feat(format): decode hyperslab selection versions 1 and 2 in VDS mappings
libhdf5 serializes a VDS hyperslab as version 1 (irregular, 4-byte block corners) for the default format bounds, and as version 2 (regular, 8-byte) for unlimited selections in the 1.10 format. Only version 3 was accepted, so every h5py VDS written with default libver failed with "only version-3 hyperslab selections are supported" (5 libhdf5 test files in the sweep). Decode all three versions following H5S__hyper_deserialize, including irregular hyperslabs (a union of blocks, enumerated in row-major order as libhdf5 iterates them) and the all-ones "unlimited" count/block marker. SerializedSelection exposes the raw form for unlimited-mapping support. Test: vds_interop::vds_version1_irregular_hyperslab_selections compares default-libver h5py VDS reads (contiguous, strided and 2-D block mappings) with libhdf5's values. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
This commit is contained in:
osobh
@@ -273,6 +273,15 @@
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- CI keeps zlib-ng building and tested; the arm64 job no longer needs cmake.
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### Correctness
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- `clawhdf5-format` virtual datasets (VDS), checked against HDF5 2.0 through
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h5py (`crates/clawhdf5/tests/vds_interop.rs`):
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- Hyperslab selection versions 1 and 2 were refused ("only version-3
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hyperslab selections are supported"). Version 1 is what libhdf5 writes for
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every VDS created with the default format bounds (h5py's default), so
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those could not be read at all; version 2 is its encoding of an unlimited
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selection. Both are decoded now, as are irregular hyperslabs (a union of
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blocks, read in row-major order as libhdf5 iterates them).
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`SerializedSelection` exposes the raw form, including unlimited counts.
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- `clawhdf5-format` reader — **values returned wrong with no error:**
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- Fixed Array and Extensible Array chunk indexes were laid out by the
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dataset's current shape instead of its max shape (23 libhdf5 test files,
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@@ -229,44 +229,47 @@ impl Selection {
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/// self-describing in length, so the count lets a caller walk a packed list
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/// of selections — as the Virtual Dataset global-heap block does).
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///
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/// Only the forms needed for VDS assembly are decoded: `ALL`, `NONE`, and
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/// **regular** hyperslabs serialized at **version 3** (the encoding HDF5
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/// 1.10+/2.0 emit). Point selections, irregular hyperslabs, and older
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/// hyperslab versions return an error rather than mis-decoding.
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/// Decodes `ALL`, `NONE`, and hyperslabs at every version libhdf5 writes
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/// (1: irregular, 4-byte coordinates — the default-format encoding; 2:
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/// regular, 8-byte; 3: either, variable width). A regular hyperslab maps
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/// to [`Selection::Hyperslab`]; an *irregular* one (a union of blocks)
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/// maps to a single-block hyperslab when it has one block, and otherwise to
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/// [`Selection::Points`] listing the union in row-major order (the order
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/// libhdf5 iterates it in). Unlimited counts/blocks decode as `u64::MAX`
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/// (see [`SerializedSelection::decode`] for the raw form). Point
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/// selections are refused: libhdf5 does not allow them in virtual datasets
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/// either.
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pub fn decode_serialized(data: &[u8]) -> Result<(Selection, usize), FormatError> {
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if data.len() < 8 {
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return Err(FormatError::UnexpectedEof {
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expected: 8,
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available: data.len(),
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});
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let (raw, len) = SerializedSelection::decode(data)?;
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let sel = match raw {
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SerializedSelection::All => Selection::All,
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SerializedSelection::None => Selection::None,
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SerializedSelection::Regular {
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start,
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stride,
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count,
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block,
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} => Selection::Hyperslab {
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start,
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stride,
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count,
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block,
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},
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SerializedSelection::Blocks { rank, starts, ends } => {
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if starts.len() == rank {
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let block = starts.iter().zip(&ends).map(|(&s, &e)| e - s + 1).collect();
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Selection::Hyperslab {
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start: starts,
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stride: vec![1; rank],
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count: vec![1; rank],
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block,
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}
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let sel_type = u32::from_le_bytes([data[0], data[1], data[2], data[3]]);
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let version = u32::from_le_bytes([data[4], data[5], data[6], data[7]]);
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match sel_type {
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// ALL / NONE: type(4) + version(4) + reserved(4) + length(4) = 16 bytes.
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3 | 0 => {
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if data.len() < 16 {
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return Err(FormatError::UnexpectedEof {
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expected: 16,
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available: data.len(),
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});
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}
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let sel = if sel_type == 3 {
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Selection::All
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} else {
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Selection::None
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Selection::Points(blocks_union_coords(rank, &starts, &ends)?)
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}
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}
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};
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Ok((sel, 16))
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}
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2 => decode_hyperslab_serialized(data, version),
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1 => Err(FormatError::ChunkedReadError(
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"VDS point selections are not supported".into(),
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)),
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_ => Err(FormatError::ChunkedReadError(
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"unknown dataspace selection type".into(),
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)),
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}
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Ok((sel, len))
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}
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/// Enumerate the selected element indices of a **1-D** dataspace of the
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@@ -314,6 +317,11 @@ impl Selection {
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"VDS selection rank does not match dataspace rank".into(),
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));
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}
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if count.iter().chain(block.iter()).any(|&v| v == UNLIMITED) {
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return Err(FormatError::ChunkedReadError(
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"unlimited selection must be clipped before it is enumerated".into(),
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));
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}
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// Selected coordinates along each dimension, in order.
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let mut per_dim: Vec<Vec<u64>> = Vec::with_capacity(rank);
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for d in 0..rank {
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@@ -400,59 +408,174 @@ impl Selection {
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}
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}
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/// Decode an `H5S_SEL_HYPER` selection in its serialized form. Only version-3
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/// **regular** hyperslabs are supported.
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fn decode_hyperslab_serialized(
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data: &[u8],
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version: u32,
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) -> Result<(Selection, usize), FormatError> {
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if version != 3 {
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return Err(FormatError::ChunkedReadError(
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"only version-3 hyperslab selections are supported".into(),
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));
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/// Hyperslab count/block value meaning "unlimited" (`H5S_UNLIMITED`).
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pub const UNLIMITED: u64 = u64::MAX;
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/// Largest number of elements an irregular selection is expanded to when it
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/// is converted to a point list by [`Selection::decode_serialized`].
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const MAX_EXPANDED_POINTS: u64 = 1 << 26;
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/// A selection exactly as `H5S_select_serialize` stores it, before it is
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/// applied to any dataspace.
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///
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/// Unlike [`Selection`] this keeps an irregular hyperslab as its list of
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/// blocks, and a regular hyperslab's count/block may be [`UNLIMITED`] (the
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/// unlimited selections used by unlimited and "printf" virtual dataset
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/// mappings).
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#[derive(Debug, Clone, PartialEq)]
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pub enum SerializedSelection {
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/// `H5S_SEL_ALL`.
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All,
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/// `H5S_SEL_NONE`.
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None,
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/// A regular hyperslab. `count[d]` or `block[d]` may be [`UNLIMITED`].
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Regular {
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start: Vec<u64>,
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stride: Vec<u64>,
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count: Vec<u64>,
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block: Vec<u64>,
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},
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/// An irregular hyperslab: the union of `starts.len() / rank` blocks, each
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/// given by its first (`starts`) and last (`ends`, inclusive) coordinate,
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/// flattened block-major.
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Blocks {
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rank: usize,
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starts: Vec<u64>,
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ends: Vec<u64>,
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},
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}
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fn sel_err(msg: &str) -> FormatError {
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FormatError::ChunkedReadError(msg.into())
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}
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/// Bounds-checked little-endian reader over a serialized selection.
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struct SelReader<'a> {
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data: &'a [u8],
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pos: usize,
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}
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impl SelReader<'_> {
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fn take(&mut self, n: usize) -> Result<&[u8], FormatError> {
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let end = self.pos.checked_add(n).filter(|&e| e <= self.data.len());
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let end = end.ok_or(FormatError::UnexpectedEof {
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expected: self.pos.saturating_add(n),
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available: self.data.len(),
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})?;
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let s = &self.data[self.pos..end];
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self.pos = end;
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Ok(s)
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}
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// type(4) ver(4) flags(1) enc_size(1) rank(4) [start,stride,count,block]*rank
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if data.len() < 14 {
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return Err(FormatError::UnexpectedEof {
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expected: 14,
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available: data.len(),
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});
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fn uint(&mut self, size: usize) -> Result<u64, FormatError> {
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let bytes = self.take(size)?;
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Ok(bytes
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.iter()
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.enumerate()
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.fold(0u64, |v, (i, &b)| v | (b as u64) << (i * 8)))
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}
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let flags = data[8];
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let enc_size = data[9] as usize;
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// Bit 0 set => regular hyperslab. Irregular hyperslabs list explicit blocks.
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if flags & 0x01 == 0 {
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return Err(FormatError::ChunkedReadError(
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"irregular VDS hyperslab selections are not supported".into(),
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));
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fn remaining(&self) -> usize {
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self.data.len() - self.pos
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}
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if enc_size != 2 && enc_size != 4 && enc_size != 8 {
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return Err(FormatError::ChunkedReadError(
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"unsupported hyperslab coordinate encoding size".into(),
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));
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}
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let rank = u32::from_le_bytes([data[10], data[11], data[12], data[13]]) as usize;
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// HDF5 caps dataspace rank at 32 (H5S_MAX_RANK). Reject anything larger so a
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// corrupt rank can't drive a huge allocation or read loop.
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if rank > 32 {
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return Err(FormatError::ChunkedReadError(
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"hyperslab selection rank exceeds maximum (32)".into(),
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));
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}
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let mut pos = 14;
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let read_coord = |data: &[u8], pos: usize| -> Result<u64, FormatError> {
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if pos + enc_size > data.len() {
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return Err(FormatError::UnexpectedEof {
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expected: pos + enc_size,
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available: data.len(),
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});
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}
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let mut v = 0u64;
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for (i, &b) in data[pos..pos + enc_size].iter().enumerate() {
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v |= (b as u64) << (i * 8);
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}
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Ok(v)
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}
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impl SerializedSelection {
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/// Decode a serialized selection, returning it and the number of bytes it
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/// occupies. Mirrors libhdf5's `H5S_select_deserialize`: `ALL`/`NONE` and
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/// hyperslab versions 1-3 are decoded; point selections (which libhdf5
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/// refuses in virtual datasets) and malformed input are errors.
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pub fn decode(data: &[u8]) -> Result<(SerializedSelection, usize), FormatError> {
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let mut r = SelReader { data, pos: 0 };
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let sel_type = r.uint(4)?;
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let version = r.uint(4)?;
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match sel_type {
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// ALL / NONE: type(4) + version(4) + reserved(4) + length(4).
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0 | 3 => {
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r.take(8)?;
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let sel = if sel_type == 3 {
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SerializedSelection::All
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} else {
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SerializedSelection::None
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};
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Ok((sel, r.pos))
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}
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2 => {
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let sel = decode_hyperslab(&mut r, version)?;
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Ok((sel, r.pos))
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}
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1 => Err(sel_err(
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"VDS point selections are not supported (libhdf5 rejects them too)",
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)),
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_ => Err(sel_err("unknown dataspace selection type")),
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}
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}
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/// The single dimension in which this selection is unlimited, if any.
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pub fn unlimited_dim(&self) -> Option<usize> {
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match self {
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SerializedSelection::Regular { count, block, .. } => count
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.iter()
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.zip(block)
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.position(|(&c, &b)| c == UNLIMITED || b == UNLIMITED),
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_ => None,
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}
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}
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/// The rank the selection was serialized with (`None` for ALL/NONE, which
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/// carry no rank).
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pub fn rank(&self) -> Option<usize> {
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match self {
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SerializedSelection::Regular { start, .. } => Some(start.len()),
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SerializedSelection::Blocks { rank, .. } => Some(*rank),
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_ => None,
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}
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}
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}
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/// `H5S__hyper_deserialize`: after the type and version words.
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fn decode_hyperslab(r: &mut SelReader, version: u64) -> Result<SerializedSelection, FormatError> {
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const REGULAR: u8 = 0x01;
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let (flags, enc_size) = match version {
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// v1: reserved(4) + length(4), always irregular, 4-byte coordinates.
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1 => {
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r.take(8)?;
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(0u8, 4usize)
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}
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// v2: flags(1) + length(4), 8-byte coordinates.
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2 => {
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let flags = r.take(1)?[0];
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r.take(4)?;
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(flags, 8)
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}
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// v3: flags(1) + encoding size(1).
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3 => {
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let flags = r.take(1)?[0];
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let enc = r.take(1)?[0] as usize;
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(flags, enc)
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}
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_ => return Err(sel_err("unsupported hyperslab selection version")),
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};
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if flags & !REGULAR != 0 {
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return Err(sel_err("unknown hyperslab selection flags"));
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}
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if !matches!(enc_size, 2 | 4 | 8) {
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return Err(sel_err("unsupported hyperslab coordinate encoding size"));
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}
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let rank = r.uint(4)? as usize;
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// HDF5 caps dataspace rank at 32 (H5S_MAX_RANK). Reject anything else so a
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// corrupt rank can't drive a huge allocation or read loop.
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if rank == 0 || rank > 32 {
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return Err(sel_err("hyperslab selection rank must be 1..=32"));
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}
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// The all-ones value of the encoding width means "unlimited".
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let unlim_raw = if enc_size == 8 {
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u64::MAX
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} else {
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(1u64 << (enc_size * 8)) - 1
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};
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if flags & REGULAR != 0 {
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let (mut start, mut stride, mut count, mut block) = (
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Vec::with_capacity(rank),
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Vec::with_capacity(rank),
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@@ -460,24 +583,104 @@ fn decode_hyperslab_serialized(
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Vec::with_capacity(rank),
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);
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for _ in 0..rank {
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start.push(read_coord(data, pos)?);
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pos += enc_size;
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stride.push(read_coord(data, pos)?);
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pos += enc_size;
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count.push(read_coord(data, pos)?);
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pos += enc_size;
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block.push(read_coord(data, pos)?);
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pos += enc_size;
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start.push(r.uint(enc_size)?);
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stride.push(r.uint(enc_size)?);
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let c = r.uint(enc_size)?;
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count.push(if c == unlim_raw { UNLIMITED } else { c });
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let b = r.uint(enc_size)?;
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block.push(if b == unlim_raw { UNLIMITED } else { b });
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}
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Ok((
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Selection::Hyperslab {
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let unlimited = count
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.iter()
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.zip(&block)
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.filter(|&(&c, &b)| c == UNLIMITED || b == UNLIMITED)
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.count();
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if unlimited > 1 {
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return Err(sel_err(
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"hyperslab selection is unlimited in more than one dimension",
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));
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}
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for d in 0..rank {
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// Overlapping blocks are not a valid regular hyperslab.
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if count[d] > 1 && block[d] != UNLIMITED && block[d] > stride[d] {
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return Err(sel_err("regular hyperslab blocks overlap"));
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}
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}
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return Ok(SerializedSelection::Regular {
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start,
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stride,
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count,
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block,
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},
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pos,
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))
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});
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}
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// Irregular: number of blocks, then each block's start and end corners.
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let nblocks = r.uint(enc_size)?;
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let per_block = (rank * 2 * enc_size) as u64;
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// Untrusted count: it must fit in what is left of the buffer.
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if nblocks
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.checked_mul(per_block)
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.is_none_or(|need| need > r.remaining() as u64)
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{
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return Err(FormatError::UnexpectedEof {
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expected: r
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.pos
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.saturating_add(nblocks.saturating_mul(per_block) as usize),
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available: r.data.len(),
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});
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}
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let n = nblocks as usize * rank;
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let (mut starts, mut ends) = (Vec::with_capacity(n), Vec::with_capacity(n));
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for _ in 0..nblocks {
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for _ in 0..rank {
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starts.push(r.uint(enc_size)?);
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}
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for _ in 0..rank {
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ends.push(r.uint(enc_size)?);
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}
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}
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if starts.iter().zip(&ends).any(|(s, e)| e < s) {
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return Err(sel_err("hyperslab block ends before it starts"));
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}
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Ok(SerializedSelection::Blocks { rank, starts, ends })
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}
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/// The coordinates of the union of the given blocks, in row-major order.
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fn blocks_union_coords(
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rank: usize,
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starts: &[u64],
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ends: &[u64],
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) -> Result<Vec<Vec<u64>>, FormatError> {
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let mut total = 0u64;
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for (s, e) in starts.chunks_exact(rank).zip(ends.chunks_exact(rank)) {
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let vol = s
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.iter()
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.zip(e)
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.try_fold(1u64, |acc, (&s, &e)| acc.checked_mul(e - s + 1));
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total = vol
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.and_then(|v| total.checked_add(v))
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.filter(|&t| t <= MAX_EXPANDED_POINTS)
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.ok_or_else(|| sel_err("irregular hyperslab selection is too large to expand"))?;
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}
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let mut out = Vec::with_capacity(total as usize);
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||||
for (s, e) in starts.chunks_exact(rank).zip(ends.chunks_exact(rank)) {
|
||||
let mut cur = s.to_vec();
|
||||
'block: loop {
|
||||
out.push(cur.clone());
|
||||
for d in (0..rank).rev() {
|
||||
if cur[d] < e[d] {
|
||||
cur[d] += 1;
|
||||
continue 'block;
|
||||
}
|
||||
cur[d] = s[d];
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
// Lexicographic order of coordinates is row-major order.
|
||||
out.sort_unstable();
|
||||
out.dedup();
|
||||
Ok(out)
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
@@ -642,11 +845,100 @@ mod tests {
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_irregular_hyperslab_rejected() {
|
||||
fn decode_truncated_irregular_hyperslab_is_error() {
|
||||
// Irregular, rank 1, but the block count is missing.
|
||||
let bytes = [0x02u8, 0, 0, 0, 0x03, 0, 0, 0, 0x00, 0x02, 0x01, 0, 0, 0];
|
||||
assert!(Selection::decode_serialized(&bytes).is_err());
|
||||
}
|
||||
|
||||
/// Version 1 as libhdf5 writes it for the default (earliest) format bounds:
|
||||
/// type, version, reserved(4), length(4), rank(4), nblocks(4), then each
|
||||
/// block's start and inclusive end corner as 4-byte values.
|
||||
fn v1_blocks(rank: u32, blocks: &[(&[u32], &[u32])]) -> Vec<u8> {
|
||||
let mut b = Vec::new();
|
||||
for w in [2u32, 1, 0, 0, rank, blocks.len() as u32] {
|
||||
b.extend_from_slice(&w.to_le_bytes());
|
||||
}
|
||||
for (s, e) in blocks {
|
||||
for v in s.iter().chain(e.iter()) {
|
||||
b.extend_from_slice(&v.to_le_bytes());
|
||||
}
|
||||
}
|
||||
b
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_v1_irregular_single_block() {
|
||||
// Exactly what h5py/HDF5 2.0 writes for `[0:4]` with default libver.
|
||||
let bytes = v1_blocks(1, &[(&[0], &[3])]);
|
||||
let (sel, used) = Selection::decode_serialized(&bytes).unwrap();
|
||||
assert_eq!(used, bytes.len());
|
||||
assert_eq!(sel.iter_linear_1d(8).unwrap(), vec![0, 1, 2, 3]);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_v1_irregular_union_is_row_major() {
|
||||
// Blocks given out of order and overlapping still enumerate once each,
|
||||
// in row-major order (libhdf5 iterates the union, not the list).
|
||||
let bytes = v1_blocks(2, &[(&[1, 0], &[1, 1]), (&[0, 2], &[1, 2])]);
|
||||
let (sel, used) = Selection::decode_serialized(&bytes).unwrap();
|
||||
assert_eq!(used, bytes.len());
|
||||
// (0,2) (1,0) (1,1) (1,2) in a 2x3 space.
|
||||
assert_eq!(sel.iter_linear(&[2, 3]).unwrap(), vec![2, 3, 4, 5]);
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_v2_regular_with_unlimited_count() {
|
||||
// v2: flags(1) + length(4), then 8-byte start/stride/count/block.
|
||||
let mut b = Vec::new();
|
||||
b.extend_from_slice(&2u32.to_le_bytes());
|
||||
b.extend_from_slice(&2u32.to_le_bytes());
|
||||
b.push(0x01);
|
||||
b.extend_from_slice(&36u32.to_le_bytes());
|
||||
b.extend_from_slice(&1u32.to_le_bytes());
|
||||
for v in [0u64, 10, u64::MAX, 10] {
|
||||
b.extend_from_slice(&v.to_le_bytes());
|
||||
}
|
||||
let (raw, used) = SerializedSelection::decode(&b).unwrap();
|
||||
assert_eq!(used, b.len());
|
||||
assert_eq!(raw.unlimited_dim(), Some(0));
|
||||
assert_eq!(
|
||||
raw,
|
||||
SerializedSelection::Regular {
|
||||
start: vec![0],
|
||||
stride: vec![10],
|
||||
count: vec![UNLIMITED],
|
||||
block: vec![10],
|
||||
}
|
||||
);
|
||||
// An unclipped unlimited selection cannot be enumerated.
|
||||
let (sel, _) = Selection::decode_serialized(&b).unwrap();
|
||||
assert!(sel.iter_linear_1d(100).is_err());
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_v3_two_byte_all_ones_is_unlimited() {
|
||||
let bytes = [
|
||||
0x02, 0, 0, 0, 0x03, 0, 0, 0, 0x01, 0x02, 0x01, 0, 0, 0, //
|
||||
0x00, 0x00, 0x01, 0x00, 0x01, 0x00, 0xFF, 0xFF,
|
||||
];
|
||||
let (raw, _) = SerializedSelection::decode(&bytes).unwrap();
|
||||
assert_eq!(raw.unlimited_dim(), Some(0));
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_irregular_block_count_beyond_buffer_is_error() {
|
||||
let mut b = v1_blocks(1, &[(&[0], &[3])]);
|
||||
b[20..24].copy_from_slice(&u32::MAX.to_le_bytes());
|
||||
assert!(Selection::decode_serialized(&b).is_err());
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn decode_point_selection_is_refused() {
|
||||
let bytes = [1u8, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0];
|
||||
assert!(Selection::decode_serialized(&bytes).is_err());
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn iter_linear_2d_block_row_major() {
|
||||
// A 2x2 block at the top-left of a 4x4 space => linear 0,1,4,5.
|
||||
|
||||
@@ -0,0 +1,156 @@
|
||||
//! Virtual Dataset (VDS) reads checked against libhdf5 (through h5py).
|
||||
//!
|
||||
//! Each test has h5py build virtual datasets and their source files in a temp
|
||||
//! directory, record what libhdf5 reads back (shape and values) next to them,
|
||||
//! and then compares that with what clawhdf5 reads from the same files.
|
||||
//!
|
||||
//! Skipped when python3 or h5py is unavailable, unless
|
||||
//! `CLAWHDF5_REQUIRE_INTEROP=1`.
|
||||
|
||||
use std::path::Path;
|
||||
use std::process::Command;
|
||||
|
||||
use clawhdf5::File;
|
||||
|
||||
/// The Python interpreter to drive interop checks with (`CLAWHDF5_PYTHON`
|
||||
/// lets these run against a virtualenv holding h5py).
|
||||
fn python() -> String {
|
||||
std::env::var("CLAWHDF5_PYTHON").unwrap_or_else(|_| "python3".to_string())
|
||||
}
|
||||
|
||||
/// When `CLAWHDF5_REQUIRE_INTEROP=1` (set in CI), a missing Python dependency
|
||||
/// is a test failure instead of a silent skip.
|
||||
fn interop_required() -> bool {
|
||||
std::env::var("CLAWHDF5_REQUIRE_INTEROP").is_ok_and(|v| v == "1")
|
||||
}
|
||||
|
||||
fn python_available() -> bool {
|
||||
Command::new(python())
|
||||
.args(["-c", "import h5py, numpy"])
|
||||
.output()
|
||||
.map(|o| o.status.success())
|
||||
.unwrap_or(false)
|
||||
}
|
||||
|
||||
macro_rules! skip_if_no_python {
|
||||
() => {
|
||||
if !python_available() {
|
||||
assert!(
|
||||
!interop_required(),
|
||||
"CLAWHDF5_REQUIRE_INTEROP=1 but python3 with h5py is not available"
|
||||
);
|
||||
eprintln!("SKIP: python3 with h5py not available");
|
||||
return;
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
/// Prelude for every generator script: `expect(file, dset, tag)` records what
|
||||
/// libhdf5 reads for `file:dset` as `<tag>.expect` (shape line, values line).
|
||||
const PRELUDE: &str = r#"
|
||||
import h5py, numpy as np
|
||||
def expect(fn, dset, tag):
|
||||
with h5py.File(fn, "r") as f:
|
||||
d = f[dset]
|
||||
a = d[...]
|
||||
with open(tag + ".expect", "w") as out:
|
||||
out.write(" ".join(str(n) for n in d.shape) + "\n")
|
||||
out.write(" ".join(repr(float(v)) for v in a.ravel()) + "\n")
|
||||
"#;
|
||||
|
||||
/// Run `body` (after [`PRELUDE`]) with `dir` as the working directory, so
|
||||
/// relative source file names land next to the virtual file.
|
||||
fn generate(dir: &Path, body: &str) {
|
||||
let script = format!("{PRELUDE}\n{body}");
|
||||
let out = Command::new(python())
|
||||
.args(["-c", &script])
|
||||
.current_dir(dir)
|
||||
.output()
|
||||
.expect("failed to run python");
|
||||
assert!(
|
||||
out.status.success(),
|
||||
"generator failed:\nSTDOUT: {}\nSTDERR: {}",
|
||||
String::from_utf8_lossy(&out.stdout),
|
||||
String::from_utf8_lossy(&out.stderr)
|
||||
);
|
||||
}
|
||||
|
||||
/// What libhdf5 read for `tag`: (shape, values as f64).
|
||||
fn expected(dir: &Path, tag: &str) -> (Vec<u64>, Vec<f64>) {
|
||||
let text = std::fs::read_to_string(dir.join(format!("{tag}.expect"))).unwrap();
|
||||
let mut lines = text.lines();
|
||||
let parse_line = |l: Option<&str>| -> Vec<String> {
|
||||
l.unwrap_or("")
|
||||
.split_whitespace()
|
||||
.map(str::to_string)
|
||||
.collect()
|
||||
};
|
||||
let shape = parse_line(lines.next())
|
||||
.iter()
|
||||
.map(|s| s.parse().unwrap())
|
||||
.collect();
|
||||
let values = parse_line(lines.next())
|
||||
.iter()
|
||||
.map(|s| s.parse().unwrap())
|
||||
.collect();
|
||||
(shape, values)
|
||||
}
|
||||
|
||||
/// Assert clawhdf5 reads `file:dset` exactly as libhdf5 did for `tag`.
|
||||
fn assert_matches_libhdf5(dir: &Path, file: &str, dset: &str, tag: &str) {
|
||||
let (shape, values) = expected(dir, tag);
|
||||
let f = File::open(dir.join(file)).unwrap();
|
||||
let ds = f.dataset(dset).unwrap();
|
||||
assert_eq!(
|
||||
ds.shape().unwrap(),
|
||||
shape,
|
||||
"{tag}: shape differs from libhdf5"
|
||||
);
|
||||
let got = ds
|
||||
.read_f64()
|
||||
.unwrap_or_else(|e| panic!("{tag}: read failed: {e}"));
|
||||
assert_eq!(got.len(), values.len(), "{tag}: element count differs");
|
||||
for (i, (g, e)) in got.iter().zip(&values).enumerate() {
|
||||
assert!(
|
||||
g == e || (g.is_nan() && e.is_nan()),
|
||||
"{tag}: element {i} is {g}, libhdf5 reads {e}\n ours: {got:?}\n libhdf5: {values:?}"
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Selection encodings
|
||||
// ---------------------------------------------------------------------------
|
||||
|
||||
/// Files written with the default (earliest) format bounds serialize every
|
||||
/// VDS hyperslab as a version-1 *irregular* selection (4-byte block corners),
|
||||
/// and a strided selection as many blocks. These were refused outright.
|
||||
#[test]
|
||||
fn vds_version1_irregular_hyperslab_selections() {
|
||||
skip_if_no_python!();
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
generate(
|
||||
dir.path(),
|
||||
r#"
|
||||
with h5py.File("src.h5", "w") as s:
|
||||
s.create_dataset("a", data=np.arange(12.0))
|
||||
s.create_dataset("m", data=np.arange(20.0).reshape(4, 5))
|
||||
with h5py.File("v1.h5", "w") as f: # default libver: hyperslab version 1
|
||||
f.create_dataset("local", data=np.arange(10.0) * -1)
|
||||
lay = h5py.VirtualLayout(shape=(12,), dtype="f8")
|
||||
lay[0:4] = h5py.VirtualSource(".", "local", shape=(10,))[2:6]
|
||||
lay[4:10] = h5py.VirtualSource("src.h5", "a", shape=(12,))[::2]
|
||||
lay[10:12] = h5py.VirtualSource("src.h5", "a", shape=(12,))[10:12]
|
||||
f.create_virtual_dataset("strided", lay)
|
||||
lay = h5py.VirtualLayout(shape=(4, 6), dtype="f8")
|
||||
lay[:, 0:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 3:5]
|
||||
lay[:, 2:6:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 0:2]
|
||||
lay[:, 3:6:2] = h5py.VirtualSource("src.h5", "m", shape=(4, 5))[:, 2:4]
|
||||
f.create_virtual_dataset("grid", lay)
|
||||
expect("v1.h5", "strided", "strided")
|
||||
expect("v1.h5", "grid", "grid")
|
||||
"#,
|
||||
);
|
||||
assert_matches_libhdf5(dir.path(), "v1.h5", "strided", "strided");
|
||||
assert_matches_libhdf5(dir.path(), "v1.h5", "grid", "grid");
|
||||
}
|
||||
@@ -71,7 +71,8 @@ the VDS item, which is marked.
|
||||
- **Virtual datasets:**
|
||||
- **Wrong data:** unmapped regions read as 0 instead of the fill value.
|
||||
- `%b` printf-style source names are not expanded.
|
||||
- Hyperslab selection versions 1 and 2 are refused.
|
||||
- ~~Hyperslab selection versions 1 and 2 are refused.~~ Fixed 2026-09-25:
|
||||
versions 1-3 and irregular hyperslabs are decoded.
|
||||
- **Files with a user block:** the base address is not applied.
|
||||
- **Old-style shared messages (version 1)** read the wrong address.
|
||||
- **Groups and links:**
|
||||
|
||||
Reference in New Issue
Block a user