typesize: usize, src: &[u8], dest: &mut [u8]) {
let bsize = src.len();
if flags & FLAG_SHUFFLE != 0 && typesize > 1 {
let n = bsize / typesize;
for i in 0..n {
for b in 0..typesize {
dest[b * n + i] = src[i * typesize + b];
}
}
dest[n * typesize..].copy_from_slice(&src[n * typesize..]);
} else if flags & FLAG_BITSHUFFLE != 0 && bsize >= typesize {
let n = bsize / typesize;
if n.is_multiple_of(8) {
let body = n * typesize;
bitshuffle_block(&src[..body], &mut dest[..body], n, typesize);
dest[body..].copy_from_slice(&src[body..]);
} else {
dest.copy_from_slice(src);
}
} else {
dest.copy_from_slice(src);
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::filter_pipeline::{FILTER_BLOSC, FilterDescription};
/// A blosclz stream: literal "abc", then a 9-byte match 3 back (a run
/// of "abc"), then literal "Z".
#[test]
fn blosclz_decodes_literals_and_overlapping_matches() {
// Match: length (ctrl >> 5) + 2 = 8, distance ofs + code + 1 = 3.
let stream = [2, b'a', b'b', b'c', (6 << 5), 2, 0, b'Z'];
let mut out = [0u8; 12];
assert_eq!(blosclz_decompress(&stream, &mut out), 12);
assert_eq!(&out, b"abcabcabcabZ");
// A stream cut inside a match is malformed.
let mut out = [0u8; 11];
assert_eq!(blosclz_decompress(&stream[..6], &mut out), 0);
// A match before the start of the output is malformed.
assert_eq!(blosclz_decompress(&[0, b'a', 32, 5, 0, b'x'], &mut out), 0);
}
fn desc(cd: Vec<u32>) -> FilterDescription {
FilterDescription {
filter_id: FILTER_BLOSC,
name: None,
flags: 0,
client_data: cd,
}
}
#[test]
fn frame_round_trips_every_codec_and_shuffle() {
for ts in [1usize, 2, 4, 8, 3, 32] {
for n in [0usize, 5, 100, 1000, 70_000, 300_001] {
if n * ts > 1 << 20 && ts > 1 {
continue;
}
let data: Vec<u8> = (0..n * ts)
.map(|i| ((i / ts) % 200) as u8 ^ (i % ts) as u8)
.collect();
for codec in [1u32, 3, 4, 5] {
for shuffle in [0u32, 1, 2] {
for level in [0u32, 5] {
let f = desc(vec![2, 2, ts as u32, 0, level, shuffle, codec]);
let ctx = FilterContext {
filter: &f,
element_size: ts,
max_output: data.len(),
};
let enc = blosc_encode(&data, &ctx).unwrap();
let dec = blosc_decode(&enc, &ctx).unwrap_or_else(|e| {
panic!("ts={ts} n={n} codec={codec} shuffle={shuffle}: {e}")
});
assert!(
dec == data,
"ts={ts} n={n} codec={codec} shuffle={shuffle} level={level}"
);
}
}
}
}
}
}
#[test]
fn rejects_bad_frames() {
let data = vec![9u8; 50_000];
let f = desc(vec![2, 2, 4, 0, 5, 1, 1]);
let ctx = FilterContext {
filter: &f,
element_size: 4,
max_output: data.len(),
};
let enc = blosc_encode(&data, &ctx).unwrap();
assert!(blosc_decode(&enc[..enc.len() - 3], &ctx).is_err());
let small = FilterContext {
max_output: 49_999,
..ctx
};
assert!(blosc_decode(&enc, &small).is_err());
let mut v3 = enc.clone();
v3[0] = 3;
assert!(blosc_decode(&v3, &ctx).is_err());
let f0 = desc(vec![2, 2, 4, 0, 5, 1, 0]);
let ctx0 = FilterContext { filter: &f0, ..ctx };
assert!(blosc_encode(&data, &ctx0).is_err());
}
}
+3 -1
View File
@@ -73,8 +73,10 @@ pub mod fill_value;
pub mod filter_pipeline; pub mod filter_pipeline;
pub mod filter_registry; pub mod filter_registry;
pub mod filters; pub mod filters;
#[cfg(feature = "bitshuffle")] #[cfg(any(feature = "bitshuffle", feature = "blosc"))]
mod filters_bitshuffle; mod filters_bitshuffle;
#[cfg(feature = "blosc")]
pub mod filters_blosc;
#[cfg(feature = "bzip2")] #[cfg(feature = "bzip2")]
mod filters_bzip2; mod filters_bzip2;
#[cfg(feature = "lzf")] #[cfg(feature = "lzf")]
@@ -770,6 +770,22 @@ impl DatasetBuilder {
self.with_plugin_filter(crate::chunked_write::PluginFilter::Bzip2 { level }) self.with_plugin_filter(crate::chunked_write::PluginFilter::Bzip2 { level })
} }
/// Enable Blosc (filter 32001) with `codec` at `level` (0-9) after
/// `shuffle`. Implies chunked storage; no extra HDF5 shuffle is added.
/// Requires the `blosc` cargo feature.
pub fn with_blosc(
&mut self,
codec: crate::chunked_write::BloscCodec,
level: u32,
shuffle: crate::chunked_write::BloscShuffle,
) -> &mut Self {
self.with_plugin_filter(crate::chunked_write::PluginFilter::Blosc {
codec,
level,
shuffle,
})
}
/// Enable Pcodec lossless numerical compression (private clawhdf5 filter /// Enable Pcodec lossless numerical compression (private clawhdf5 filter
/// ID 480). /// ID 480).
/// ///
+3
View File
@@ -46,6 +46,9 @@ pcodec = ["clawhdf5-format/pcodec"]
lzf = ["clawhdf5-format/lzf"] lzf = ["clawhdf5-format/lzf"]
bitshuffle = ["clawhdf5-format/bitshuffle"] bitshuffle = ["clawhdf5-format/bitshuffle"]
bzip2 = ["clawhdf5-format/bzip2"] bzip2 = ["clawhdf5-format/bzip2"]
blosc = ["clawhdf5-format/blosc"]
# Every plugin filter.
plugin-filters = ["lzf", "bitshuffle", "bzip2", "blosc"]
# Dataset::verify_provenance() — recompute a dataset's SHA-256 and compare # Dataset::verify_provenance() — recompute a dataset's SHA-256 and compare
# against its stored _provenance_sha256 attribute. On by default, matching # against its stored _provenance_sha256 attribute. On by default, matching
# clawhdf5-format's own default-on `provenance` feature. # clawhdf5-format's own default-on `provenance` feature.
@@ -76,7 +76,7 @@ try:
except ImportError: except ImportError:
hdf5plugin = None hdf5plugin = None
path = sys.argv[1] path = sys.argv[1]
FILTERS = eval(sys.argv[2]) FILTERS = eval('(' + sys.argv[2] + ')')
cases = [ cases = [
('<u1', (1000,), (128,), 'ramp'), ('<u1', (1000,), (128,), 'ramp'),
('<i2', (37, 53), (10, 16), 'ramp'), ('<i2', (37, 53), (10, 16), 'ramp'),
@@ -303,6 +303,56 @@ fn bzip2_written_by_clawhdf5_reads_in_hdf5plugin() {
}); });
} }
#[cfg(feature = "blosc")]
#[test]
fn blosc_written_by_hdf5plugin_reads_exactly() {
if !have_python("h5py, hdf5plugin") {
return;
}
// Every codec hdf5plugin's Blosc offers, each shuffle mode, and levels
// from "store" to maximum.
check_h5py_written(
"blosc",
r#"[(f'{c} {s} {l}', hdf5plugin.Blosc(cname=c, clevel=l, shuffle=s))
for c in ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd']
for s, l in [(hdf5plugin.Blosc.NOSHUFFLE, 5),
(hdf5plugin.Blosc.SHUFFLE, 9),
(hdf5plugin.Blosc.BITSHUFFLE, 1)]]
+ [('blosclz level 0', hdf5plugin.Blosc(cname='blosclz', clevel=0))]"#,
);
}
#[cfg(feature = "blosc")]
#[test]
fn blosc_written_by_clawhdf5_reads_in_hdf5plugin() {
use clawhdf5_format::chunked_write::{BloscCodec, BloscShuffle};
if !have_python("h5py, hdf5plugin") {
return;
}
for codec in [
BloscCodec::Lz4,
BloscCodec::Snappy,
BloscCodec::Zlib,
BloscCodec::Zstd,
] {
for (shuffle, level) in [
(BloscShuffle::None, 5),
(BloscShuffle::Byte, 9),
(BloscShuffle::Bit, 1),
(BloscShuffle::Byte, 0),
] {
check_ours_read_by_h5py(
&format!("blosc_{codec:?}_{shuffle:?}_{level}"),
32001,
"blosc",
|ds| {
ds.with_blosc(codec, level, shuffle);
},
);
}
}
}
#[cfg(feature = "lzf")] #[cfg(feature = "lzf")]
#[test] #[test]
fn lzf_written_by_h5py_reads_exactly() { fn lzf_written_by_h5py_reads_exactly() {