From 0c114bf0b89e427d3ef6c16aa78839cc9f74f209 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Mon, 17 Jun 2024 22:41:31 +1000 Subject: [PATCH 1/6] Add support for variable length data types Data type sizes are now represented by `DataTypeSize` instead of usize Also adds `ArraySize`. Both are `Fixed` only for now. Need to support `Variable` throughout the codebase. Change codec API in prep for variable sized data types Enable `{Array,DataType}Size::Variable` Implement `CowArrayBytes::validate()` and add `CodecError::InvalidVariableSizedArrayOffsets` Use `CowArrayBytes::validate()` impl `From` for `CowArrayBytes` for various types Array `_element` methods now use `T: Element` Add `vlen` codec metadata Fix codecs bench Implement an experimental vlen codec Use `impl Into>` in array methods Use `RawBytesCow` consistently Remove various vlen todo's Cleanup `ArrayBytes` Use `ArrayError::InvalidElementValue` for invalid string encodings Add `ArraySubset::contains()` Add `FillValue::new_empty()` Add remaining vlen support to array `store_` methods and improve vlen validation Add remaining vlen support to array `retrieve_` methods Partial decoding in the vlen filter Fix async vlen errors Sharding codec vlen support Add vlen support to sharding partial decoder vlen support for sharded_readable_ext `offsets_u64_to_usize` handle 32-bit system Minor FillValue doc update Remove unused ArraySubset methods and add related convenience functions Add cities test Add `Arrow32` vlen encoding Add support for Interleave32 (Zarr V2) vlen encoding fmt clippy Set minimum version for num-complex Fix `ArrayBytes` from `&[u8; N]` for rust < 1.77 Add `binary` data type Vlen improve docs and test various encodings. Fix `cities.csv` encoding. `vlen` change encoding names Validate `vlen` codec `length32` encoding against `zarr-python` v2 Don't store `zarrs` metadata in cities test output Split `vlen` into `vlen` and `vlen_interleaved` Vlen supports separate index/dat encoding with full codec chains. Fix typesize in vlen `index_codecs` metadata Add support for `String` fill value metadata Add `FillValueMetadata::Unsupported` `ArrayMetadata` can be serialised and deserialised with an unsupported `fill_value`, but `Array` creation will fail. vlen cleanup Change vlen codec identifiers given they are experimental Move duplicate `extract_decoded_regions` fn into `array_bytes` + other minor changes Minor vlen_partial_decoder cleanup Add support for `zarr-python` nonconformant `|O` V2 data type Support conversion of Zarr V2 arrats with `vlen-*` codecs to V3 Update root docs for new vlen related codecs/data types Cleanup `get_vlen_bytes_and_offsets` --- CHANGELOG.md | 34 +- Cargo.toml | 6 +- benches/codecs.rs | 8 +- doc/status/codecs.md | 44 +- doc/status/data_types.md | 9 +- examples/sharded_array_write_read.rs | 12 +- src/array.rs | 25 +- src/array/array_async_readable.rs | 285 +- src/array/array_async_readable_writable.rs | 151 +- src/array/array_async_writable.rs | 121 +- src/array/array_builder.rs | 26 +- src/array/array_bytes.rs | 598 + src/array/array_errors.rs | 11 +- src/array/array_representation.rs | 78 +- src/array/array_sync_readable.rs | 284 +- src/array/array_sync_readable_writable.rs | 145 +- src/array/array_sync_sharded_readable_ext.rs | 211 +- src/array/array_sync_writable.rs | 135 +- src/array/codec.rs | 128 +- .../codec/array_partial_decoder_cache.rs | 40 +- src/array/codec/array_to_array/bitround.rs | 73 +- .../array_to_array/bitround/bitround_codec.rs | 25 +- .../bitround/bitround_partial_decoder.rs | 26 +- src/array/codec/array_to_array/transpose.rs | 81 +- .../transpose/transpose_codec.rs | 146 +- .../transpose/transpose_partial_decoder.rs | 197 +- src/array/codec/array_to_bytes.rs | 2 + src/array/codec/array_to_bytes/bytes.rs | 28 +- .../codec/array_to_bytes/bytes/bytes_codec.rs | 87 +- .../bytes/bytes_partial_decoder.rs | 112 +- src/array/codec/array_to_bytes/codec_chain.rs | 174 +- src/array/codec/array_to_bytes/pcodec.rs | 26 +- .../array_to_bytes/pcodec/pcodec_codec.rs | 28 +- .../pcodec/pcodec_partial_decoder.rs | 45 +- src/array/codec/array_to_bytes/sharding.rs | 58 +- .../array_to_bytes/sharding/sharding_codec.rs | 302 +- .../sharding/sharding_partial_decoder.rs | 620 +- src/array/codec/array_to_bytes/vlen.rs | 198 + .../codec/array_to_bytes/vlen/vlen_codec.rs | 305 + .../vlen/vlen_partial_decoder.rs | 178 + .../codec/array_to_bytes/vlen_interleaved.rs | 83 + .../vlen_interleaved_codec.rs | 157 + .../vlen_interleaved_partial_decoder.rs | 119 + src/array/codec/array_to_bytes/zfp.rs | 33 +- .../codec/array_to_bytes/zfp/zfp_codec.rs | 30 +- .../array_to_bytes/zfp/zfp_partial_decoder.rs | 41 +- .../codec/byte_interval_partial_decoder.rs | 11 +- .../codec/bytes_partial_decoder_cache.rs | 9 +- src/array/codec/bytes_to_bytes/blosc.rs | 18 +- .../codec/bytes_to_bytes/blosc/blosc_codec.rs | 11 +- .../blosc/blosc_partial_decoder.rs | 13 +- src/array/codec/bytes_to_bytes/bz2.rs | 18 +- .../codec/bytes_to_bytes/bz2/bz2_codec.rs | 10 +- .../bytes_to_bytes/bz2/bz2_partial_decoder.rs | 9 +- .../bytes_to_bytes/crc32c/crc32c_codec.rs | 10 +- .../crc32c/crc32c_partial_decoder.rs | 9 +- .../codec/bytes_to_bytes/gzip/gzip_codec.rs | 10 +- .../gzip/gzip_partial_decoder.rs | 9 +- .../test_unbounded/test_unbounded_codec.rs | 12 +- .../test_unbounded_partial_decoder.rs | 9 +- .../codec/bytes_to_bytes/zstd/zstd_codec.rs | 10 +- .../zstd/zstd_partial_decoder.rs | 9 +- src/array/data_type.rs | 128 +- src/array/element.rs | 267 + src/array/fill_value.rs | 25 + src/array_subset.rs | 238 +- src/metadata/array.rs | 54 +- src/metadata/v2/array.rs | 7 +- src/metadata/v2/codec/blosc.rs | 46 +- src/metadata/v3.rs | 4 + src/metadata/v3/codec/vlen.rs | 84 + src/metadata/v3/codec/vlen_interleaved.rs | 37 + src/metadata/v3/fill_value.rs | 77 +- src/storage/storage_async.rs | 2 +- src/storage/store/store_async/opendal.rs | 2 +- src/storage/store/store_sync/opendal.rs | 2 +- tests/array_async.rs | 234 +- tests/array_sync.rs | 264 +- tests/cities.rs | 132 + tests/data/cities.csv | 47868 ++++++++++++++++ tests/data/v2/cities.zarr/.zarray | 18 + tests/data/v2/cities.zarr/0 | Bin 0 -> 11835 bytes tests/data/v2/cities.zarr/1 | Bin 0 -> 12423 bytes tests/data/v2/cities.zarr/10 | Bin 0 -> 13146 bytes tests/data/v2/cities.zarr/11 | Bin 0 -> 13092 bytes tests/data/v2/cities.zarr/12 | Bin 0 -> 13491 bytes tests/data/v2/cities.zarr/13 | Bin 0 -> 13343 bytes tests/data/v2/cities.zarr/14 | Bin 0 -> 13323 bytes tests/data/v2/cities.zarr/15 | Bin 0 -> 13353 bytes tests/data/v2/cities.zarr/16 | Bin 0 -> 13283 bytes tests/data/v2/cities.zarr/17 | Bin 0 -> 13655 bytes tests/data/v2/cities.zarr/18 | Bin 0 -> 13309 bytes tests/data/v2/cities.zarr/19 | Bin 0 -> 13626 bytes tests/data/v2/cities.zarr/2 | Bin 0 -> 12776 bytes tests/data/v2/cities.zarr/20 | Bin 0 -> 13293 bytes tests/data/v2/cities.zarr/21 | Bin 0 -> 13595 bytes tests/data/v2/cities.zarr/22 | Bin 0 -> 13544 bytes 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src/metadata/v3/codec/vlen.rs create mode 100644 src/metadata/v3/codec/vlen_interleaved.rs create mode 100644 tests/cities.rs create mode 100644 tests/data/cities.csv create mode 100644 tests/data/v2/cities.zarr/.zarray create mode 100644 tests/data/v2/cities.zarr/0 create mode 100644 tests/data/v2/cities.zarr/1 create mode 100644 tests/data/v2/cities.zarr/10 create mode 100644 tests/data/v2/cities.zarr/11 create mode 100644 tests/data/v2/cities.zarr/12 create mode 100644 tests/data/v2/cities.zarr/13 create mode 100644 tests/data/v2/cities.zarr/14 create mode 100644 tests/data/v2/cities.zarr/15 create mode 100644 tests/data/v2/cities.zarr/16 create mode 100644 tests/data/v2/cities.zarr/17 create mode 100644 tests/data/v2/cities.zarr/18 create mode 100644 tests/data/v2/cities.zarr/19 create mode 100644 tests/data/v2/cities.zarr/2 create mode 100644 tests/data/v2/cities.zarr/20 create mode 100644 tests/data/v2/cities.zarr/21 create mode 100644 tests/data/v2/cities.zarr/22 create mode 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tests/data/v3/cities.zarr/zarr.json diff --git a/CHANGELOG.md b/CHANGELOG.md index d85801a7..2086bd88 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,14 +7,46 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +### Added + - Add `ArrayBytes`, `RawBytes`, `RawBytesOffsets`, and `ArrayBytesError` + - These can represent array data with fixed and variable length data types + - Add `array::Element[Owned]` traits representing array elements + - Supports conversion to and from `ArrayBytes` + - Add `array::ElementFixedLength` marker trait + - Add experimental `vlen` and `vlen_interleaved` codec for variable length data types + - `vlen_interleaved` is for legacy support of Zarr V2 `vlen-utf8`/`vlen-bytes`/`vlen-array` codecs + - Add `DataType::{String,Binary}` data types + - These are likely to become standardised in the future and are not feature gated + - Add `ArraySubset::contains()` + - Add `FillValueMetadata::{String,Unsupported}` + - `ArrayMetadata` can be serialised and deserialised with an unsupported `fill_value`, but `Array` creation will fail. + - Implement `From<{[u8; N],&[u8; N],String,&str}>` for `FillValue` + - Add `ArraySize` and `DataTypeSize` + - Add `DataType::fixed_size()` that returns `Option`. Returns `None` for variable length data types. + - Add `ArrayError::IncompatibleElementType` (replaces `ArrayError::IncompatibleElementSize`) + - Add `ArrayError::InvalidElementValue` + ### Changed - Use `[async_]retrieve_array_subset_opt` internally in `Array::[async_]retrieve_chunks_opt` - **Breaking**: Replace `[Async]ArrayPartialDecoderTraits::element_size()` with `data_type()` + - Array `_store` methods now use `impl Into>` instead of `&[u8]` for the input bytes + - **Breaking**: Array `_store_{elements,ndarray}` methods now use `T: Element` instead of `T: bytemuck::Pod` + - **Breaking**: Array `_retrieve_{elements,ndarray}` methods now use `T: ElementOwned` instead of `T: bytemuck::Pod` + - Optimised `Array::[async_]store_array_subset_opt` when the subset is a subset of a single chunk + - Make `transmute_to_bytes` public + - Relax `ndarray_into_vec` from `T: bytemuck:Pod` to `T: Clone` + - **Breaking**: `DataType::size()` now returns a `DataTypeSize` instead of `usize` + - **Breaking**: `ArrayCodecTraits::{encode/decode}` have been specialised into `ArrayTo{Array,Bytes}CodecTraits::{encode/decode}` ### Removed - **Breaking**: Remove `into_array_view` array and codec API - This was not fully utilised, not applicable to variable sized data types, and quite unsafe for a public API - - Remove internal `ChunksPerShardError` and just use `CodecError::Other` + - **Breaking**: Remove internal `ChunksPerShardError` and just use `CodecError::Other` + - **Breaking**: Remove `array_subset::{ArrayExtractBytesError,ArrayStoreBytesError}` + - **Breaking**: Remove `ArraySubset::{extract,store}_bytes[_unchecked]`, they are replaced by methods in `ArrayBytes` + - **Breaking**: Remove `array::validate_element_size` and `ArrayError::IncompatibleElementSize` + - The internal validation in array `_element` methods is now more strict than just matching the element size + - Example: `u16` must match `uint16` data type and will not match `int16` or `float16` ### Fixed - Fix an unnecessary copy in `async_store_set_partial_values` diff --git a/Cargo.toml b/Cargo.toml index c2d450b7..c2bbe2cc 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -43,7 +43,7 @@ async-lock = { version = "3.2.0", optional = true } async-recursion = { version = "1.0.5", optional = true } async-trait = { version = "0.1.74", optional = true } blosc-sys = { version = "0.3.4", package = "blosc-src", features = ["snappy", "lz4", "zlib", "zstd"], optional = true } -bytemuck = { version = "1.14.0", features = ["extern_crate_alloc", "must_cast"] } +bytemuck = { version = "1.14.0", features = ["extern_crate_alloc", "must_cast", "min_const_generics"] } bytes = "1.6.0" bzip2 = { version = "0.4.4", optional = true, features = ["static"] } crc32c = { version = "0.6.5", optional = true } @@ -75,6 +75,10 @@ zfp-sys = {version = "0.1.15", features = ["static"], optional = true } zip = { version = "2.1.3", optional = true } zstd = { version = "0.13.1", features = ["zstdmt"], optional = true } +[dependencies.num-complex] +version = "0.4.3" +features = ["bytemuck"] + [dev-dependencies] chrono = "0.4" criterion = "0.5.1" diff --git a/benches/codecs.rs b/benches/codecs.rs index 25441c0c..f44bfaff 100644 --- a/benches/codecs.rs +++ b/benches/codecs.rs @@ -8,9 +8,10 @@ use zarrs::array::{ codec::{ array_to_bytes::bytes::Endianness, bytes_to_bytes::blosc::{BloscCompressor, BloscShuffleMode}, - ArrayCodecTraits, BloscCodec, BytesCodec, BytesToBytesCodecTraits, CodecOptions, + ArrayCodecTraits, ArrayToBytesCodecTraits, BloscCodec, BytesCodec, BytesToBytesCodecTraits, + CodecOptions, }, - BytesRepresentation, ChunkRepresentation, DataType, + BytesRepresentation, ChunkRepresentation, DataType, Element, }; fn codec_bytes(c: &mut Criterion) { @@ -35,12 +36,13 @@ fn codec_bytes(c: &mut Criterion) { .unwrap(); let data = vec![0u8; size3.try_into().unwrap()]; + let bytes = Element::into_array_bytes(&DataType::UInt8, &data).unwrap(); group.throughput(Throughput::Bytes(size3)); // encode and decode have the same implementation group.bench_function(BenchmarkId::new("encode_decode", size3), |b| { b.iter(|| { codec - .encode(Cow::Borrowed(&data), &rep, &CodecOptions::default()) + .encode(bytes.clone(), &rep, &CodecOptions::default()) .unwrap() }); }); diff --git a/doc/status/codecs.md b/doc/status/codecs.md index a4587c7c..205aa0f3 100644 --- a/doc/status/codecs.md +++ b/doc/status/codecs.md @@ -1,16 +1,18 @@ -| Codec Type | Codec† | ZEP | V3 | V2 | Feature Flag* | -| -------------- | ------------------------- | ----------------- | ------- | ------- | ------------- | -| Array to Array | [transpose] | [ZEP0001] | ✓ | | **transpose** | -| | [bitround] (experimental) | | ✓ | | bitround | -| Array to Bytes | [bytes] | [ZEP0001] | ✓ | | | -| | [sharding_indexed] | [ZEP0002] | ✓ | | **sharding** | -| | [zfp] (experimental) | | ✓ | | zfp | -| | [pcodec] (experimental) | | ✓ | | pcodec | -| Bytes to Bytes | [blosc] | [ZEP0001] | ✓ | ✓ | **blosc** | -| | [gzip] | [ZEP0001] | ✓ | ✓ | **gzip** | -| | [crc32c] | [ZEP0002] | ✓ | | **crc32c** | -| | [zstd] | [zarr-specs #256] | ✓ | | zstd | -| | [bz2] (experimental) | | ✓ | ✓ | bz2 | +| Codec Type | Codec† | ZEP | V3 | V2 | Feature Flag* | +| -------------- | -------------------------------------- | ----------------- | ------- | ------- | ------------- | +| Array to Array | [transpose] | [ZEP0001] | ✓ | | **transpose** | +| | [bitround] (experimental) | | ✓ | | bitround | +| Array to Bytes | [bytes] | [ZEP0001] | ✓ | | | +| | [sharding_indexed] | [ZEP0002] | ✓ | | **sharding** | +| | [zfp] (experimental) | | ✓ | | zfp | +| | [pcodec] (experimental) | | ✓ | | pcodec | +| | [vlen] (experimental) | | ✓ | | | +| | V3 [vlen_interleaved] (experimental)
V2 vlen-utf8/vlen-bytes/vlen-array | | ✓ | ✓ | | +| Bytes to Bytes | [blosc] | [ZEP0001] | ✓ | ✓ | **blosc** | +| | [gzip] | [ZEP0001] | ✓ | ✓ | **gzip** | +| | [crc32c] | [ZEP0002] | ✓ | | **crc32c** | +| | [zstd] | [zarr-specs #256] | ✓ | | zstd | +| | [bz2] (experimental) | | ✓ | ✓ | bz2 | \* Bolded feature flags are part of the default set of features.
@@ -31,12 +33,16 @@ [crc32c]: crate::array::codec::bytes_to_bytes::crc32c [zstd]: crate::array::codec::bytes_to_bytes::zstd [bz2]: crate::array::codec::bytes_to_bytes::bz2 +[vlen]: crate::array::codec::array_to_bytes::vlen +[vlen_interleaved]: crate::array::codec::array_to_bytes::vlen_interleaved The `"name"` of of experimental codecs in array metadata links the codec documentation in this crate. -| Experimental Codec | Name / URI | -| ------------------ | ------------------------------------------------- | -| `bitround` | | -| `zfp` | | -| `pcodec` | | -| `bz2` | | +| Experimental Codec | Name / URI | +| ------------------ | -------------------------------------------------------- | +| `bitround` | | +| `zfp` | | +| `pcodec` | | +| `bz2` | | +| `vlen` | | +| `vlen_interleaved` | | diff --git a/doc/status/data_types.md b/doc/status/data_types.md index 05875056..bf66c75a 100644 --- a/doc/status/data_types.md +++ b/doc/status/data_types.md @@ -1,8 +1,12 @@ -| Data Type | ZEP | V3 | V2 | Feature Flag | +| Data Type† | ZEP | V3 | V2 | Feature Flag | | --------- | --- | ----- | -- | ------------ | | [bool]
[int8] [int16] [int32] [int64] [uint8] [uint16] [uint32] [uint64]
[float16] [float32] [float64]
[complex64] [complex128] | [ZEP0001] | ✓ | ✓ | | [r* (raw bits)] | [ZEP0001] | ✓ | | | | [bfloat16] | [zarr-specs #130] | ✓ | | | +| [string] (experimental) | [ZEP0007 (draft)] | ✓ | | | +| [binary] (experimental) | [ZEP0007 (draft)] | ✓ | | | + +† Experimental data types are recommended for evaluation only. [bool]: crate::array::data_type::DataType::Bool [int8]: crate::array::data_type::DataType::Int8 @@ -20,6 +24,9 @@ [complex128]: crate::array::data_type::DataType::Complex128 [bfloat16]: crate::array::data_type::DataType::BFloat16 [r* (raw bits)]: crate::array::data_type::DataType::RawBits +[string]: crate::array::data_type::DataType::String +[binary]: crate::array::data_type::DataType::Binary [ZEP0001]: https://zarr.dev/zeps/accepted/ZEP0001.html [zarr-specs #130]: https://github.com/zarr-developers/zarr-specs/issues/130 +[ZEP0007 (draft)]: https://github.com/zarr-developers/zeps/pull/47 diff --git a/examples/sharded_array_write_read.rs b/examples/sharded_array_write_read.rs index d312e8c5..5a05368c 100644 --- a/examples/sharded_array_write_read.rs +++ b/examples/sharded_array_write_read.rs @@ -137,15 +137,15 @@ fn sharded_array_write_read() -> Result<(), Box> { ArraySubset::new_with_start_shape(vec![0, 4], inner_chunk_shape.clone())?, ]; let decoded_inner_chunks_bytes = partial_decoder.partial_decode(&inner_chunks_to_decode)?; - let decoded_inner_chunks_ndarray = decoded_inner_chunks_bytes - .into_iter() - .map(|bytes| bytes_to_ndarray::(&inner_chunk_shape, bytes.to_vec())) - .collect::, _>>()?; println!("Decoded inner chunks:"); for (inner_chunk_subset, decoded_inner_chunk) in - std::iter::zip(inner_chunks_to_decode, decoded_inner_chunks_ndarray) + std::iter::zip(inner_chunks_to_decode, decoded_inner_chunks_bytes) { - println!("{inner_chunk_subset}\n{decoded_inner_chunk}\n"); + let ndarray = bytes_to_ndarray::( + &inner_chunk_shape, + decoded_inner_chunk.into_fixed()?.into_owned(), + )?; + println!("{inner_chunk_subset}\n{ndarray}\n"); } // Show the hierarchy diff --git a/src/array.rs b/src/array.rs index f7f46bdc..4599af0f 100644 --- a/src/array.rs +++ b/src/array.rs @@ -22,6 +22,7 @@ //! The documentation for [`Array`] details how to interact with arrays. mod array_builder; +mod array_bytes; mod array_errors; mod array_metadata_options; mod array_representation; @@ -33,6 +34,7 @@ pub mod codec; pub mod concurrency; pub mod data_type; mod dimension_name; +mod element; mod endianness; mod fill_value; mod nan_representations; @@ -47,9 +49,10 @@ use std::sync::Arc; pub use self::{ array_builder::ArrayBuilder, + array_bytes::{ArrayBytes, ArrayBytesError, RawBytes, RawBytesOffsets}, array_errors::{ArrayCreateError, ArrayError}, array_metadata_options::ArrayMetadataOptions, - array_representation::{ArrayRepresentation, ChunkRepresentation}, + array_representation::{ArrayRepresentation, ArraySize, ChunkRepresentation}, bytes_representation::BytesRepresentation, chunk_grid::ChunkGrid, chunk_key_encoding::{ChunkKeyEncoding, ChunkKeySeparator}, @@ -57,8 +60,9 @@ pub use self::{ codec::ArrayCodecTraits, codec::CodecChain, concurrency::RecommendedConcurrency, - data_type::DataType, + data_type::{DataType, DataTypeSize}, dimension_name::DimensionName, + element::{Element, ElementFixedLength}, endianness::{Endianness, NATIVE_ENDIAN}, fill_value::FillValue, nan_representations::{ZARR_NAN_BF16, ZARR_NAN_F16, ZARR_NAN_F32, ZARR_NAN_F64}, @@ -641,9 +645,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Convert an ndarray into a vec with standard layout -fn ndarray_into_vec( - array: ndarray::Array, -) -> Vec { +fn ndarray_into_vec(array: ndarray::Array) -> Vec { if array.is_standard_layout() { array } else { @@ -695,7 +697,7 @@ pub fn transmute_to_bytes_vec(from: Vec) -> Vec { /// Transmute from `&[T]` to `&[u8]`. #[must_use] -fn transmute_to_bytes(from: &[T]) -> &[u8] { +pub fn transmute_to_bytes(from: &[T]) -> &[u8] { bytemuck::must_cast_slice(from) } @@ -733,17 +735,6 @@ fn iter_u64_to_usize<'a, I: Iterator>(iter: I) -> Vec { .collect::>() } -fn validate_element_size(data_type: &DataType) -> Result<(), ArrayError> { - if data_type.size() == std::mem::size_of::() { - Ok(()) - } else { - Err(ArrayError::IncompatibleElementSize( - data_type.size(), - std::mem::size_of::(), - )) - } -} - #[cfg(feature = "ndarray")] /// Convert a vector of elements to an [`ndarray::ArrayD`]. /// diff --git a/src/array/array_async_readable.rs b/src/array/array_async_readable.rs index 7bb48eb1..e540e59e 100644 --- a/src/array/array_async_readable.rs +++ b/src/array/array_async_readable.rs @@ -13,15 +13,16 @@ use crate::{ }; use super::{ + array_bytes::{merge_chunks_vlen, update_bytes_flen}, codec::{ - options::CodecOptions, ArrayCodecTraits, ArrayToBytesCodecTraits, - AsyncArrayPartialDecoderTraits, AsyncStoragePartialDecoder, + options::CodecOptions, ArrayToBytesCodecTraits, AsyncArrayPartialDecoderTraits, + AsyncStoragePartialDecoder, }, concurrency::concurrency_chunks_and_codec, - transmute_from_bytes_vec, + element::ElementOwned, unsafe_cell_slice::UnsafeCellSlice, - validate_element_size, Array, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV2, - ArrayMetadataV3, + Array, ArrayBytes, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV2, + ArrayMetadataV3, DataTypeSize, }; #[cfg(feature = "ndarray")] @@ -93,14 +94,14 @@ impl Array { pub async fn async_retrieve_chunk_if_exists( &self, chunk_indices: &[u64], - ) -> Result>, ArrayError> { + ) -> Result>, ArrayError> { self.async_retrieve_chunk_if_exists_opt(chunk_indices, &CodecOptions::default()) .await } /// Async variant of [`retrieve_chunk_elements_if_exists`](Array::retrieve_chunk_elements_if_exists). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_elements_if_exists( + pub async fn async_retrieve_chunk_elements_if_exists( &self, chunk_indices: &[u64], ) -> Result>, ArrayError> { @@ -111,7 +112,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_ndarray_if_exists`](Array::retrieve_chunk_ndarray_if_exists). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_ndarray_if_exists( + pub async fn async_retrieve_chunk_ndarray_if_exists( &self, chunk_indices: &[u64], ) -> Result>, ArrayError> { @@ -144,14 +145,17 @@ impl Array { /// Async variant of [`retrieve_chunk`](Array::retrieve_chunk). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk(&self, chunk_indices: &[u64]) -> Result, ArrayError> { + pub async fn async_retrieve_chunk( + &self, + chunk_indices: &[u64], + ) -> Result, ArrayError> { self.async_retrieve_chunk_opt(chunk_indices, &CodecOptions::default()) .await } /// Async variant of [`retrieve_chunk_elements`](Array::retrieve_chunk_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_elements( + pub async fn async_retrieve_chunk_elements( &self, chunk_indices: &[u64], ) -> Result, ArrayError> { @@ -162,7 +166,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_ndarray`](Array::retrieve_chunk_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_ndarray( + pub async fn async_retrieve_chunk_ndarray( &self, chunk_indices: &[u64], ) -> Result, ArrayError> { @@ -172,14 +176,17 @@ impl Array { /// Async variant of [`retrieve_chunks`](Array::retrieve_chunks). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunks(&self, chunks: &ArraySubset) -> Result, ArrayError> { + pub async fn async_retrieve_chunks( + &self, + chunks: &ArraySubset, + ) -> Result, ArrayError> { self.async_retrieve_chunks_opt(chunks, &CodecOptions::default()) .await } /// Async variant of [`retrieve_chunks_elements`](Array::retrieve_chunks_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunks_elements( + pub async fn async_retrieve_chunks_elements( &self, chunks: &ArraySubset, ) -> Result, ArrayError> { @@ -190,7 +197,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunks_ndarray`](Array::retrieve_chunks_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunks_ndarray( + pub async fn async_retrieve_chunks_ndarray( &self, chunks: &ArraySubset, ) -> Result, ArrayError> { @@ -204,14 +211,14 @@ impl Array { &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { self.async_retrieve_chunk_subset_opt(chunk_indices, chunk_subset, &CodecOptions::default()) .await } /// Async variant of [`retrieve_chunk_subset_elements`](Array::retrieve_chunk_subset_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_subset_elements( + pub async fn async_retrieve_chunk_subset_elements( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -227,7 +234,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_subset_ndarray`](Array::retrieve_chunk_subset_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_chunk_subset_ndarray( + pub async fn async_retrieve_chunk_subset_ndarray( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -245,14 +252,14 @@ impl Array { pub async fn async_retrieve_array_subset( &self, array_subset: &ArraySubset, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { self.async_retrieve_array_subset_opt(array_subset, &CodecOptions::default()) .await } /// Async variant of [`retrieve_array_subset_elements`](Array::retrieve_array_subset_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_array_subset_elements( + pub async fn async_retrieve_array_subset_elements( &self, array_subset: &ArraySubset, ) -> Result, ArrayError> { @@ -263,7 +270,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_array_subset_ndarray`](Array::retrieve_array_subset_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_retrieve_array_subset_ndarray( + pub async fn async_retrieve_array_subset_ndarray( &self, array_subset: &ArraySubset, ) -> Result, ArrayError> { @@ -291,7 +298,7 @@ impl Array { &self, chunk_indices: &[u64], options: &CodecOptions, - ) -> Result>, ArrayError> { + ) -> Result>, ArrayError> { if chunk_indices.len() != self.dimensionality() { return Err(ArrayError::InvalidChunkGridIndicesError( chunk_indices.to_vec(), @@ -311,7 +318,7 @@ impl Array { .map_err(ArrayError::StorageError)?; if let Some(chunk_encoded) = chunk_encoded { let chunk_representation = self.chunk_array_representation(chunk_indices)?; - let chunk_decoded = self + let bytes = self .codecs() .decode( Cow::Borrowed(&chunk_encoded), @@ -319,16 +326,11 @@ impl Array { options, ) .map_err(ArrayError::CodecError)?; - let chunk_decoded_size = - chunk_representation.num_elements_usize() * chunk_representation.data_type().size(); - if chunk_decoded.len() == chunk_decoded_size { - Ok(Some(chunk_decoded.into_owned())) - } else { - Err(ArrayError::UnexpectedChunkDecodedSize( - chunk_decoded.len(), - chunk_decoded_size, - )) - } + bytes.validate( + chunk_representation.num_elements(), + chunk_representation.data_type().size(), + )?; + Ok(Some(bytes.into_owned())) } else { Ok(None) } @@ -340,7 +342,7 @@ impl Array { &self, chunk_indices: &[u64], options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { let chunk = self .async_retrieve_chunk_if_exists_opt(chunk_indices, options) .await?; @@ -348,43 +350,49 @@ impl Array { Ok(chunk) } else { let chunk_representation = self.chunk_array_representation(chunk_indices)?; - let fill_value = chunk_representation.fill_value().as_ne_bytes(); - Ok(fill_value.repeat(chunk_representation.num_elements_usize())) + Ok(ArrayBytes::new_fill_value( + chunk_representation.num_elements_usize(), + self.fill_value(), + )) } } /// Async variant of [`retrieve_chunk_elements_if_exists_opt`](Array::retrieve_chunk_elements_if_exists_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_elements_if_exists_opt( + pub async fn async_retrieve_chunk_elements_if_exists_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result>, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self + if let Some(bytes) = self .async_retrieve_chunk_if_exists_opt(chunk_indices, options) - .await?; - Ok(bytes.map(|bytes| transmute_from_bytes_vec::(bytes))) + .await? + { + let elements = T::from_array_bytes(self.data_type(), bytes)?; + Ok(Some(elements)) + } else { + Ok(None) + } } /// Async variant of [`retrieve_chunk_elements_opt`](Array::retrieve_chunk_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_elements_opt( + pub async fn async_retrieve_chunk_elements_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; let bytes = self .async_retrieve_chunk_opt(chunk_indices, options) .await?; - Ok(transmute_from_bytes_vec::(bytes)) + let elements = T::from_array_bytes(self.data_type(), bytes)?; + Ok(elements) } #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_ndarray_if_exists_opt`](Array::retrieve_chunk_ndarray_if_exists_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_ndarray_if_exists_opt( + pub async fn async_retrieve_chunk_ndarray_if_exists_opt( &self, chunk_indices: &[u64], options: &CodecOptions, @@ -407,7 +415,7 @@ impl Array { #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_ndarray_opt`](Array::retrieve_chunk_ndarray_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_ndarray_opt( + pub async fn async_retrieve_chunk_ndarray_opt( &self, chunk_indices: &[u64], options: &CodecOptions, @@ -467,7 +475,7 @@ impl Array { &self, chunks: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { if chunks.dimensionality() != self.dimensionality() { return Err(ArrayError::InvalidArraySubset( chunks.clone(), @@ -482,25 +490,24 @@ impl Array { /// Async variant of [`retrieve_chunks_elements_opt`](Array::retrieve_chunks_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunks_elements_opt( + pub async fn async_retrieve_chunks_elements_opt( &self, chunks: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; let bytes = self.async_retrieve_chunks_opt(chunks, options).await?; - Ok(transmute_from_bytes_vec::(bytes)) + let elements = T::from_array_bytes(self.data_type(), bytes)?; + Ok(elements) } #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunks_ndarray_opt`](Array::retrieve_chunks_ndarray_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunks_ndarray_opt( + pub async fn async_retrieve_chunks_ndarray_opt( &self, chunks: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; let array_subset = self.chunks_subset(chunks)?; let elements = self .async_retrieve_chunks_elements_opt(chunks, options) @@ -515,7 +522,7 @@ impl Array { &self, array_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { if array_subset.dimensionality() != self.dimensionality() { return Err(ArrayError::InvalidArraySubset( array_subset.clone(), @@ -535,10 +542,10 @@ impl Array { // Retrieve chunk bytes let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => Ok(self - .fill_value() - .as_ne_bytes() - .repeat(array_subset.num_elements_usize())), + 0 => Ok(ArrayBytes::new_fill_value( + array_subset.num_elements_usize(), + self.fill_value(), + )), 1 => { let chunk_indices = chunks.start(); let chunk_subset = self.chunk_subset(chunk_indices)?; @@ -557,11 +564,6 @@ impl Array { } } _ => { - // Decode chunks and copy to output - let size_output = - usize::try_from(array_subset.num_elements() * self.data_type().size() as u64) - .unwrap(); - // Calculate chunk/codec concurrency let chunk_representation = self.chunk_array_representation(&vec![0; self.dimensionality()])?; @@ -574,84 +576,109 @@ impl Array { &codec_concurrency, ); - // let mut output = vec![0; size_output]; - // let output_slice = output.as_mut_slice(); - let mut output = Vec::with_capacity(size_output); - { - let output = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); - let retrieve_chunk = |chunk_indices: Vec| { - let options = options.clone(); - async move { - let chunk_subset = self.chunk_subset(&chunk_indices)?; - let chunk_subset_overlap = chunk_subset.overlap(array_subset)?; - let chunk_subset_bytes = self - .async_retrieve_chunk_subset_opt( - &chunk_indices, - &chunk_subset_overlap.relative_to(chunk_subset.start())?, - &options, + match chunk_representation.data_type().size() { + DataTypeSize::Variable => { + let retrieve_chunk = |chunk_indices: Vec| { + let options = options.clone(); + async move { + let chunk_subset = self.chunk_subset(&chunk_indices)?; + let chunk_subset_overlap = chunk_subset.overlap(array_subset)?; + Ok::<_, ArrayError>(( + self.async_retrieve_chunk_subset_opt( + &chunk_indices, + &chunk_subset_overlap.relative_to(chunk_subset.start())?, + &options, + ) + .await?, + chunk_subset_overlap.relative_to(array_subset.start())?, + )) + } + }; + + // TODO: chunk_concurrent_limit + let chunk_bytes_and_subsets = futures::future::try_join_all( + chunks.indices().iter().map(retrieve_chunk), + ) + .await?; + + Ok(merge_chunks_vlen( + chunk_bytes_and_subsets, + array_subset.shape(), + )?) + } + DataTypeSize::Fixed(data_type_size) => { + let size_output = + usize::try_from(array_subset.num_elements() * data_type_size as u64) + .unwrap(); + let mut output = Vec::with_capacity(size_output); + { + let output = + UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); + let retrieve_chunk = |chunk_indices: Vec| { + let options = options.clone(); + async move { + let chunk_subset = self.chunk_subset(&chunk_indices)?; + let chunk_subset_overlap = + chunk_subset.overlap(array_subset)?; + let chunk_subset_bytes = self + .async_retrieve_chunk_subset_opt( + &chunk_indices, + &chunk_subset_overlap + .relative_to(chunk_subset.start())?, + &options, + ) + .await?; + let chunk_subset_bytes = chunk_subset_bytes.into_fixed()?; + let output = unsafe { output.get() }; + update_bytes_flen( + output, + array_subset.shape(), + &chunk_subset_bytes, + &chunk_subset_overlap.relative_to(array_subset.start())?, + data_type_size, + ); + Ok::<_, ArrayError>(()) + } + }; + + futures::stream::iter(&chunks.indices()) + .map(Ok) + .try_for_each_concurrent( + Some(chunk_concurrent_limit), + retrieve_chunk, ) .await?; - let contiguous_indices = unsafe { - chunk_subset_overlap - .relative_to(array_subset.start())? - .contiguous_linearised_indices_unchecked(array_subset.shape()) - }; - let element_size = self.data_type().size(); - let length = - contiguous_indices.contiguous_elements_usize() * element_size; - let mut decoded_offset = 0; - // FIXME: Par iteration? - let output = unsafe { output.get() }; - for (array_subset_element_index, _num_elements) in &contiguous_indices { - let output_offset = usize::try_from(array_subset_element_index) - .unwrap() - * element_size; - debug_assert!((output_offset + length) <= output.len()); - debug_assert!( - (decoded_offset + length) <= chunk_subset_bytes.len() - ); - output[output_offset..output_offset + length].copy_from_slice( - &chunk_subset_bytes[decoded_offset..decoded_offset + length], - ); - decoded_offset += length; - } - Ok::<_, ArrayError>(()) } - }; - futures::stream::iter(&chunks.indices()) - .map(Ok) - .try_for_each_concurrent(Some(chunk_concurrent_limit), retrieve_chunk) - .await?; + unsafe { output.set_len(size_output) }; + Ok(ArrayBytes::from(output)) + } } - unsafe { output.set_len(size_output) }; - Ok(output) } } } /// Async variant of [`retrieve_array_subset_elements_opt`](Array::retrieve_array_subset_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_array_subset_elements_opt( + pub async fn async_retrieve_array_subset_elements_opt( &self, array_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; let bytes = self .async_retrieve_array_subset_opt(array_subset, options) .await?; - Ok(transmute_from_bytes_vec::(bytes)) + let elements = T::from_array_bytes(self.data_type(), bytes)?; + Ok(elements) } #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_array_subset_ndarray_opt`](Array::retrieve_array_subset_ndarray_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_array_subset_ndarray_opt( + pub async fn async_retrieve_array_subset_ndarray_opt( &self, array_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in async_retrieve_array_subset_elements let elements = self .async_retrieve_array_subset_elements_opt(array_subset, options) .await?; @@ -665,7 +692,7 @@ impl Array { chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { let chunk_representation = self.chunk_array_representation(chunk_indices)?; if !chunk_subset.inbounds(&chunk_representation.shape_u64()) { return Err(ArrayError::InvalidArraySubset( @@ -683,52 +710,42 @@ impl Array { data_key(self.path(), chunk_indices, self.chunk_key_encoding()), )); - let partial_decoder = self + let bytes = self .codecs() .async_partial_decoder(input_handle, &chunk_representation, options) - .await?; - let decoded_bytes = partial_decoder + .await? .partial_decode_opt(&[chunk_subset.clone()], options) .await? - .pop() - .unwrap(); - - let expected_size = chunk_subset.num_elements_usize() * self.data_type().size(); - if decoded_bytes.len() == chunk_subset.num_elements_usize() * self.data_type().size() { - Ok(decoded_bytes.into_owned()) - } else { - Err(ArrayError::UnexpectedChunkDecodedSize( - decoded_bytes.len(), - expected_size, - )) - } + .remove(0) + .into_owned(); + bytes.validate(chunk_subset.num_elements(), self.data_type().size())?; + Ok(bytes) } /// Async variant of [`retrieve_chunk_subset_elements_opt`](Array::retrieve_chunk_subset_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_subset_elements_opt( + pub async fn async_retrieve_chunk_subset_elements_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; let bytes = self .async_retrieve_chunk_subset_opt(chunk_indices, chunk_subset, options) .await?; - Ok(transmute_from_bytes_vec::(bytes)) + let elements = T::from_array_bytes(self.data_type(), bytes)?; + Ok(elements) } #[cfg(feature = "ndarray")] /// Async variant of [`retrieve_chunk_subset_ndarray_opt`](Array::retrieve_chunk_subset_ndarray_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_retrieve_chunk_subset_ndarray_opt( + pub async fn async_retrieve_chunk_subset_ndarray_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in async_retrieve_chunk_subset_elements let elements = self .async_retrieve_chunk_subset_elements_opt(chunk_indices, chunk_subset, options) .await?; diff --git a/src/array/array_async_readable_writable.rs b/src/array/array_async_readable_writable.rs index 575c7cd8..bf948731 100644 --- a/src/array/array_async_readable_writable.rs +++ b/src/array/array_async_readable_writable.rs @@ -1,22 +1,22 @@ use futures::{StreamExt, TryStreamExt}; use crate::{ - array::validate_element_size, array_subset::ArraySubset, - storage::AsyncReadableWritableStorageTraits, + array::ArrayBytes, array_subset::ArraySubset, storage::AsyncReadableWritableStorageTraits, }; use super::{ - codec::options::CodecOptions, concurrency::concurrency_chunks_and_codec, Array, ArrayError, + array_bytes::update_array_bytes, codec::options::CodecOptions, + concurrency::concurrency_chunks_and_codec, Array, ArrayError, Element, }; impl Array { /// Async variant of [`store_chunk_subset`](Array::store_chunk_subset). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_store_chunk_subset( + pub async fn async_store_chunk_subset<'a>( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - chunk_subset_bytes: &[u8], + chunk_subset_bytes: impl Into>, ) -> Result<(), ArrayError> { self.async_store_chunk_subset_opt( chunk_indices, @@ -29,7 +29,7 @@ impl Array( + pub async fn async_store_chunk_subset_elements( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -48,7 +48,7 @@ impl Array> + Send, D: ndarray::Dimension, >( @@ -68,10 +68,10 @@ impl Array( &self, array_subset: &ArraySubset, - subset_bytes: &[u8], + subset_bytes: impl Into>, ) -> Result<(), ArrayError> { self.async_store_array_subset_opt(array_subset, subset_bytes, &CodecOptions::default()) .await @@ -79,7 +79,7 @@ impl Array( + pub async fn async_store_array_subset_elements( &self, array_subset: &ArraySubset, subset_elements: &[T], @@ -96,7 +96,7 @@ impl Array> + Send, D: ndarray::Dimension, >( @@ -118,11 +118,11 @@ impl Array( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - chunk_subset_bytes: &[u8], + chunk_subset_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { let chunk_shape = self @@ -138,75 +138,58 @@ impl Array() * self.data_type().size() as u64; - if chunk_subset_bytes.len() as u64 != expected_length { - return Err(ArrayError::InvalidBytesInputSize( - chunk_subset_bytes.len(), - expected_length, - )); - } if chunk_subset.shape() == chunk_shape && chunk_subset.start().iter().all(|&x| x == 0) { // The subset spans the whole chunk, so store the bytes directly and skip decoding self.async_store_chunk_opt(chunk_indices, chunk_subset_bytes, options) .await } else { + let chunk_subset_bytes = chunk_subset_bytes.into(); + chunk_subset_bytes.validate(chunk_subset.num_elements(), self.data_type().size())?; + // Lock the chunk // let key = data_key(self.path(), chunk_indices, self.chunk_key_encoding()); // let mutex = self.storage.mutex(&key).await?; // let _lock = mutex.lock(); // Decode the entire chunk - let mut chunk_bytes = self + let chunk_bytes_old = self .async_retrieve_chunk_opt(chunk_indices, options) .await?; - // Update the intersecting subset of the chunk - let element_size = self.data_type().size(); - let mut offset = 0; - let contiguous_indices = - unsafe { chunk_subset.contiguous_linearised_indices_unchecked(&chunk_shape) }; - let length = contiguous_indices.contiguous_elements_usize() * element_size; - for (chunk_element_index, _num_elements) in &contiguous_indices { - let chunk_offset = usize::try_from(chunk_element_index).unwrap() * element_size; - debug_assert!(chunk_offset + length <= chunk_bytes.len()); - debug_assert!(offset + length <= chunk_subset_bytes.len()); - chunk_bytes[chunk_offset..chunk_offset + length] - .copy_from_slice(&chunk_subset_bytes[offset..offset + length]); - offset += length; - } + // Update the chunk + let chunk_bytes_new = update_array_bytes( + chunk_bytes_old, + chunk_shape, + chunk_subset_bytes, + chunk_subset, + self.data_type().size(), + ); // Store the updated chunk - self.async_store_chunk_opt(chunk_indices, &chunk_bytes, options) + self.async_store_chunk_opt(chunk_indices, chunk_bytes_new, options) .await } } /// Async variant of [`store_chunk_subset_elements_opt`](Array::store_chunk_subset_elements_opt). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub async fn async_store_chunk_subset_elements_opt( + pub async fn async_store_chunk_subset_elements_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, chunk_subset_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunk_subset_elements = crate::array::transmute_to_bytes(chunk_subset_elements); - self.async_store_chunk_subset_opt( - chunk_indices, - chunk_subset, - chunk_subset_elements, - options, - ) - .await + let chunk_subset_bytes = T::into_array_bytes(self.data_type(), chunk_subset_elements)?; + self.async_store_chunk_subset_opt(chunk_indices, chunk_subset, chunk_subset_bytes, options) + .await } /// Async variant of [`store_chunk_subset_ndarray_opt`](Array::store_chunk_subset_ndarray_opt). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub async fn async_store_chunk_subset_ndarray_opt< - T: bytemuck::Pod + Send + Sync, + T: Element + Send + Sync, TArray: Into> + Send, D: ndarray::Dimension, >( @@ -216,7 +199,6 @@ impl Array Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunk_subset_array: ndarray::Array = chunk_subset_array.into(); let subset = ArraySubset::new_with_start_shape( chunk_subset_start.to_vec(), @@ -239,10 +221,10 @@ impl Array( &self, array_subset: &ArraySubset, - subset_bytes: &[u8], + subset_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { // Validation @@ -252,13 +234,6 @@ impl Array Array Array| { - let chunk_subset_in_array = unsafe { - self.chunk_grid() - .subset_unchecked(&chunk_indices, self.shape()) - .unwrap() - }; - let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset_in_array) }; + let chunk_subset = self.chunk_subset(&chunk_indices).unwrap(); // FIXME: unwrap + let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset) }; let chunk_subset_in_array_subset = unsafe { overlap.relative_to_unchecked(array_subset.start()) }; let array_subset_in_chunk_subset = - unsafe { overlap.relative_to_unchecked(chunk_subset_in_array.start()) }; - let chunk_subset_bytes = unsafe { - chunk_subset_in_array_subset.extract_bytes_unchecked( - subset_bytes, + unsafe { overlap.relative_to_unchecked(chunk_subset.start()) }; + let chunk_subset_bytes = subset_bytes + .extract_array_subset( + &chunk_subset_in_array_subset, array_subset.shape(), - self.data_type().size(), + self.data_type(), ) - }; + .unwrap(); // FIXME: unwrap let options = options.clone(); async move { self.async_store_chunk_subset_opt( &chunk_indices, &array_subset_in_chunk_subset, - &chunk_subset_bytes, + chunk_subset_bytes, &options, ) .await @@ -356,15 +313,14 @@ impl Array( + pub async fn async_store_array_subset_elements_opt( &self, array_subset: &ArraySubset, subset_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let subset_elements = crate::array::transmute_to_bytes(subset_elements); - self.async_store_array_subset_opt(array_subset, subset_elements, options) + let subset_bytes = T::into_array_bytes(self.data_type(), subset_elements)?; + self.async_store_array_subset_opt(array_subset, subset_bytes, options) .await } @@ -372,7 +328,7 @@ impl Array> + Send, D: ndarray::Dimension, >( @@ -381,7 +337,6 @@ impl Array Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let subset_array: ndarray::Array = subset_array.into(); let subset = ArraySubset::new_with_start_shape( subset_start.to_vec(), diff --git a/src/array/array_async_writable.rs b/src/array/array_async_writable.rs index 2e4701f4..cb22ee5c 100644 --- a/src/array/array_async_writable.rs +++ b/src/array/array_async_writable.rs @@ -1,9 +1,9 @@ -use std::{borrow::Cow, sync::Arc}; +use std::sync::Arc; use futures::{StreamExt, TryStreamExt}; use crate::{ - array::validate_element_size, + array::ArrayBytes, array_subset::ArraySubset, metadata::MetadataEraseVersion, storage::{ @@ -13,9 +13,9 @@ use crate::{ }; use super::{ - codec::{options::CodecOptions, ArrayCodecTraits}, + codec::{options::CodecOptions, ArrayToBytesCodecTraits}, concurrency::concurrency_chunks_and_codec, - Array, ArrayError, ArrayMetadata, ArrayMetadataOptions, + Array, ArrayError, ArrayMetadata, ArrayMetadataOptions, Element, }; impl Array { @@ -44,10 +44,10 @@ impl Array { /// Async variant of [`store_chunk`](Array::store_chunk). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunk( + pub async fn async_store_chunk<'a>( &self, chunk_indices: &[u64], - chunk_bytes: &[u8], + chunk_bytes: impl Into>, ) -> Result<(), ArrayError> { self.async_store_chunk_opt(chunk_indices, chunk_bytes, &CodecOptions::default()) .await @@ -55,7 +55,7 @@ impl Array { /// Async variant of [`store_chunk_elements`](Array::store_chunk_elements). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunk_elements( + pub async fn async_store_chunk_elements( &self, chunk_indices: &[u64], chunk_elements: &[T], @@ -68,7 +68,7 @@ impl Array { /// Async variant of [`store_chunk_ndarray`](Array::store_chunk_ndarray). #[allow(clippy::missing_errors_doc)] pub async fn async_store_chunk_ndarray< - T: bytemuck::Pod + Send + Sync, + T: Element + Send + Sync, TArray: Into> + Send, D: ndarray::Dimension, >( @@ -83,10 +83,10 @@ impl Array { /// Async variant of [`store_chunks`](Array::store_chunks). #[allow(clippy::missing_errors_doc)] #[allow(clippy::similar_names)] - pub async fn async_store_chunks( + pub async fn async_store_chunks<'a>( &self, chunks: &ArraySubset, - chunks_bytes: &[u8], + chunks_bytes: impl Into>, ) -> Result<(), ArrayError> { self.async_store_chunks_opt(chunks, chunks_bytes, &CodecOptions::default()) .await @@ -94,7 +94,7 @@ impl Array { /// Async variant of [`store_chunks_elements`](Array::store_chunks_elements). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunks_elements( + pub async fn async_store_chunks_elements( &self, chunks: &ArraySubset, chunks_elements: &[T], @@ -107,7 +107,7 @@ impl Array { /// Async variant of [`store_chunks_ndarray`](Array::store_chunks_ndarray). #[allow(clippy::missing_errors_doc)] pub async fn async_store_chunks_ndarray< - T: bytemuck::Pod + Send + Sync, + T: Element + Send + Sync, TArray: Into> + Send, D: ndarray::Dimension, >( @@ -213,24 +213,25 @@ impl Array { /// Async variant of [`store_chunk_opt`](Array::store_chunk_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunk_opt( + pub async fn async_store_chunk_opt<'a>( &self, chunk_indices: &[u64], - chunk_bytes: &[u8], + chunk_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { + let chunk_bytes = chunk_bytes.into(); + // Validation let chunk_array_representation = self.chunk_array_representation(chunk_indices)?; - if chunk_bytes.len() as u64 != chunk_array_representation.size() { - return Err(ArrayError::InvalidBytesInputSize( - chunk_bytes.len(), - chunk_array_representation.size(), - )); - } + chunk_bytes.validate( + chunk_array_representation.num_elements(), + chunk_array_representation.data_type().size(), + )?; - if !options.store_empty_chunks() && self.fill_value().equals_all(chunk_bytes) { + let is_fill_value = + !options.store_empty_chunks() && chunk_bytes.is_fill_value(self.fill_value()); + if is_fill_value { self.async_erase_chunk(chunk_indices).await?; - Ok(()) } else { let storage_handle = Arc::new(StorageHandle::new(self.storage.clone())); let storage_transformer = self @@ -238,11 +239,7 @@ impl Array { .create_async_writable_transformer(storage_handle); let chunk_encoded = self .codecs() - .encode( - Cow::Borrowed(chunk_bytes), - &chunk_array_representation, - options, - ) + .encode(chunk_bytes, &chunk_array_representation, options) .map_err(ArrayError::CodecError)?; let chunk_encoded = AsyncBytes::from(chunk_encoded.to_vec()); crate::storage::async_store_chunk( @@ -252,22 +249,21 @@ impl Array { self.chunk_key_encoding(), chunk_encoded, ) - .await - .map_err(ArrayError::StorageError) + .await?; } + Ok(()) } /// Async variant of [`store_chunk_elements_opt`](Array::store_chunk_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunk_elements_opt( + pub async fn async_store_chunk_elements_opt( &self, chunk_indices: &[u64], chunk_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunk_elements = crate::array::transmute_to_bytes(chunk_elements); - self.async_store_chunk_opt(chunk_indices, chunk_elements, options) + let bytes = T::into_array_bytes(self.data_type(), chunk_elements)?; + self.async_store_chunk_opt(chunk_indices, bytes, options) .await } @@ -275,7 +271,7 @@ impl Array { /// Async variant of [`store_chunk_ndarray_opt`](Array::store_chunk_ndarray_opt). #[allow(clippy::missing_errors_doc)] pub async fn async_store_chunk_ndarray_opt< - T: bytemuck::Pod + Send + Sync, + T: Element + Send + Sync, TArray: Into> + Send, D: ndarray::Dimension, >( @@ -284,7 +280,6 @@ impl Array { chunk_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunk_array: ndarray::Array = chunk_array.into(); let chunk_shape = self.chunk_shape_usize(chunk_indices)?; if chunk_array.shape() == chunk_shape { @@ -302,30 +297,27 @@ impl Array { /// Async variant of [`store_chunks_opt`](Array::store_chunks_opt). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] #[allow(clippy::similar_names)] - pub async fn async_store_chunks_opt( + pub async fn async_store_chunks_opt<'a>( &self, chunks: &ArraySubset, - chunks_bytes: &[u8], + chunks_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => {} + 0 => { + let chunks_bytes = chunks_bytes.into(); + chunks_bytes.validate(0, self.data_type().size())?; + } 1 => { let chunk_indices = chunks.start(); self.async_store_chunk_opt(chunk_indices, chunks_bytes, options) .await?; } _ => { + let chunks_bytes = chunks_bytes.into(); let array_subset = self.chunks_subset(chunks)?; - let element_size = self.data_type().size(); - let expected_size = element_size as u64 * array_subset.num_elements(); - if chunks_bytes.len() as u64 != expected_size { - return Err(ArrayError::InvalidBytesInputSize( - chunks_bytes.len(), - expected_size, - )); - } + chunks_bytes.validate(array_subset.num_elements(), self.data_type().size())?; // Calculate chunk/codec concurrency let chunk_representation = @@ -340,30 +332,17 @@ impl Array { ); let store_chunk = |chunk_indices: Vec| { - let chunk_subset_in_array = unsafe { - self.chunk_grid() - .subset_unchecked(&chunk_indices, self.shape()) - .unwrap() // FIXME: Unwrap - }; - let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset_in_array) }; - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - let chunk_bytes = unsafe { - chunk_subset_in_array_subset.extract_bytes_unchecked( - chunks_bytes, + let chunk_subset = self.chunk_subset(&chunk_indices).unwrap(); // FIXME: unwrap + let chunk_bytes = chunks_bytes + .extract_array_subset( + &chunk_subset.relative_to(array_subset.start()).unwrap(), // FIXME: unwrap array_subset.shape(), - element_size, + self.data_type(), ) - }; - - debug_assert_eq!( - chunk_subset_in_array.num_elements(), - chunk_subset_in_array_subset.num_elements() - ); - + .unwrap(); // FIXME: unwrap let options = options.clone(); async move { - self.async_store_chunk_opt(&chunk_indices, &chunk_bytes, &options) + self.async_store_chunk_opt(&chunk_indices, chunk_bytes, &options) .await } }; @@ -379,15 +358,14 @@ impl Array { /// Async variant of [`store_chunks_elements_opt`](Array::store_chunks_elements_opt). #[allow(clippy::missing_errors_doc)] - pub async fn async_store_chunks_elements_opt( + pub async fn async_store_chunks_elements_opt( &self, chunks: &ArraySubset, chunks_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunks_elements = crate::array::transmute_to_bytes(chunks_elements); - self.async_store_chunks_opt(chunks, chunks_elements, options) + let chunks_bytes = T::into_array_bytes(self.data_type(), chunks_elements)?; + self.async_store_chunks_opt(chunks, chunks_bytes, options) .await } @@ -395,7 +373,7 @@ impl Array { /// Async variant of [`store_chunks_ndarray_opt`](Array::store_chunks_ndarray_opt). #[allow(clippy::missing_errors_doc)] pub async fn async_store_chunks_ndarray_opt< - T: bytemuck::Pod + Send + Sync, + T: Element + Send + Sync, TArray: Into> + Send, D: ndarray::Dimension, >( @@ -404,7 +382,6 @@ impl Array { chunks_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunks_array: ndarray::Array = chunks_array.into(); let chunks_subset = self.chunks_subset(chunks)?; let chunks_shape = chunks_subset.shape_usize(); diff --git a/src/array/array_builder.rs b/src/array/array_builder.rs index cc74e11c..269d7906 100644 --- a/src/array/array_builder.rs +++ b/src/array/array_builder.rs @@ -5,7 +5,8 @@ use crate::{metadata::v3::AdditionalFields, node::NodePath, storage::StorageTran use super::{ chunk_key_encoding::{ChunkKeyEncoding, DefaultChunkKeyEncoding}, codec::{ - ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, BytesCodec, BytesToBytesCodecTraits, + array_to_bytes::vlen::VlenCodec, ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, + BytesCodec, BytesToBytesCodecTraits, }, data_type::IncompatibleFillValueError, Array, ArrayCreateError, ArrayMetadata, ArrayMetadataV3, ArrayShape, ChunkGrid, @@ -93,6 +94,7 @@ impl ArrayBuilder { chunk_grid: ChunkGrid, fill_value: FillValue, ) -> Self { + let is_fixed_size = data_type.fixed_size().is_some(); Self { shape, data_type, @@ -100,7 +102,12 @@ impl ArrayBuilder { chunk_key_encoding: ChunkKeyEncoding::new(DefaultChunkKeyEncoding::default()), fill_value, array_to_array_codecs: Vec::default(), - array_to_bytes_codec: Box::::default(), + array_to_bytes_codec: if is_fixed_size { + Box::::default() + } else { + Box::::default() + // Box::::default() + }, bytes_to_bytes_codecs: Vec::default(), attributes: serde_json::Map::default(), storage_transformers: StorageTransformerChain::default(), @@ -287,12 +294,15 @@ impl ArrayBuilder { )); } } - if self.data_type.size() != self.fill_value.size() { - return Err(IncompatibleFillValueError::new( - self.data_type.name(), - self.fill_value.clone(), - ) - .into()); + + if let Some(data_type_size) = self.data_type.fixed_size() { + if data_type_size != self.fill_value.size() { + return Err(IncompatibleFillValueError::new( + self.data_type.name(), + self.fill_value.clone(), + ) + .into()); + } } let codec_chain = CodecChain::new( diff --git a/src/array/array_bytes.rs b/src/array/array_bytes.rs new file mode 100644 index 00000000..5bed39d7 --- /dev/null +++ b/src/array/array_bytes.rs @@ -0,0 +1,598 @@ +use std::borrow::Cow; + +use itertools::Itertools; +use thiserror::Error; + +use crate::{ + array_subset::{ArraySubset, IncompatibleArraySubsetAndShapeError}, + byte_range::extract_byte_ranges_concat_unchecked, +}; + +use super::{codec::CodecError, ravel_indices, ArrayShape, DataType, DataTypeSize, FillValue}; + +/// Array element bytes. +pub type RawBytes<'a> = Cow<'a, [u8]>; + +/// Array element byte offsets. +pub type RawBytesOffsets<'a> = Cow<'a, [usize]>; + +/// Fixed or variable length array bytes. +/// +/// Offsets are [`None`] if bytes are composed of fixed size data types. +#[derive(Clone, Debug, PartialEq)] +pub enum ArrayBytes<'a> { + /// Bytes for a fixed length array. + Fixed(RawBytes<'a>), + /// Bytes and element byte offsets for a variable length array. + Variable(RawBytes<'a>, RawBytesOffsets<'a>), +} + +/// Errors related to [`ArrayBytes<'_>`] and [`ArrayBytes`]. +#[derive(Debug, Error)] +pub enum ArrayBytesError { + /// Invalid use of a fixed length method. + #[error("Used a fixed length (flen) method on a variable length (vlen) array")] + UsedFixedLengthMethodOnVariableLengthArray, +} + +impl<'a> ArrayBytes<'a> { + /// Create a new fixed length array bytes from `bytes`. + pub fn new_flen(bytes: impl Into>) -> Self { + Self::Fixed(bytes.into()) + } + + /// Create a new variable length array bytes from `bytes` and `offsets`. + pub fn new_vlen( + bytes: impl Into>, + offsets: impl Into>, + ) -> Self { + Self::Variable(bytes.into(), offsets.into()) + } + + /// Create a new [`ArrayBytes`] with `num_elements` composed entirely of the `fill_value`. + #[must_use] + pub fn new_fill_value(num_elements: usize, fill_value: &FillValue) -> Self { + if fill_value.size() == 0 { + Self::new_vlen( + fill_value.as_ne_bytes().repeat(num_elements), + (0..=num_elements) + .map(|i| i * fill_value.size()) + .collect::>(), + ) + } else { + Self::new_flen(fill_value.as_ne_bytes().repeat(num_elements)) + } + } + + /// Convert the array bytes into fixed size bytes. + /// + /// # Errors + /// Returns a [`CodecError::ExpectedFixedLengthBytes`] if the bytes are variable length. + pub fn into_fixed(self) -> Result, CodecError> { + match self { + Self::Fixed(bytes) => Ok(bytes), + Self::Variable(_, _) => Err(CodecError::ExpectedFixedLengthBytes), + } + } + + /// Convert the array bytes into variable sized bytes and element byte offsets. + /// + /// # Errors + /// Returns a [`CodecError::ExpectedVariableLengthBytes`] if the bytes are fixed length. + pub fn into_variable(self) -> Result<(RawBytes<'a>, RawBytesOffsets<'a>), CodecError> { + match self { + Self::Fixed(_) => Err(CodecError::ExpectedVariableLengthBytes), + Self::Variable(bytes, offsets) => Ok((bytes, offsets)), + } + } + + /// Returns the size (in bytes) of the underlying element bytes. + /// + /// This only considers the size of the element bytes, and does not include the elemenet offsets for a variable sized array. + #[must_use] + pub fn size(&self) -> usize { + match self { + Self::Fixed(bytes) | Self::Variable(bytes, _) => bytes.len(), + } + } + + /// Return the byte offsets for variable sized bytes. Returns [`None`] for fixed size bytes. + #[must_use] + pub fn offsets(&self) -> Option<&RawBytesOffsets<'a>> { + match self { + Self::Fixed(_) => None, + Self::Variable(_, offsets) => Some(offsets), + } + } + + /// Convert into owned [`ArrayBytes<'_>`]. + #[must_use] + pub fn into_owned<'b>(self) -> ArrayBytes<'b> { + match self { + Self::Fixed(bytes) => ArrayBytes::<'b>::new_flen(bytes.into_owned()), + Self::Variable(bytes, offsets) => { + ArrayBytes::<'b>::new_vlen(bytes.into_owned(), offsets.into_owned()) + } + } + } + + /// Validate that the array has a valid encoding. + /// + /// For a fixed-length array, check it matches the expected size. + /// For a variable-length array, check that the offsets are monotonically increasing and the largest offset is equal to the array length. + /// Always returns without error for an array with fixed-length data. + /// + /// # Errors + /// Returns an error if the array is not valid. + pub fn validate( + &self, + num_elements: u64, + data_type_size: DataTypeSize, + ) -> Result<(), CodecError> { + validate_bytes(self, num_elements, data_type_size) + } + + /// Returns [`true`] if the array is empty for the given fill value. + #[must_use] + pub fn is_fill_value(&self, fill_value: &FillValue) -> bool { + match self { + Self::Fixed(bytes) => fill_value.equals_all(bytes), + Self::Variable(bytes, _offsets) => fill_value.equals_all(bytes), + } + } + + /// Extract a subset of the array bytes. + /// + /// # Errors + /// Returns a [`CodecError::InvalidArraySubsetError`] if the `array_shape` is incompatible with `subset`. + /// + /// # Panics + /// Panics if indices in the subset exceed [`usize::MAX`]. + pub fn extract_array_subset( + &self, + subset: &ArraySubset, + array_shape: &[u64], + data_type: &DataType, + ) -> Result, CodecError> { + match self { + ArrayBytes::Variable(bytes, offsets) => { + let indices = subset.linearised_indices(array_shape).map_err(|_| { + IncompatibleArraySubsetAndShapeError::new(subset.clone(), array_shape.to_vec()) + })?; + let mut bytes_length = 0; + for index in &indices { + let index = usize::try_from(index).unwrap(); + let curr = offsets[index]; + let next = offsets[index + 1]; + debug_assert!(next >= curr); + bytes_length += next - curr; + } + let mut ss_bytes = Vec::with_capacity(bytes_length); + let mut ss_offsets = Vec::with_capacity(1 + indices.len()); + for index in &indices { + let index = usize::try_from(index).unwrap(); + let curr = offsets[index]; + let next = offsets[index + 1]; + ss_offsets.push(ss_bytes.len()); + ss_bytes.extend_from_slice(&bytes[curr..next]); + } + ss_offsets.push(ss_bytes.len()); + Ok(ArrayBytes::new_vlen(ss_bytes, ss_offsets)) + } + ArrayBytes::Fixed(bytes) => { + let byte_ranges = + subset.byte_ranges(array_shape, data_type.fixed_size().unwrap())?; + let bytes = unsafe { extract_byte_ranges_concat_unchecked(bytes, &byte_ranges) }; + Ok(ArrayBytes::new_flen(bytes)) + } + } + } +} + +/// Validate fixed length array bytes for a given array size. +fn validate_bytes_flen(bytes: &RawBytes, array_size: u64) -> Result<(), CodecError> { + if bytes.len() as u64 == array_size { + Ok(()) + } else { + Err(CodecError::UnexpectedChunkDecodedSize( + bytes.len(), + array_size, + )) + } +} + +/// Validate variable length array bytes for an array with `num_elements`. +fn validate_bytes_vlen( + bytes: &RawBytes, + offsets: &RawBytesOffsets, + num_elements: u64, +) -> Result<(), CodecError> { + if offsets.len() as u64 != num_elements + 1 { + return Err(CodecError::InvalidVariableSizedArrayOffsets); + } + let len = bytes.len(); + let mut offset_last = 0; + for offset in offsets.iter() { + if *offset < offset_last || *offset > len { + return Err(CodecError::InvalidVariableSizedArrayOffsets); + } + offset_last = *offset; + } + if offset_last == len { + Ok(()) + } else { + Err(CodecError::InvalidVariableSizedArrayOffsets) + } +} + +/// Validate array bytes. +fn validate_bytes( + bytes: &ArrayBytes<'_>, + num_elements: u64, + data_type_size: DataTypeSize, +) -> Result<(), CodecError> { + match (bytes, data_type_size) { + (ArrayBytes::Fixed(bytes), DataTypeSize::Fixed(data_type_size)) => { + validate_bytes_flen(bytes, num_elements * data_type_size as u64) + } + (ArrayBytes::Variable(bytes, offsets), DataTypeSize::Variable) => { + validate_bytes_vlen(bytes, offsets, num_elements) + } + (ArrayBytes::Fixed(_), DataTypeSize::Variable) => Err(CodecError::Other( + "Used fixed length array bytes with a variable sized data type.".to_string(), + )), + (ArrayBytes::Variable(_, _), DataTypeSize::Fixed(_)) => Err(CodecError::Other( + "Used variable length array bytes with a fixed length data type.".to_string(), + )), + } +} + +/// This function is used internally by various array/codec methods to write the bytes of a chunk subset into an output with an associated array subset. +/// This approach only works for fixed length data types. +pub(crate) fn update_bytes_flen( + output_bytes: &mut [u8], + output_shape: &[u64], + subset_bytes: &RawBytes, + subset: &ArraySubset, + data_type_size: usize, +) { + debug_assert_eq!( + output_bytes.len(), + usize::try_from(output_shape.iter().product::()).unwrap() * data_type_size + ); + debug_assert_eq!( + subset_bytes.len(), + subset.num_elements_usize() * data_type_size, + ); + + let contiguous_indices = + unsafe { subset.contiguous_linearised_indices_unchecked(output_shape) }; + let length = contiguous_indices.contiguous_elements_usize() * data_type_size; + let mut decoded_offset = 0; + // TODO: Par iteration? + for (array_subset_element_index, _num_elements) in &contiguous_indices { + let output_offset = usize::try_from(array_subset_element_index).unwrap() * data_type_size; + debug_assert!((output_offset + length) <= output_bytes.len()); + debug_assert!((decoded_offset + length) <= subset_bytes.len()); + output_bytes[output_offset..output_offset + length] + .copy_from_slice(&subset_bytes[decoded_offset..decoded_offset + length]); + decoded_offset += length; + } +} + +pub(crate) fn update_bytes_vlen<'a>( + output_bytes: &RawBytes, + output_offsets: &RawBytesOffsets, + output_shape: ArrayShape, + subset_bytes: &RawBytes, + subset_offsets: &RawBytesOffsets, + subset: &ArraySubset, +) -> ArrayBytes<'a> { + // Get the current and new length of the bytes in the chunk subset + let size_subset_new = { + let chunk_subset_indices = subset + .relative_to(subset.start()) + .unwrap() + .linearised_indices(subset.shape()) + .unwrap(); + chunk_subset_indices + .iter() + .map(|index| { + let index = usize::try_from(index).unwrap(); + subset_offsets[index + 1] - subset_offsets[index] + }) + .sum::() + }; + let size_subset_old = { + let chunk_indices = subset.linearised_indices(&output_shape).unwrap(); + chunk_indices + .iter() + .map(|index| { + let index = usize::try_from(index).unwrap(); + output_offsets[index + 1] - output_offsets[index] + }) + .sum::() + }; + + // Populate new offsets and bytes + let mut offsets_new = Vec::with_capacity(output_offsets.len()); + let bytes_new_len = (output_bytes.len() + size_subset_new) + .checked_sub(size_subset_old) + .unwrap(); + let mut bytes_new = Vec::with_capacity(bytes_new_len); + let indices = ArraySubset::new_with_shape(output_shape).indices(); + for (chunk_index, indices) in indices.iter().enumerate() { + offsets_new.push(bytes_new.len()); + if subset.contains(&indices) { + let subset_indices = indices + .iter() + .zip(subset.start()) + .map(|(i, s)| i - s) + .collect::>(); + let subset_index = + usize::try_from(ravel_indices(&subset_indices, subset.shape())).unwrap(); + let start = subset_offsets[subset_index]; + let end = subset_offsets[subset_index + 1]; + bytes_new.extend_from_slice(&subset_bytes[start..end]); + } else { + let start = output_offsets[chunk_index]; + let end = output_offsets[chunk_index + 1]; + bytes_new.extend_from_slice(&output_bytes[start..end]); + } + } + offsets_new.push(bytes_new.len()); + + ArrayBytes::new_vlen(bytes_new, offsets_new) +} + +/// Update the intersecting subset of the chunk +/// This function is used internally by [`store_chunk_subset_opt`] and [`async_store_chunk_subset_opt`] +pub(crate) fn update_array_bytes<'a>( + output_bytes: ArrayBytes, + output_shape: ArrayShape, + subset_bytes: ArrayBytes, + subset: &ArraySubset, + data_type_size: DataTypeSize, +) -> ArrayBytes<'a> { + match (output_bytes, subset_bytes, data_type_size) { + ( + ArrayBytes::Variable(chunk_bytes, chunk_offsets), + ArrayBytes::Variable(chunk_subset_bytes, chunk_subset_offsets), + DataTypeSize::Variable, + ) => update_bytes_vlen( + &chunk_bytes, + &chunk_offsets, + output_shape, + &chunk_subset_bytes, + &chunk_subset_offsets, + subset, + ), + ( + ArrayBytes::Fixed(chunk_bytes), + ArrayBytes::Fixed(chunk_subset_bytes), + DataTypeSize::Fixed(data_type_size), + ) => { + let mut chunk_bytes = chunk_bytes.into_owned(); + update_bytes_flen( + &mut chunk_bytes, + &output_shape, + &chunk_subset_bytes, + subset, + data_type_size, + ); + ArrayBytes::new_flen(chunk_bytes) + } + (_, _, _) => { + unreachable!("Validation should occur outside of this function") + } + } +} + +/// Merge a set of chunks into an array subset. +/// +/// This function is used internally by [`retrieve_array_subset_opt`] and [`async_retrieve_array_subset_opt`]. +pub(crate) fn merge_chunks_vlen<'a>( + chunk_bytes_and_subsets: Vec<(ArrayBytes<'_>, ArraySubset)>, + array_shape: &[u64], +) -> Result, CodecError> { + let num_elements = usize::try_from(array_shape.iter().product::()).unwrap(); + + #[cfg(debug_assertions)] + { + // Validate the input + let mut element_in_input = vec![0; num_elements]; + for (_, chunk_subset) in &chunk_bytes_and_subsets { + // println!("{chunk_subset:?}"); + let indices = chunk_subset.linearised_indices(array_shape).unwrap(); + for idx in &indices { + let idx = usize::try_from(idx).unwrap(); + element_in_input[idx] += 1; + } + } + assert!(element_in_input.iter().all(|v| *v == 1)); + } + + // Get the size of each element + // TODO: Go parallel + let mut element_sizes = vec![0; num_elements]; + for (chunk_bytes, chunk_subset) in &chunk_bytes_and_subsets { + let chunk_offsets = chunk_bytes.offsets().unwrap(); + debug_assert_eq!(chunk_offsets.len() as u64, chunk_subset.num_elements() + 1); + let indices = chunk_subset.linearised_indices(array_shape).unwrap(); + debug_assert_eq!(chunk_offsets.len(), indices.len() + 1); + for (subset_idx, (curr, next)) in indices.iter().zip(chunk_offsets.iter().tuple_windows()) { + debug_assert!(next >= curr); + let subset_idx = usize::try_from(subset_idx).unwrap(); + element_sizes[subset_idx] = next - curr; + } + } + + // Convert to offsets with a cumulative sum + // TODO: Parallel cum sum + let mut offsets = Vec::with_capacity(element_sizes.len() + 1); + offsets.push(0); // first offset is always zero + offsets.extend(element_sizes.iter().scan(0, |acc, &sz| { + *acc += sz; + Some(*acc) + })); + + // Write bytes + // TODO: Go parallel + let mut bytes = vec![0; *offsets.last().unwrap()]; + for (chunk_bytes, chunk_subset) in chunk_bytes_and_subsets { + let (chunk_bytes, chunk_offsets) = chunk_bytes.into_variable()?; + let indices = chunk_subset.linearised_indices(array_shape).unwrap(); + for (subset_idx, (&chunk_curr, &chunk_next)) in + indices.iter().zip(chunk_offsets.iter().tuple_windows()) + { + let subset_idx = usize::try_from(subset_idx).unwrap(); + let subset_curr = offsets[subset_idx]; + let subset_next = offsets[subset_idx + 1]; + bytes[subset_curr..subset_next].copy_from_slice(&chunk_bytes[chunk_curr..chunk_next]); + } + } + + Ok(ArrayBytes::new_vlen(bytes, offsets)) +} + +pub(crate) fn extract_decoded_regions_vlen<'a>( + bytes: &[u8], + offsets: &[usize], + decoded_regions: &[ArraySubset], + array_shape: &[u64], +) -> Result>, CodecError> { + let mut out = Vec::with_capacity(decoded_regions.len()); + for decoded_region in decoded_regions { + let indices = decoded_region.linearised_indices(array_shape)?; + let mut region_bytes_len = 0; + for index in &indices { + let index = usize::try_from(index).unwrap(); + let curr = offsets[index]; + let next = offsets[index + 1]; + debug_assert!(next >= curr); + region_bytes_len += next - curr; + } + let mut region_offsets = Vec::with_capacity(decoded_region.num_elements_usize() + 1); + let mut region_bytes = Vec::with_capacity(region_bytes_len); + for index in &indices { + region_offsets.push(region_bytes.len()); + let index = usize::try_from(index).unwrap(); + let curr = offsets[index]; + let next = offsets[index + 1]; + region_bytes.extend_from_slice(&bytes[curr..next]); + } + region_offsets.push(region_bytes.len()); + out.push(ArrayBytes::new_vlen(region_bytes, region_offsets)); + } + Ok(out) +} + +impl<'a> From> for ArrayBytes<'a> { + fn from(bytes: RawBytes<'a>) -> Self { + Self::new_flen(bytes) + } +} + +// impl<'a, 'b> From<&ArrayBytes<'a>> for ArrayBytes<'b> { +// fn from(bytes: &ArrayBytes<'a>) -> Self { +// match bytes { +// Self::Fixed(bytes) => { +// let bytes = bytes.to_vec(); +// ArrayBytes::<'b>::new_flen(bytes) +// }, +// Self::Variable(bytes, offsets) => { +// let bytes: RawBytes<'b> = bytes.to_vec().into(); +// let offsets: RawBytesOffsets<'b> = offsets.to_vec().into(); +// ArrayBytes::new_vlen(bytes, offsets) +// } +// } +// } +// } + +// impl<'a> From> for ArrayBytes<'a> { +// fn from(bytes: ArrayBytes<'_>) -> Self { +// match bytes { +// ArrayBytes::Fixed(bytes) => ArrayBytes::new_flen(bytes) +// ArrayBytes::Variable(bytes, offsets) => ArrayBytes::new_vlen(bytes, offsets) +// } +// } +// } + +impl<'a> From<&'a [u8]> for ArrayBytes<'a> { + fn from(bytes: &'a [u8]) -> Self { + ArrayBytes::new_flen(bytes) + } +} + +impl From> for ArrayBytes<'_> { + fn from(bytes: Vec) -> Self { + ArrayBytes::new_flen(bytes) + } +} + +impl<'a, const N: usize> From<&'a [u8; N]> for ArrayBytes<'a> { + fn from(bytes: &'a [u8; N]) -> Self { + // NOTE: as_slice() is needed for rust <1.77 + ArrayBytes::new_flen(bytes.as_slice()) + } +} + +#[cfg(test)] +mod tests { + use std::error::Error; + use std::mem::size_of; + + use crate::array::Element; + + use super::*; + + #[test] + fn array_bytes_flen() -> Result<(), Box> { + let data = [0u32, 1, 2, 3, 4]; + let bytes = Element::into_array_bytes(&DataType::UInt32, &data)?; + let ArrayBytes::Fixed(bytes) = bytes else { + panic!() + }; + assert_eq!(bytes.len(), size_of::() * data.len()); + + Ok(()) + } + + #[test] + fn array_bytes_str() -> Result<(), Box> { + let data = ["a", "bb", "ccc"]; + let bytes = Element::into_array_bytes(&DataType::String, &data)?; + let ArrayBytes::Variable(bytes, offsets) = bytes else { + panic!() + }; + assert_eq!(bytes, "abbccc".as_bytes()); + assert_eq!(*offsets, [0, 1, 3, 6]); + + Ok(()) + } + + #[test] + fn test_flen_update_subset() { + let mut bytes_array = vec![0u8; 4 * 4]; + update_bytes_flen( + &mut bytes_array, + &vec![4, 4], + &vec![1u8, 2].into(), + &ArraySubset::new_with_ranges(&[1..2, 1..3]), + 1, + ); + + update_bytes_flen( + &mut bytes_array, + &vec![4, 4], + &vec![3u8, 4].into(), + &ArraySubset::new_with_ranges(&[3..4, 0..2]), + 1, + ); + + debug_assert_eq!( + bytes_array, + vec![0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 3, 4, 0, 0] + ); + } +} diff --git a/src/array/array_errors.rs b/src/array/array_errors.rs index 7d078fac..ff628d6d 100644 --- a/src/array/array_errors.rs +++ b/src/array/array_errors.rs @@ -97,9 +97,16 @@ pub enum ArrayError { #[error("got chunk decoded shape {_0:?}, expected {_1:?}")] UnexpectedChunkDecodedShape(ArrayShape, ArrayShape), /// Incompatible element size. - #[error("got element size {_0}, expected {_1}")] - IncompatibleElementSize(usize, usize), + #[error("the element types does not match the data type")] + IncompatibleElementType, /// Invalid data shape. #[error("data has shape {_0:?}, expected {_1:?}")] InvalidDataShape(Vec, Vec), + /// Invalid element value. + /// + /// For example + /// - a bool array with a value not equal to 0 (false) or 1 (true). + /// - a string with invalid utf-8 encoding. + #[error("Invalid element value")] + InvalidElementValue, } diff --git a/src/array/array_representation.rs b/src/array/array_representation.rs index 51897f29..d74a81ab 100644 --- a/src/array/array_representation.rs +++ b/src/array/array_representation.rs @@ -1,6 +1,9 @@ use std::num::NonZeroU64; -use super::{data_type::IncompatibleFillValueError, ArrayShape, DataType, FillValue}; +use super::{ + data_type::{DataTypeSize, IncompatibleFillValueError}, + ArrayShape, DataType, FillValue, +}; use derive_more::Display; /// The shape, data type, and fill value of an `array`. @@ -24,6 +27,23 @@ pub type ArrayRepresentation = ArrayRepresentationBase; /// The array representation of a chunk, which must have nonzero dimensions. pub type ChunkRepresentation = ArrayRepresentationBase; +/// The size of an array/chunk. +#[derive(Copy, Clone, Debug, Eq, PartialEq)] +pub enum ArraySize { + /// Fixed size. + Fixed { + /// The number of elements. + num_elements: u64, + /// The data type size (in bytes). + data_type_size: usize, + }, + /// Variable sized. + Variable { + /// The number of elements. + num_elements: u64, + }, +} + impl ArrayRepresentationBase where TDim: Into + core::fmt::Debug + Copy, @@ -38,17 +58,26 @@ where data_type: DataType, fill_value: FillValue, ) -> Result { - if data_type.size() == fill_value.size() { - Ok(Self { + match data_type.size() { + DataTypeSize::Fixed(size) => { + if size == fill_value.size() { + Ok(Self { + array_shape, + data_type, + fill_value, + }) + } else { + Err(IncompatibleFillValueError::new( + data_type.name(), + fill_value, + )) + } + } + DataTypeSize::Variable => Ok(Self { array_shape, data_type, fill_value, - }) - } else { - Err(IncompatibleFillValueError::new( - data_type.name(), - fill_value, - )) + }), } } @@ -62,7 +91,9 @@ where data_type: DataType, fill_value: FillValue, ) -> Self { - debug_assert_eq!(data_type.size(), fill_value.size()); + if let Some(data_type_size) = data_type.fixed_size() { + debug_assert_eq!(data_type_size, fill_value.size()); + } Self { array_shape, data_type, @@ -123,23 +154,26 @@ where /// Return the element size. #[must_use] - pub fn element_size(&self) -> usize { - self.fill_value.size() + pub fn element_size(&self) -> DataTypeSize { + self.data_type().size() } - /// Return the total size in bytes. - /// - /// Equal to the product of each element of its shape and the element size. + /// Returns the element size in bytes with a fixed-size data type, otherwise returns [`None`]. #[must_use] - pub fn size(&self) -> u64 { - self.num_elements() * self.element_size() as u64 + pub fn fixed_element_size(&self) -> Option { + self.data_type().fixed_size() } - /// Return the total size in bytes as a [`usize`]. - /// - /// Equal to the product of each element of its shape and the element size. + /// Return the array size. #[must_use] - pub fn size_usize(&self) -> usize { - self.num_elements_usize() * self.element_size() + pub fn size(&self) -> ArraySize { + let num_elements = self.num_elements(); + match self.element_size() { + DataTypeSize::Fixed(data_type_size) => ArraySize::Fixed { + num_elements, + data_type_size, + }, + DataTypeSize::Variable => ArraySize::Variable { num_elements }, + } } } diff --git a/src/array/array_sync_readable.rs b/src/array/array_sync_readable.rs index 8004473e..ecb17187 100644 --- a/src/array/array_sync_readable.rs +++ b/src/array/array_sync_readable.rs @@ -4,7 +4,7 @@ use rayon::iter::{IntoParallelIterator, ParallelIterator}; use rayon_iter_concurrent_limit::iter_concurrent_limit; use crate::{ - array::ArrayMetadataV2, + array::{ArrayBytes, ArrayMetadataV2}, array_subset::ArraySubset, metadata::MetadataRetrieveVersion, node::NodePath, @@ -15,14 +15,15 @@ use crate::{ }; use super::{ + array_bytes::{merge_chunks_vlen, update_bytes_flen}, codec::{ - options::CodecOptions, ArrayCodecTraits, ArrayPartialDecoderTraits, - ArrayToBytesCodecTraits, StoragePartialDecoder, + options::CodecOptions, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, + StoragePartialDecoder, }, concurrency::concurrency_chunks_and_codec, - transmute_from_bytes_vec, + element::ElementOwned, unsafe_cell_slice::UnsafeCellSlice, - validate_element_size, Array, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV3, + Array, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV3, DataTypeSize, }; #[cfg(feature = "ndarray")] @@ -105,7 +106,7 @@ impl Array { pub fn retrieve_chunk_if_exists( &self, chunk_indices: &[u64], - ) -> Result>, ArrayError> { + ) -> Result>, ArrayError> { self.retrieve_chunk_if_exists_opt(chunk_indices, &CodecOptions::default()) } @@ -118,7 +119,7 @@ impl Array { /// - `chunk_indices` are invalid, /// - there is a codec decoding error, or /// - an underlying store error. - pub fn retrieve_chunk_elements_if_exists( + pub fn retrieve_chunk_elements_if_exists( &self, chunk_indices: &[u64], ) -> Result>, ArrayError> { @@ -138,7 +139,7 @@ impl Array { /// /// # Panics /// Will panic if a chunk dimension is larger than `usize::MAX`. - pub fn retrieve_chunk_ndarray_if_exists( + pub fn retrieve_chunk_ndarray_if_exists( &self, chunk_indices: &[u64], ) -> Result>, ArrayError> { @@ -178,7 +179,7 @@ impl Array { /// /// # Panics /// Panics if the number of elements in the chunk exceeds `usize::MAX`. - pub fn retrieve_chunk(&self, chunk_indices: &[u64]) -> Result, ArrayError> { + pub fn retrieve_chunk(&self, chunk_indices: &[u64]) -> Result, ArrayError> { self.retrieve_chunk_opt(chunk_indices, &CodecOptions::default()) } @@ -191,7 +192,7 @@ impl Array { /// - `chunk_indices` are invalid, /// - there is a codec decoding error, or /// - an underlying store error. - pub fn retrieve_chunk_elements( + pub fn retrieve_chunk_elements( &self, chunk_indices: &[u64], ) -> Result, ArrayError> { @@ -211,7 +212,7 @@ impl Array { /// /// # Panics /// Will panic if a chunk dimension is larger than `usize::MAX`. - pub fn retrieve_chunk_ndarray( + pub fn retrieve_chunk_ndarray( &self, chunk_indices: &[u64], ) -> Result, ArrayError> { @@ -264,7 +265,7 @@ impl Array { /// /// # Panics /// Panics if the number of array elements in the chunk exceeds `usize::MAX`. - pub fn retrieve_chunks(&self, chunks: &ArraySubset) -> Result, ArrayError> { + pub fn retrieve_chunks(&self, chunks: &ArraySubset) -> Result, ArrayError> { self.retrieve_chunks_opt(chunks, &CodecOptions::default()) } @@ -275,7 +276,7 @@ impl Array { /// /// # Panics /// Panics if the number of array elements in the chunks exceeds `usize::MAX`. - pub fn retrieve_chunks_elements( + pub fn retrieve_chunks_elements( &self, chunks: &ArraySubset, ) -> Result, ArrayError> { @@ -290,7 +291,7 @@ impl Array { /// /// # Panics /// Panics if the number of array elements in the chunks exceeds `usize::MAX`. - pub fn retrieve_chunks_ndarray( + pub fn retrieve_chunks_ndarray( &self, chunks: &ArraySubset, ) -> Result, ArrayError> { @@ -312,7 +313,7 @@ impl Array { &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { self.retrieve_chunk_subset_opt(chunk_indices, chunk_subset, &CodecOptions::default()) } @@ -324,7 +325,7 @@ impl Array { /// - the chunk subset is invalid, /// - there is a codec decoding error, or /// - an underlying store error. - pub fn retrieve_chunk_subset_elements( + pub fn retrieve_chunk_subset_elements( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -348,7 +349,7 @@ impl Array { /// /// # Panics /// Will panic if the number of elements in `chunk_subset` is `usize::MAX` or larger. - pub fn retrieve_chunk_subset_ndarray( + pub fn retrieve_chunk_subset_ndarray( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -373,7 +374,10 @@ impl Array { /// /// # Panics /// Panics if attempting to reference a byte beyond `usize::MAX`. - pub fn retrieve_array_subset(&self, array_subset: &ArraySubset) -> Result, ArrayError> { + pub fn retrieve_array_subset( + &self, + array_subset: &ArraySubset, + ) -> Result, ArrayError> { self.retrieve_array_subset_opt(array_subset, &CodecOptions::default()) } @@ -386,7 +390,7 @@ impl Array { /// - an array subset is invalid or out of bounds of the array, /// - there is a codec decoding error, or /// - an underlying store error. - pub fn retrieve_array_subset_elements( + pub fn retrieve_array_subset_elements( &self, array_subset: &ArraySubset, ) -> Result, ArrayError> { @@ -404,7 +408,7 @@ impl Array { /// /// # Panics /// Will panic if any dimension in `chunk_subset` is `usize::MAX` or larger. - pub fn retrieve_array_subset_ndarray( + pub fn retrieve_array_subset_ndarray( &self, array_subset: &ArraySubset, ) -> Result, ArrayError> { @@ -432,7 +436,7 @@ impl Array { &self, chunk_indices: &[u64], options: &CodecOptions, - ) -> Result>, ArrayError> { + ) -> Result>, ArrayError> { if chunk_indices.len() != self.dimensionality() { return Err(ArrayError::InvalidChunkGridIndicesError( chunk_indices.to_vec(), @@ -451,7 +455,7 @@ impl Array { .map_err(ArrayError::StorageError)?; if let Some(chunk_encoded) = chunk_encoded { let chunk_representation = self.chunk_array_representation(chunk_indices)?; - let chunk_decoded = self + let bytes = self .codecs() .decode( Cow::Borrowed(&chunk_encoded), @@ -459,16 +463,11 @@ impl Array { options, ) .map_err(ArrayError::CodecError)?; - let chunk_decoded_size = - chunk_representation.num_elements_usize() * chunk_representation.data_type().size(); - if chunk_decoded.len() == chunk_decoded_size { - Ok(Some(chunk_decoded.into_owned())) - } else { - Err(ArrayError::UnexpectedChunkDecodedSize( - chunk_decoded.len(), - chunk_decoded_size, - )) - } + bytes.validate( + chunk_representation.num_elements(), + chunk_representation.data_type().size(), + )?; + Ok(Some(bytes.into_owned())) } else { Ok(None) } @@ -480,50 +479,54 @@ impl Array { &self, chunk_indices: &[u64], options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { let chunk = self.retrieve_chunk_if_exists_opt(chunk_indices, options)?; if let Some(chunk) = chunk { Ok(chunk) } else { let chunk_representation = self.chunk_array_representation(chunk_indices)?; - let fill_value = chunk_representation.fill_value().as_ne_bytes(); - Ok(fill_value.repeat(chunk_representation.num_elements_usize())) + Ok(ArrayBytes::new_fill_value( + chunk_representation.num_elements_usize(), + self.fill_value(), + )) } } /// Explicit options version of [`retrieve_chunk_elements_if_exists`](Array::retrieve_chunk_elements_if_exists). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_elements_if_exists_opt( + pub fn retrieve_chunk_elements_if_exists_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result>, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_chunk_if_exists_opt(chunk_indices, options)?; - Ok(bytes.map(|bytes| transmute_from_bytes_vec::(bytes))) + if let Some(bytes) = self.retrieve_chunk_if_exists_opt(chunk_indices, options)? { + Ok(Some(T::from_array_bytes(self.data_type(), bytes)?)) + } else { + Ok(None) + } } /// Explicit options version of [`retrieve_chunk_elements`](Array::retrieve_chunk_elements). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_elements_opt( + pub fn retrieve_chunk_elements_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_chunk_opt(chunk_indices, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_chunk_opt(chunk_indices, options)?, + ) } #[cfg(feature = "ndarray")] /// Explicit options version of [`retrieve_chunk_ndarray_if_exists`](Array::retrieve_chunk_ndarray_if_exists). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_ndarray_if_exists_opt( + pub fn retrieve_chunk_ndarray_if_exists_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result>, ArrayError> { - // validate_element_size::(self.data_type())?; // in retrieve_chunk_elements_if_exists let shape = self .chunk_grid() .chunk_shape_u64(chunk_indices, self.shape())? @@ -539,12 +542,11 @@ impl Array { #[cfg(feature = "ndarray")] /// Explicit options version of [`retrieve_chunk_ndarray`](Array::retrieve_chunk_ndarray). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_ndarray_opt( + pub fn retrieve_chunk_ndarray_opt( &self, chunk_indices: &[u64], options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in retrieve_chunk_elements let shape = self .chunk_grid() .chunk_shape_u64(chunk_indices, self.shape())? @@ -561,7 +563,7 @@ impl Array { &self, chunks: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { if chunks.dimensionality() != self.dimensionality() { return Err(ArrayError::InvalidArraySubset( chunks.clone(), @@ -575,25 +577,22 @@ impl Array { /// Explicit options version of [`retrieve_chunks_elements`](Array::retrieve_chunks_elements). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunks_elements_opt( + pub fn retrieve_chunks_elements_opt( &self, chunks: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_chunks_opt(chunks, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes(self.data_type(), self.retrieve_chunks_opt(chunks, options)?) } #[cfg(feature = "ndarray")] /// Explicit options version of [`retrieve_chunks_ndarray`](Array::retrieve_chunks_ndarray). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunks_ndarray_opt( + pub fn retrieve_chunks_ndarray_opt( &self, chunks: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in retrieve_chunks_elements_opt let array_subset = self.chunks_subset(chunks)?; let elements = self.retrieve_chunks_elements_opt::(chunks, options)?; elements_to_ndarray(array_subset.shape(), elements) @@ -601,11 +600,12 @@ impl Array { /// Explicit options version of [`retrieve_array_subset`](Array::retrieve_array_subset). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] + #[allow(clippy::too_many_lines)] pub fn retrieve_array_subset_opt( &self, array_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { if array_subset.dimensionality() != self.dimensionality() { return Err(ArrayError::InvalidArraySubset( array_subset.clone(), @@ -625,10 +625,10 @@ impl Array { // Retrieve chunk bytes let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => Ok(self - .fill_value() - .as_ne_bytes() - .repeat(array_subset.num_elements_usize())), + 0 => Ok(ArrayBytes::new_fill_value( + array_subset.num_elements_usize(), + self.fill_value(), + )), 1 => { let chunk_indices = chunks.start(); let chunk_subset = self.chunk_subset(chunk_indices)?; @@ -646,13 +646,10 @@ impl Array { } } _ => { - // Allocate the output - let size_output = array_subset.num_elements_usize() * self.data_type().size(); - let mut output = Vec::with_capacity(size_output); - - // Calculate chunk/codec concurrency let chunk_representation = self.chunk_array_representation(&vec![0; self.dimensionality()])?; + + // Calculate chunk/codec concurrency let codec_concurrency = self.recommended_codec_concurrency(&chunk_representation)?; let (chunk_concurrent_limit, options) = concurrency_chunks_and_codec( @@ -662,73 +659,100 @@ impl Array { &codec_concurrency, ); - { - let output = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); - let retrieve_chunk = |chunk_indices: Vec| { - let chunk_subset = self.chunk_subset(&chunk_indices)?; - let chunk_subset_overlap = chunk_subset.overlap(array_subset)?; - let chunk_subset_bytes = self.retrieve_chunk_subset_opt( - &chunk_indices, - &chunk_subset_overlap.relative_to(chunk_subset.start())?, - &options, - )?; - let contiguous_indices = unsafe { - chunk_subset_overlap - .relative_to(array_subset.start())? - .contiguous_linearised_indices_unchecked(array_subset.shape()) + match chunk_representation.data_type().size() { + DataTypeSize::Variable => { + // Retrieve all the chunks + let retrieve_chunk = |chunk_indices: Vec| -> Result< + (ArrayBytes<'_>, ArraySubset), + ArrayError, + > { + let chunk_subset = self.chunk_subset(&chunk_indices)?; + let chunk_subset_overlap = chunk_subset.overlap(array_subset)?; + Ok(( + self.retrieve_chunk_subset_opt( + &chunk_indices, + &chunk_subset_overlap.relative_to(chunk_subset.start())?, + &options, + )?, + chunk_subset_overlap.relative_to(array_subset.start())?, + )) }; - let element_size = self.data_type().size(); - let length = contiguous_indices.contiguous_elements_usize() * element_size; - let mut decoded_offset = 0; - // FIXME: Par iteration? - let output = unsafe { output.get() }; - for (array_subset_element_index, _num_elements) in &contiguous_indices { - let output_offset = - usize::try_from(array_subset_element_index).unwrap() * element_size; - debug_assert!((output_offset + length) <= output.len()); - debug_assert!((decoded_offset + length) <= chunk_subset_bytes.len()); - output[output_offset..output_offset + length].copy_from_slice( - &chunk_subset_bytes[decoded_offset..decoded_offset + length], - ); - decoded_offset += length; + let chunk_indices = chunks.indices(); + let chunk_bytes_and_subsets = iter_concurrent_limit!( + chunk_concurrent_limit, + chunk_indices, + map, + retrieve_chunk + ) + .collect::, _>>()?; + + Ok(merge_chunks_vlen( + chunk_bytes_and_subsets, + array_subset.shape(), + )?) + } + DataTypeSize::Fixed(data_type_size) => { + // Allocate the output + let size_output = array_subset.num_elements_usize() * data_type_size; + let mut output = Vec::with_capacity(size_output); + + { + let output = + UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); + let retrieve_chunk = |chunk_indices: Vec| { + let chunk_subset = self.chunk_subset(&chunk_indices)?; + let chunk_subset_overlap = chunk_subset.overlap(array_subset)?; + let chunk_subset_bytes = self.retrieve_chunk_subset_opt( + &chunk_indices, + &chunk_subset_overlap.relative_to(chunk_subset.start())?, + &options, + )?; + update_bytes_flen( + unsafe { output.get() }, + array_subset.shape(), + &chunk_subset_bytes.into_fixed()?, + &chunk_subset_overlap.relative_to(array_subset.start())?, + data_type_size, + ); + Ok::<_, ArrayError>(()) + }; + let indices = chunks.indices(); + iter_concurrent_limit!( + chunk_concurrent_limit, + indices, + try_for_each, + retrieve_chunk + )?; } - Ok::<_, ArrayError>(()) - }; - let indices = chunks.indices(); - iter_concurrent_limit!( - chunk_concurrent_limit, - indices, - try_for_each, - retrieve_chunk - )?; + unsafe { output.set_len(size_output) }; + Ok(ArrayBytes::from(output)) + } } - unsafe { output.set_len(size_output) }; - Ok(output) } } } /// Explicit options version of [`retrieve_array_subset_elements`](Array::retrieve_array_subset_elements). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_array_subset_elements_opt( + pub fn retrieve_array_subset_elements_opt( &self, array_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_array_subset_opt(array_subset, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_array_subset_opt(array_subset, options)?, + ) } #[cfg(feature = "ndarray")] /// Explicit options version of [`retrieve_array_subset_ndarray`](Array::retrieve_array_subset_ndarray). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_array_subset_ndarray_opt( + pub fn retrieve_array_subset_ndarray_opt( &self, array_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in retrieve_array_subset_elements_opt let elements = self.retrieve_array_subset_elements_opt::(array_subset, options)?; elements_to_ndarray(array_subset.shape(), elements) } @@ -740,7 +764,7 @@ impl Array { chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result, ArrayError> { let chunk_representation = self.chunk_array_representation(chunk_indices)?; if !chunk_subset.inbounds(&chunk_representation.shape_u64()) { return Err(ArrayError::InvalidArraySubset( @@ -749,7 +773,7 @@ impl Array { )); } - let decoded_bytes = if chunk_subset.start().iter().all(|&o| o == 0) + let bytes = if chunk_subset.start().iter().all(|&o| o == 0) && chunk_subset.shape() == chunk_representation.shape_u64() { // Fast path if `chunk_subset` encompasses the whole chunk @@ -764,51 +788,39 @@ impl Array { data_key(self.path(), chunk_indices, self.chunk_key_encoding()), )); - unsafe { - self.codecs() - .partial_decoder(input_handle, &chunk_representation, options)? - .partial_decode_opt(&[chunk_subset.clone()], options)? - .pop() - .unwrap_unchecked() - .into_owned() - } + self.codecs() + .partial_decoder(input_handle, &chunk_representation, options)? + .partial_decode_opt(&[chunk_subset.clone()], options)? + .remove(0) + .into_owned() }; - - let total_size = decoded_bytes.len(); - let expected_size = chunk_subset.num_elements_usize() * self.data_type().size(); - if total_size == chunk_subset.num_elements_usize() * self.data_type().size() { - Ok(decoded_bytes) - } else { - Err(ArrayError::UnexpectedChunkDecodedSize( - total_size, - expected_size, - )) - } + bytes.validate(chunk_subset.num_elements(), self.data_type().size())?; + Ok(bytes) } /// Explicit options version of [`retrieve_chunk_subset_elements`](Array::retrieve_chunk_subset_elements). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_subset_elements_opt( + pub fn retrieve_chunk_subset_elements_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_chunk_subset_opt(chunk_indices, chunk_subset, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_chunk_subset_opt(chunk_indices, chunk_subset, options)?, + ) } #[cfg(feature = "ndarray")] /// Explicit options version of [`retrieve_chunk_subset_ndarray`](Array::retrieve_chunk_subset_ndarray). #[allow(clippy::missing_errors_doc)] - pub fn retrieve_chunk_subset_ndarray_opt( + pub fn retrieve_chunk_subset_ndarray_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - // validate_element_size::(self.data_type())?; // in retrieve_chunk_subset_elements let elements = self.retrieve_chunk_subset_elements_opt::(chunk_indices, chunk_subset, options)?; elements_to_ndarray(chunk_subset.shape(), elements) diff --git a/src/array/array_sync_readable_writable.rs b/src/array/array_sync_readable_writable.rs index f728c889..28dc1185 100644 --- a/src/array/array_sync_readable_writable.rs +++ b/src/array/array_sync_readable_writable.rs @@ -1,11 +1,10 @@ use rayon::iter::{IntoParallelIterator, ParallelIterator}; -use crate::{ - array::validate_element_size, array_subset::ArraySubset, storage::ReadableWritableStorageTraits, -}; +use crate::{array::ArrayBytes, array_subset::ArraySubset, storage::ReadableWritableStorageTraits}; use super::{ - codec::options::CodecOptions, concurrency::concurrency_chunks_and_codec, Array, ArrayError, + array_bytes::update_array_bytes, codec::options::CodecOptions, + concurrency::concurrency_chunks_and_codec, Array, ArrayError, Element, }; impl Array { @@ -23,11 +22,11 @@ impl Array /// # Panics /// Panics if attempting to reference a byte beyond `usize::MAX`. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunk_subset( + pub fn store_chunk_subset<'a>( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - chunk_subset_bytes: &[u8], + chunk_subset_bytes: impl Into>, ) -> Result<(), ArrayError> { self.store_chunk_subset_opt( chunk_indices, @@ -47,7 +46,7 @@ impl Array /// - the size of `T` does not match the data type size, or /// - a [`store_chunk_subset`](Array::store_chunk_subset) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunk_subset_elements( + pub fn store_chunk_subset_elements( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, @@ -70,7 +69,7 @@ impl Array /// # Errors /// Returns an [`ArrayError`] if a [`store_chunk_subset_elements`](Array::store_chunk_subset_elements) error condition is met. pub fn store_chunk_subset_ndarray< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -99,10 +98,10 @@ impl Array /// - there is a codec encoding error, or /// - an underlying store error. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_array_subset( + pub fn store_array_subset<'a>( &self, array_subset: &ArraySubset, - subset_bytes: &[u8], + subset_bytes: impl Into>, ) -> Result<(), ArrayError> { self.store_array_subset_opt(array_subset, subset_bytes, &CodecOptions::default()) } @@ -117,7 +116,7 @@ impl Array /// - the size of `T` does not match the data type size, or /// - a [`store_array_subset`](Array::store_array_subset) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_array_subset_elements( + pub fn store_array_subset_elements( &self, array_subset: &ArraySubset, subset_elements: &[T], @@ -139,7 +138,7 @@ impl Array /// Returns an [`ArrayError`] if a [`store_array_subset_elements`](Array::store_array_subset_elements) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub fn store_array_subset_ndarray< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -156,11 +155,11 @@ impl Array /// Explicit options version of [`store_chunk_subset`](Array::store_chunk_subset). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunk_subset_opt( + pub fn store_chunk_subset_opt<'a>( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, - chunk_subset_bytes: &[u8], + chunk_subset_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { let chunk_shape = self @@ -176,67 +175,55 @@ impl Array chunk_shape, )); } - let expected_length = - chunk_subset.shape().iter().product::() * self.data_type().size() as u64; - if chunk_subset_bytes.len() as u64 != expected_length { - return Err(ArrayError::InvalidBytesInputSize( - chunk_subset_bytes.len(), - expected_length, - )); - } if chunk_subset.shape() == chunk_shape && chunk_subset.start().iter().all(|&x| x == 0) { // The subset spans the whole chunk, so store the bytes directly and skip decoding self.store_chunk_opt(chunk_indices, chunk_subset_bytes, options) } else { + let chunk_subset_bytes = chunk_subset_bytes.into(); + chunk_subset_bytes.validate(chunk_subset.num_elements(), self.data_type().size())?; + // Lock the chunk // let key = data_key(self.path(), chunk_indices, self.chunk_key_encoding()); // let mutex = self.storage.mutex(&key)?; // let _lock = mutex.lock(); // Decode the entire chunk - let mut chunk_bytes = self.retrieve_chunk_opt(chunk_indices, options)?; + let chunk_bytes_old = self.retrieve_chunk_opt(chunk_indices, options)?; + chunk_bytes_old.validate(chunk_shape.iter().product(), self.data_type().size())?; - // Update the intersecting subset of the chunk - let element_size = self.data_type().size(); - let mut offset = 0; - let contiguous_indices = - unsafe { chunk_subset.contiguous_linearised_indices_unchecked(&chunk_shape) }; - let length = contiguous_indices.contiguous_elements_usize() * element_size; - // FIXME: Par iter? - for (chunk_element_index, _num_elements) in &contiguous_indices { - let chunk_offset = usize::try_from(chunk_element_index).unwrap() * element_size; - debug_assert!(chunk_offset + length <= chunk_bytes.len()); - debug_assert!(offset + length <= chunk_subset_bytes.len()); - chunk_bytes[chunk_offset..chunk_offset + length] - .copy_from_slice(&chunk_subset_bytes[offset..offset + length]); - offset += length; - } + // Update the chunk + let chunk_bytes_new = update_array_bytes( + chunk_bytes_old, + chunk_shape, + chunk_subset_bytes, + chunk_subset, + self.data_type().size(), + ); // Store the updated chunk - self.store_chunk_opt(chunk_indices, &chunk_bytes, options) + self.store_chunk_opt(chunk_indices, chunk_bytes_new, options) } } /// Explicit options version of [`store_chunk_subset_elements`](Array::store_chunk_subset_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunk_subset_elements_opt( + pub fn store_chunk_subset_elements_opt( &self, chunk_indices: &[u64], chunk_subset: &ArraySubset, chunk_subset_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunk_subset_elements = crate::array::transmute_to_bytes(chunk_subset_elements); - self.store_chunk_subset_opt(chunk_indices, chunk_subset, chunk_subset_elements, options) + let chunk_subset_bytes = T::into_array_bytes(self.data_type(), chunk_subset_elements)?; + self.store_chunk_subset_opt(chunk_indices, chunk_subset, chunk_subset_bytes, options) } #[cfg(feature = "ndarray")] /// Explicit options version of [`store_chunk_subset_ndarray`](Array::store_chunk_subset_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub fn store_chunk_subset_ndarray_opt< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -246,7 +233,6 @@ impl Array chunk_subset_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunk_subset_array: ndarray::Array = chunk_subset_array.into(); let subset = ArraySubset::new_with_start_shape( chunk_subset_start.to_vec(), @@ -262,10 +248,11 @@ impl Array /// Explicit options version of [`store_array_subset`](Array::store_array_subset). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_array_subset_opt( + #[allow(clippy::too_many_lines)] + pub fn store_array_subset_opt<'a>( &self, array_subset: &ArraySubset, - subset_bytes: &[u8], + subset_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { // Validation @@ -275,13 +262,6 @@ impl Array self.shape().to_vec(), )); } - let expected_size = array_subset.num_elements() * self.data_type().size() as u64; - if subset_bytes.len() as u64 != expected_size { - return Err(ArrayError::InvalidBytesInputSize( - subset_bytes.len(), - expected_size, - )); - } // Find the chunks intersecting this array subset let chunks = self.chunks_in_array_subset(array_subset)?; @@ -294,38 +274,23 @@ impl Array let num_chunks = chunks.num_elements_usize(); if num_chunks == 1 { let chunk_indices = chunks.start(); - let chunk_subset_in_array = unsafe { - self.chunk_grid() - .subset_unchecked(chunk_indices, self.shape()) - .unwrap() - }; - if array_subset == &chunk_subset_in_array { + let chunk_subset = self.chunk_subset(chunk_indices)?; + if array_subset == &chunk_subset { // A fast path if the array subset matches the chunk subset // This skips the internal decoding occurring in store_chunk_subset self.store_chunk_opt(chunk_indices, subset_bytes, options)?; } else { - let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset_in_array) }; - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - let chunk_subset_bytes = unsafe { - chunk_subset_in_array_subset.extract_bytes_unchecked( - subset_bytes, - array_subset.shape(), - self.data_type().size(), - ) - }; - // Store the chunk subset - let array_subset_in_chunk_subset = - unsafe { overlap.relative_to_unchecked(chunk_subset_in_array.start()) }; self.store_chunk_subset_opt( chunk_indices, - &array_subset_in_chunk_subset, - &chunk_subset_bytes, + &array_subset.relative_to(chunk_subset.start())?, + subset_bytes, options, )?; } } else { + let subset_bytes = subset_bytes.into(); + subset_bytes.validate(array_subset.num_elements(), self.data_type().size())?; // Calculate chunk/codec concurrency let chunk_representation = self.chunk_array_representation(&vec![0; self.dimensionality()])?; @@ -338,27 +303,21 @@ impl Array ); let store_chunk = |chunk_indices: Vec| -> Result<(), ArrayError> { - let chunk_subset_in_array = unsafe { - self.chunk_grid() - .subset_unchecked(&chunk_indices, self.shape()) - .unwrap() - }; + let chunk_subset_in_array = self.chunk_subset(&chunk_indices)?; let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset_in_array) }; let chunk_subset_in_array_subset = unsafe { overlap.relative_to_unchecked(array_subset.start()) }; + let chunk_subset_bytes = subset_bytes.extract_array_subset( + &chunk_subset_in_array_subset, + array_subset.shape(), + self.data_type(), + )?; let array_subset_in_chunk_subset = unsafe { overlap.relative_to_unchecked(chunk_subset_in_array.start()) }; - let chunk_subset_bytes = unsafe { - chunk_subset_in_array_subset.extract_bytes_unchecked( - subset_bytes, - array_subset.shape(), - self.data_type().size(), - ) - }; self.store_chunk_subset_opt( &chunk_indices, &array_subset_in_chunk_subset, - &chunk_subset_bytes, + chunk_subset_bytes, &options, ) }; @@ -376,22 +335,21 @@ impl Array /// Explicit options version of [`store_array_subset_elements`](Array::store_array_subset_elements). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_array_subset_elements_opt( + pub fn store_array_subset_elements_opt( &self, array_subset: &ArraySubset, subset_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let subset_elements = crate::array::transmute_to_bytes(subset_elements); - self.store_array_subset_opt(array_subset, subset_elements, options) + let subset_bytes = T::into_array_bytes(self.data_type(), subset_elements)?; + self.store_array_subset_opt(array_subset, subset_bytes, options) } #[cfg(feature = "ndarray")] /// Explicit options version of [`store_array_subset_ndarray`](Array::store_array_subset_ndarray). #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub fn store_array_subset_ndarray_opt< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -400,7 +358,6 @@ impl Array subset_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let subset_array: ndarray::Array = subset_array.into(); let subset = ArraySubset::new_with_start_shape( subset_start.to_vec(), diff --git a/src/array/array_sync_sharded_readable_ext.rs b/src/array/array_sync_sharded_readable_ext.rs index c9207829..048733db 100644 --- a/src/array/array_sync_sharded_readable_ext.rs +++ b/src/array/array_sync_sharded_readable_ext.rs @@ -3,10 +3,13 @@ use std::{collections::HashMap, sync::Arc}; use rayon::iter::{IntoParallelIterator, ParallelIterator}; use rayon_iter_concurrent_limit::iter_concurrent_limit; +use super::array_bytes::{merge_chunks_vlen, update_bytes_flen}; +use super::element::ElementOwned; use super::{ - codec::CodecOptions, concurrency::concurrency_chunks_and_codec, transmute_from_bytes_vec, - validate_element_size, Array, ArrayError, ArrayShardedExt, ChunkGrid, UnsafeCellSlice, + codec::CodecOptions, concurrency::concurrency_chunks_and_codec, Array, ArrayError, + ArrayShardedExt, ChunkGrid, UnsafeCellSlice, }; +use super::{ArrayBytes, DataTypeSize}; use crate::storage::ReadableStorageTraits; use crate::{array::codec::ArrayPartialDecoderTraits, array_subset::ArraySubset}; @@ -93,13 +96,13 @@ pub trait ArrayShardedReadableExt, inner_chunk_indices: &[u64], options: &CodecOptions, - ) -> Result, ArrayError>; + ) -> Result; /// Read and decode the inner chunk at `chunk_indices` into a vector of its elements. /// /// See [`Array::retrieve_chunk_elements_opt`]. #[allow(clippy::missing_errors_doc)] - fn retrieve_inner_chunk_elements_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunk_elements_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunk_indices: &[u64], @@ -111,7 +114,7 @@ pub trait ArrayShardedReadableExt( + fn retrieve_inner_chunk_ndarray_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunk_indices: &[u64], @@ -127,13 +130,13 @@ pub trait ArrayShardedReadableExt, inner_chunks: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError>; + ) -> Result; /// Read and decode the inner chunks at `inner_chunks` into a vector of their elements. /// /// See [`Array::retrieve_chunks_elements_opt`]. #[allow(clippy::missing_errors_doc)] - fn retrieve_inner_chunks_elements_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunks_elements_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunks: &ArraySubset, @@ -145,7 +148,7 @@ pub trait ArrayShardedReadableExt( + fn retrieve_inner_chunks_ndarray_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunks: &ArraySubset, @@ -161,13 +164,13 @@ pub trait ArrayShardedReadableExt, array_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError>; + ) -> Result; /// Read and decode the `array_subset` of array into a vector of its elements. /// /// See [`Array::retrieve_array_subset_elements_opt`]. #[allow(clippy::missing_errors_doc)] - fn retrieve_array_subset_elements_sharded_opt<'a, T: bytemuck::Pod>( + fn retrieve_array_subset_elements_sharded_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, array_subset: &ArraySubset, @@ -179,7 +182,7 @@ pub trait ArrayShardedReadableExt( + fn retrieve_array_subset_ndarray_sharded_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, array_subset: &ArraySubset, @@ -195,7 +198,7 @@ impl ArrayShardedReadableExt cache: &ArrayShardedReadableExtCache<'a>, inner_chunk_indices: &[u64], options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result { if cache.array_is_sharded() { let array_subset = cache .inner_chunk_grid() @@ -217,29 +220,30 @@ impl ArrayShardedReadableExt let shard_subset = array_subset.relative_to(&shard_origin)?; let partial_decoder = cache.retrieve(self, shard_indices)?; - Ok(partial_decoder + let bytes = partial_decoder .partial_decode_opt(&[shard_subset], options)? - .pop() - .expect("partial_decode_opt called with one subset, returned without error") - .into_owned()) + .remove(0) + .into_owned(); + Ok(bytes) } else { self.retrieve_chunk_opt(inner_chunk_indices, options) } } - fn retrieve_inner_chunk_elements_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunk_elements_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunk_indices: &[u64], options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_inner_chunk_opt(cache, inner_chunk_indices, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_inner_chunk_opt(cache, inner_chunk_indices, options)?, + ) } #[cfg(feature = "ndarray")] - fn retrieve_inner_chunk_ndarray_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunk_ndarray_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunk_indices: &[u64], @@ -260,7 +264,7 @@ impl ArrayShardedReadableExt cache: &ArrayShardedReadableExtCache<'a>, inner_chunks: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result { if cache.array_is_sharded() { let inner_chunk_grid = cache.inner_chunk_grid(); let array_subset = inner_chunk_grid @@ -280,19 +284,20 @@ impl ArrayShardedReadableExt } } - fn retrieve_inner_chunks_elements_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunks_elements_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunks: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_inner_chunks_opt(cache, inner_chunks, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_inner_chunks_opt(cache, inner_chunks, options)?, + ) } #[cfg(feature = "ndarray")] - fn retrieve_inner_chunks_ndarray_opt<'a, T: bytemuck::Pod>( + fn retrieve_inner_chunks_ndarray_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, inner_chunks: &ArraySubset, @@ -315,12 +320,13 @@ impl ArrayShardedReadableExt super::elements_to_ndarray(array_subset.shape(), elements) } + #[allow(clippy::too_many_lines)] fn retrieve_array_subset_sharded_opt<'a>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, array_subset: &ArraySubset, options: &CodecOptions, - ) -> Result, ArrayError> { + ) -> Result { if cache.array_is_sharded() { // Find the shards intersecting this array subset let shards = self.chunks_in_array_subset(array_subset)?; @@ -334,15 +340,11 @@ impl ArrayShardedReadableExt // Retrieve chunk bytes let num_shards = shards.num_elements_usize(); if num_shards == 0 { - Ok(self - .fill_value() - .as_ne_bytes() - .repeat(array_subset.num_elements_usize())) + Ok(ArrayBytes::new_fill_value( + array_subset.num_elements_usize(), + self.fill_value(), + )) } else { - // Allocate the output - let size_output = array_subset.num_elements_usize() * self.data_type().size(); - let mut output = Vec::with_capacity(size_output); - // Calculate chunk/codec concurrency let chunk_representation = self.chunk_array_representation(&vec![0; self.dimensionality()])?; @@ -355,77 +357,106 @@ impl ArrayShardedReadableExt &codec_concurrency, ); - { - let output = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); - let retrieve_shard = |shard_indices: Vec| { - let shard_subset = self.chunk_subset(&shard_indices)?; - let shard_subset_overlap = shard_subset.overlap(array_subset)?; - // let shard_subset_bytes = self.retrieve_chunk_subset_opt( - // &shard_indices, - // &shard_subset_overlap.relative_to(shard_subset.start())?, - // &options, - // )?; - let shard_subset_bytes = cache - .retrieve(self, &shard_indices)? - .partial_decode_opt( - &[shard_subset_overlap.relative_to(shard_subset.start())?], - &options, - )? - .pop() - .unwrap() - .into_owned(); - - let contiguous_indices = unsafe { - shard_subset_overlap - .relative_to(array_subset.start())? - .contiguous_linearised_indices_unchecked(array_subset.shape()) + match self.data_type().size() { + DataTypeSize::Variable => { + let retrieve_inner_chunk = |shard_indices: Vec| -> Result< + (ArrayBytes<'_>, ArraySubset), + ArrayError, + > { + let shard_subset = self.chunk_subset(&shard_indices)?; + let shard_subset_overlap = shard_subset.overlap(array_subset)?; + let bytes = cache + .retrieve(self, &shard_indices)? + .partial_decode_opt( + &[shard_subset_overlap.relative_to(shard_subset.start())?], + &options, + )? + .remove(0) + .into_owned(); + Ok(( + bytes, + shard_subset_overlap.relative_to(array_subset.start())?, + )) }; - let element_size = self.data_type().size(); - let length = contiguous_indices.contiguous_elements_usize() * element_size; - let mut decoded_offset = 0; - // FIXME: Par iteration? - let output = unsafe { output.get() }; - for (array_subset_element_index, _num_elements) in &contiguous_indices { - let output_offset = - usize::try_from(array_subset_element_index).unwrap() * element_size; - debug_assert!((output_offset + length) <= output.len()); - debug_assert!((decoded_offset + length) <= shard_subset_bytes.len()); - output[output_offset..output_offset + length].copy_from_slice( - &shard_subset_bytes[decoded_offset..decoded_offset + length], - ); - decoded_offset += length; + + let indices = shards.indices(); + let chunk_bytes_and_subsets = iter_concurrent_limit!( + chunk_concurrent_limit, + indices, + map, + retrieve_inner_chunk + ) + .collect::, _>>()?; + + Ok(merge_chunks_vlen( + chunk_bytes_and_subsets, + array_subset.shape(), + )?) + } + DataTypeSize::Fixed(data_type_size) => { + let size_output = array_subset.num_elements_usize() * data_type_size; + let mut output = Vec::with_capacity(size_output); + { + let output = + UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut output); + let retrieve_shard_into_slice = |shard_indices: Vec| { + let shard_subset = self.chunk_subset(&shard_indices)?; + let shard_subset_overlap = shard_subset.overlap(array_subset)?; + // let shard_subset_bytes = self.retrieve_chunk_subset_opt( + // &shard_indices, + // &shard_subset_overlap.relative_to(shard_subset.start())?, + // &options, + // )?; + let bytes = cache + .retrieve(self, &shard_indices)? + .partial_decode_opt( + &[shard_subset_overlap + .relative_to(shard_subset.start())?], + &options, + )? + .remove(0) + .into_owned(); + update_bytes_flen( + unsafe { output.get() }, + array_subset.shape(), + &bytes.into_fixed()?, + &shard_subset_overlap.relative_to(array_subset.start())?, + data_type_size, + ); + Ok::<_, ArrayError>(()) + }; + let indices = shards.indices(); + iter_concurrent_limit!( + chunk_concurrent_limit, + indices, + try_for_each, + retrieve_shard_into_slice + )?; } - Ok::<_, ArrayError>(()) - }; - let indices = shards.indices(); - iter_concurrent_limit!( - chunk_concurrent_limit, - indices, - try_for_each, - retrieve_shard - )?; + unsafe { output.set_len(size_output) }; + Ok(ArrayBytes::from(output)) + } } - unsafe { output.set_len(size_output) }; - Ok(output) } } else { self.retrieve_array_subset_opt(array_subset, options) } } - fn retrieve_array_subset_elements_sharded_opt<'a, T: bytemuck::Pod>( + fn retrieve_array_subset_elements_sharded_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, array_subset: &ArraySubset, options: &CodecOptions, ) -> Result, ArrayError> { - validate_element_size::(self.data_type())?; - let bytes = self.retrieve_array_subset_sharded_opt(cache, array_subset, options)?; - Ok(transmute_from_bytes_vec::(bytes)) + T::from_array_bytes( + self.data_type(), + self.retrieve_array_subset_sharded_opt(cache, array_subset, options)?, + ) } #[cfg(feature = "ndarray")] - fn retrieve_array_subset_ndarray_sharded_opt<'a, T: bytemuck::Pod>( + fn retrieve_array_subset_ndarray_sharded_opt<'a, T: ElementOwned>( &'a self, cache: &ArrayShardedReadableExtCache<'a>, array_subset: &ArraySubset, diff --git a/src/array/array_sync_writable.rs b/src/array/array_sync_writable.rs index acbf074b..971dccbd 100644 --- a/src/array/array_sync_writable.rs +++ b/src/array/array_sync_writable.rs @@ -1,10 +1,10 @@ -use std::{borrow::Cow, sync::Arc}; +use std::sync::Arc; use rayon::iter::{IntoParallelIterator, ParallelIterator}; use rayon_iter_concurrent_limit::iter_concurrent_limit; use crate::{ - array::validate_element_size, + array::ArrayBytes, array_subset::ArraySubset, metadata::MetadataEraseVersion, storage::{ @@ -14,9 +14,9 @@ use crate::{ }; use super::{ - codec::{options::CodecOptions, ArrayCodecTraits}, + codec::{options::CodecOptions, ArrayToBytesCodecTraits}, concurrency::concurrency_chunks_and_codec, - Array, ArrayError, ArrayMetadata, ArrayMetadataOptions, + Array, ArrayError, ArrayMetadata, ArrayMetadataOptions, Element, }; impl Array { @@ -58,7 +58,11 @@ impl Array { /// - the length of `chunk_bytes` is not equal to the expected length (the product of the number of elements in the chunk and the data type size in bytes), /// - there is a codec encoding error, or /// - an underlying store error. - pub fn store_chunk(&self, chunk_indices: &[u64], chunk_bytes: &[u8]) -> Result<(), ArrayError> { + pub fn store_chunk<'a>( + &self, + chunk_indices: &[u64], + chunk_bytes: impl Into>, + ) -> Result<(), ArrayError> { self.store_chunk_opt(chunk_indices, chunk_bytes, &CodecOptions::default()) } @@ -71,7 +75,7 @@ impl Array { /// Returns an [`ArrayError`] if /// - the size of `T` does not match the data type size, or /// - a [`store_chunk`](Array::store_chunk) error condition is met. - pub fn store_chunk_elements( + pub fn store_chunk_elements( &self, chunk_indices: &[u64], chunk_elements: &[T], @@ -90,7 +94,7 @@ impl Array { /// - a [`store_chunk_elements`](Array::store_chunk_elements) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub fn store_chunk_ndarray< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -114,10 +118,10 @@ impl Array { /// - an underlying store error. #[allow(clippy::similar_names)] #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunks( + pub fn store_chunks<'a>( &self, chunks: &ArraySubset, - chunks_bytes: &[u8], + chunks_bytes: impl Into>, ) -> Result<(), ArrayError> { self.store_chunks_opt(chunks, chunks_bytes, &CodecOptions::default()) } @@ -129,7 +133,7 @@ impl Array { /// - the size of `T` does not match the data type size, or /// - a [`store_chunks`](Array::store_chunks) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] - pub fn store_chunks_elements( + pub fn store_chunks_elements( &self, chunks: &ArraySubset, chunks_elements: &[T], @@ -146,7 +150,7 @@ impl Array { /// - a [`store_chunks_elements`](Array::store_chunks_elements) error condition is met. #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] pub fn store_chunks_ndarray< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -242,24 +246,25 @@ impl Array { /// Explicit options version of [`store_chunk`](Array::store_chunk). #[allow(clippy::missing_errors_doc)] - pub fn store_chunk_opt( + pub fn store_chunk_opt<'a>( &self, chunk_indices: &[u64], - chunk_bytes: &[u8], + chunk_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { + let chunk_bytes = chunk_bytes.into(); + // Validation let chunk_array_representation = self.chunk_array_representation(chunk_indices)?; - if chunk_bytes.len() as u64 != chunk_array_representation.size() { - return Err(ArrayError::InvalidBytesInputSize( - chunk_bytes.len(), - chunk_array_representation.size(), - )); - } + chunk_bytes.validate( + chunk_array_representation.num_elements(), + chunk_array_representation.data_type().size(), + )?; - if !options.store_empty_chunks() && self.fill_value().equals_all(chunk_bytes) { + let is_fill_value = + !options.store_empty_chunks() && chunk_bytes.is_fill_value(self.fill_value()); + if is_fill_value { self.erase_chunk(chunk_indices)?; - Ok(()) } else { let storage_handle = Arc::new(StorageHandle::new(self.storage.clone())); let storage_transformer = self @@ -267,11 +272,7 @@ impl Array { .create_writable_transformer(storage_handle); let chunk_encoded = self .codecs() - .encode( - Cow::Borrowed(chunk_bytes), - &chunk_array_representation, - options, - ) + .encode(chunk_bytes, &chunk_array_representation, options) .map_err(ArrayError::CodecError)?; crate::storage::store_chunk( &*storage_transformer, @@ -279,29 +280,28 @@ impl Array { chunk_indices, self.chunk_key_encoding(), Bytes::from(chunk_encoded.into_owned()), - ) - .map_err(ArrayError::StorageError) + )?; } + Ok(()) } /// Explicit options version of [`store_chunk_elements`](Array::store_chunk_elements). #[allow(clippy::missing_errors_doc)] - pub fn store_chunk_elements_opt( + pub fn store_chunk_elements_opt( &self, chunk_indices: &[u64], chunk_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunk_elements = crate::array::transmute_to_bytes(chunk_elements); - self.store_chunk_opt(chunk_indices, chunk_elements, options) + let chunk_bytes = T::into_array_bytes(self.data_type(), chunk_elements)?; + self.store_chunk_opt(chunk_indices, chunk_bytes, options) } #[cfg(feature = "ndarray")] /// Explicit options version of [`store_chunk_ndarray`](Array::store_chunk_ndarray). #[allow(clippy::missing_errors_doc)] pub fn store_chunk_ndarray_opt< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -310,12 +310,11 @@ impl Array { chunk_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunk_array: ndarray::Array = chunk_array.into(); let chunk_shape = self.chunk_shape_usize(chunk_indices)?; if chunk_array.shape() == chunk_shape { let chunk_array = super::ndarray_into_vec(chunk_array); - self.store_chunk_elements_opt(chunk_indices, &chunk_array, options) + self.store_chunk_elements_opt(chunk_indices, chunk_array.as_slice(), options) } else { Err(ArrayError::InvalidDataShape( chunk_array.shape().to_vec(), @@ -326,30 +325,27 @@ impl Array { /// Explicit options version of [`store_chunks`](Array::store_chunks). #[allow(clippy::similar_names)] - #[allow(clippy::missing_errors_doc)] - pub fn store_chunks_opt( + #[allow(clippy::missing_errors_doc, clippy::missing_panics_doc)] + pub fn store_chunks_opt<'a>( &self, chunks: &ArraySubset, - chunks_bytes: &[u8], + chunks_bytes: impl Into>, options: &CodecOptions, ) -> Result<(), ArrayError> { let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => {} + 0 => { + let chunks_bytes = chunks_bytes.into(); + chunks_bytes.validate(0, self.data_type().size())?; + } 1 => { let chunk_indices = chunks.start(); self.store_chunk_opt(chunk_indices, chunks_bytes, options)?; } _ => { + let chunks_bytes = chunks_bytes.into(); let array_subset = self.chunks_subset(chunks)?; - let element_size = self.data_type().size(); - let expected_size = element_size as u64 * array_subset.num_elements(); - if chunks_bytes.len() as u64 != expected_size { - return Err(ArrayError::InvalidBytesInputSize( - chunks_bytes.len(), - expected_size, - )); - } + chunks_bytes.validate(array_subset.num_elements(), self.data_type().size())?; // Calculate chunk/codec concurrency let chunk_representation = @@ -364,32 +360,15 @@ impl Array { ); let store_chunk = |chunk_indices: Vec| -> Result<(), ArrayError> { - let chunk_subset_in_array = unsafe { - self.chunk_grid() - .subset_unchecked(&chunk_indices, self.shape()) - .ok_or_else(|| { - ArrayError::InvalidChunkGridIndicesError(chunk_indices.clone()) - })? - }; - let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset_in_array) }; - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - #[allow(clippy::similar_names)] - let chunk_bytes = unsafe { - chunk_subset_in_array_subset.extract_bytes_unchecked( - chunks_bytes, - array_subset.shape(), - element_size, - ) - }; - - debug_assert_eq!( - chunk_subset_in_array.num_elements(), - chunk_subset_in_array_subset.num_elements() - ); - - self.store_chunk_opt(&chunk_indices, &chunk_bytes, &options) + let chunk_subset = self.chunk_subset(&chunk_indices)?; + let chunk_bytes = chunks_bytes.extract_array_subset( + &chunk_subset.relative_to(array_subset.start())?, + array_subset.shape(), + self.data_type(), + )?; + self.store_chunk_opt(&chunk_indices, chunk_bytes, &options) }; + let indices = chunks.indices(); iter_concurrent_limit!(chunk_concurrent_limit, indices, try_for_each, store_chunk)?; } @@ -400,22 +379,21 @@ impl Array { /// Explicit options version of [`store_chunks_elements`](Array::store_chunks_elements). #[allow(clippy::missing_errors_doc)] - pub fn store_chunks_elements_opt( + pub fn store_chunks_elements_opt( &self, chunks: &ArraySubset, chunks_elements: &[T], options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; - let chunks_elements = crate::array::transmute_to_bytes(chunks_elements); - self.store_chunks_opt(chunks, chunks_elements, options) + let chunks_bytes = T::into_array_bytes(self.data_type(), chunks_elements)?; + self.store_chunks_opt(chunks, chunks_bytes, options) } #[cfg(feature = "ndarray")] /// Explicit options version of [`store_chunks_ndarray`](Array::store_chunks_ndarray). #[allow(clippy::missing_errors_doc)] pub fn store_chunks_ndarray_opt< - T: bytemuck::Pod, + T: Element, TArray: Into>, D: ndarray::Dimension, >( @@ -424,13 +402,12 @@ impl Array { chunks_array: TArray, options: &CodecOptions, ) -> Result<(), ArrayError> { - validate_element_size::(self.data_type())?; let chunks_array: ndarray::Array = chunks_array.into(); let chunks_subset = self.chunks_subset(chunks)?; let chunks_shape = chunks_subset.shape_usize(); if chunks_array.shape() == chunks_shape { let chunks_array = super::ndarray_into_vec(chunks_array); - self.store_chunks_elements_opt(chunks, &chunks_array, options) + self.store_chunks_elements_opt(chunks, chunks_array.as_slice(), options) } else { Err(ArrayError::InvalidDataShape( chunks_array.shape().to_vec(), diff --git a/src/array/codec.rs b/src/array/codec.rs index 4207b1c1..212a1c49 100644 --- a/src/array/codec.rs +++ b/src/array/codec.rs @@ -90,6 +90,7 @@ use super::{ concurrency::RecommendedConcurrency, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, DataType, }; +use super::{ArrayBytes, RawBytes}; /// A codec plugin. pub type CodecPlugin = Plugin; @@ -208,28 +209,6 @@ pub trait ArrayCodecTraits: CodecTraits { decoded_representation: &ChunkRepresentation, ) -> Result; - /// Encode a chunk. - /// - /// # Errors - /// Returns [`CodecError`] if a codec fails or `decoded_value` is incompatible with `decoded_representation`. - fn encode<'a>( - &self, - decoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - options: &CodecOptions, - ) -> Result, CodecError>; - - /// Decode a chunk. - /// - /// # Errors - /// Returns [`CodecError`] if a codec fails or the decoded output is incompatible with `decoded_representation`. - fn decode<'a>( - &self, - encoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - options: &CodecOptions, - ) -> Result, CodecError>; - /// Return the partial decode granularity. /// /// This represents the shape of the smallest subset of a chunk that can be efficiently decoded if the chunk were subdivided into a regular grid. @@ -255,7 +234,7 @@ pub trait BytesPartialDecoderTraits: Send + Sync { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError>; + ) -> Result>>, CodecError>; /// Partially decode bytes and concatenate. /// @@ -269,7 +248,7 @@ pub trait BytesPartialDecoderTraits: Send + Sync { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { Ok(self .partial_decode(decoded_regions, options)? .map(|vecs| Cow::Owned(vecs.concat()))) @@ -281,7 +260,7 @@ pub trait BytesPartialDecoderTraits: Send + Sync { /// /// # Errors /// Returns [`CodecError`] if a codec fails. - fn decode(&self, options: &CodecOptions) -> Result>, CodecError> { + fn decode(&self, options: &CodecOptions) -> Result>, CodecError> { Ok(self .partial_decode(&[ByteRange::FromStart(0, None)], options)? .map(|mut v| v.remove(0))) @@ -302,7 +281,7 @@ pub trait AsyncBytesPartialDecoderTraits: Send + Sync { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError>; + ) -> Result>>, CodecError>; /// Partially decode bytes and concatenate. /// @@ -314,8 +293,7 @@ pub trait AsyncBytesPartialDecoderTraits: Send + Sync { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>, CodecError> { - // FIXME: Remove default implementation in the next major release and implement for each codec to reduce internal allocations + ) -> Result>, CodecError> { Ok(self .partial_decode(decoded_regions, options) .await? @@ -328,7 +306,7 @@ pub trait AsyncBytesPartialDecoderTraits: Send + Sync { /// /// # Errors /// Returns [`CodecError`] if a codec fails. - async fn decode(&self, options: &CodecOptions) -> Result>, CodecError> { + async fn decode(&self, options: &CodecOptions) -> Result>, CodecError> { Ok(self .partial_decode(&[ByteRange::FromStart(0, None)], options) .await? @@ -351,7 +329,7 @@ pub trait ArrayPartialDecoderTraits: Send + Sync { fn partial_decode( &self, array_subsets: &[ArraySubset], - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { self.partial_decode_opt(array_subsets, &CodecOptions::default()) } @@ -361,7 +339,7 @@ pub trait ArrayPartialDecoderTraits: Send + Sync { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError>; + ) -> Result>, CodecError>; } #[cfg(feature = "async")] @@ -378,7 +356,7 @@ pub trait AsyncArrayPartialDecoderTraits: Send + Sync { async fn partial_decode( &self, array_subsets: &[ArraySubset], - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { self.partial_decode_opt(array_subsets, &CodecOptions::default()) .await } @@ -388,7 +366,7 @@ pub trait AsyncArrayPartialDecoderTraits: Send + Sync { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError>; + ) -> Result>, CodecError>; } /// A [`ReadableStorage`] store value partial decoder. @@ -409,7 +387,7 @@ impl BytesPartialDecoderTraits for StoragePartialDecoder { &self, decoded_regions: &[ByteRange], _options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(self .storage .get_partial_values_key(&self.key, decoded_regions)? @@ -444,7 +422,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncStoragePartialDecoder { &self, decoded_regions: &[ByteRange], _options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(self .storage .get_partial_values_key(&self.key, decoded_regions) @@ -473,6 +451,28 @@ pub trait ArrayToArrayCodecTraits: decoded_representation: &ChunkRepresentation, ) -> Result; + /// Encode a chunk. + /// + /// # Errors + /// Returns [`CodecError`] if a codec fails or `bytes` is incompatible with `decoded_representation`. + fn encode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError>; + + /// Decode a chunk. + /// + /// # Errors + /// Returns [`CodecError`] if a codec fails or the decoded output is incompatible with `decoded_representation`. + fn decode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError>; + /// Initialise a partial decoder. /// /// `parallel` only affects parallelism on initialisation, which is irrelevant for most codecs. @@ -519,6 +519,28 @@ pub trait ArrayToBytesCodecTraits: decoded_representation: &ChunkRepresentation, ) -> Result; + /// Encode a chunk. + /// + /// # Errors + /// Returns [`CodecError`] if a codec fails or `bytes` is incompatible with `decoded_representation`. + fn encode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError>; + + /// Decode a chunk. + /// + /// # Errors + /// Returns [`CodecError`] if a codec fails or the decoded output is incompatible with `decoded_representation`. + fn decode<'a>( + &self, + bytes: RawBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError>; + /// Initialise a partial decoder. /// /// # Errors @@ -569,9 +591,9 @@ pub trait BytesToBytesCodecTraits: CodecTraits + dyn_clone::DynClone + core::fmt /// Returns [`CodecError`] if a codec fails. fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, options: &CodecOptions, - ) -> Result, CodecError>; + ) -> Result, CodecError>; /// Decode chunk bytes. // @@ -579,10 +601,10 @@ pub trait BytesToBytesCodecTraits: CodecTraits + dyn_clone::DynClone + core::fmt /// Returns [`CodecError`] if a codec fails. fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, decoded_representation: &BytesRepresentation, options: &CodecOptions, - ) -> Result, CodecError>; + ) -> Result, CodecError>; /// Initialises a partial decoder. /// @@ -615,7 +637,7 @@ impl BytesPartialDecoderTraits for std::io::Cursor<&[u8]> { &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -625,12 +647,12 @@ impl BytesPartialDecoderTraits for std::io::Cursor<&[u8]> { } } -impl BytesPartialDecoderTraits for std::io::Cursor> { +impl BytesPartialDecoderTraits for std::io::Cursor> { fn partial_decode( &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -645,7 +667,7 @@ impl BytesPartialDecoderTraits for std::io::Cursor> { &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -662,7 +684,7 @@ impl AsyncBytesPartialDecoderTraits for std::io::Cursor<&[u8]> { &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -674,12 +696,12 @@ impl AsyncBytesPartialDecoderTraits for std::io::Cursor<&[u8]> { #[cfg(feature = "async")] #[async_trait::async_trait] -impl AsyncBytesPartialDecoderTraits for std::io::Cursor> { +impl AsyncBytesPartialDecoderTraits for std::io::Cursor> { async fn partial_decode( &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -696,7 +718,7 @@ impl AsyncBytesPartialDecoderTraits for std::io::Cursor> { &self, decoded_regions: &[ByteRange], _parallel: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(Some( extract_byte_ranges_read_seek(&mut self.clone(), decoded_regions)? .into_iter() @@ -733,9 +755,21 @@ pub enum CodecError { /// Unsupported data type #[error("Unsupported data type {0} for codec {1}")] UnsupportedDataType(DataType, String), + /// Offsets are not [`None`] with a fixed length data type. + #[error("Offsets are invalid or are not compatible with the data type (e.g. fixed-sized data types)")] + InvalidOffsets, /// Other #[error("{_0}")] Other(String), + /// Invalid variable sized array offsets. + #[error("Invalid variable sized array offsets")] + InvalidVariableSizedArrayOffsets, + /// Expected fixed length bytes. + #[error("Expected fixed length array bytes")] + ExpectedFixedLengthBytes, + /// Expected variable length bytes. + #[error("Expected variable length array bytes")] + ExpectedVariableLengthBytes, } impl From<&str> for CodecError { diff --git a/src/array/codec/array_partial_decoder_cache.rs b/src/array/codec/array_partial_decoder_cache.rs index 6ed0858b..d83c37e7 100644 --- a/src/array/codec/array_partial_decoder_cache.rs +++ b/src/array/codec/array_partial_decoder_cache.rs @@ -1,11 +1,6 @@ //! A cache for partial decoders. -use std::{borrow::Cow, marker::PhantomData}; - -use crate::{ - array::{ChunkRepresentation, DataType}, - array_subset::IncompatibleArraySubsetAndShapeError, -}; +use crate::array::{ArrayBytes, ChunkRepresentation, DataType}; use super::{ArrayPartialDecoderTraits, ArraySubset, CodecError, CodecOptions}; @@ -15,8 +10,7 @@ use super::AsyncArrayPartialDecoderTraits; /// A cache for an [`ArrayPartialDecoderTraits`] partial decoder. pub struct ArrayPartialDecoderCache<'a> { decoded_representation: ChunkRepresentation, - cache: Vec, - phantom: PhantomData<&'a ()>, + cache: ArrayBytes<'a>, } impl<'a> ArrayPartialDecoderCache<'a> { @@ -29,7 +23,7 @@ impl<'a> ArrayPartialDecoderCache<'a> { decoded_representation: ChunkRepresentation, options: &CodecOptions, ) -> Result { - let cache = input_handle + let bytes = input_handle .partial_decode_opt( &[ArraySubset::new_with_shape( decoded_representation.shape_u64(), @@ -40,8 +34,7 @@ impl<'a> ArrayPartialDecoderCache<'a> { .into_owned(); Ok(Self { decoded_representation, - cache, - phantom: PhantomData, + cache: bytes, }) } @@ -55,7 +48,7 @@ impl<'a> ArrayPartialDecoderCache<'a> { decoded_representation: ChunkRepresentation, options: &CodecOptions, ) -> Result, CodecError> { - let cache = input_handle + let bytes = input_handle .partial_decode_opt( &[ArraySubset::new_with_shape( decoded_representation.shape_u64(), @@ -67,8 +60,7 @@ impl<'a> ArrayPartialDecoderCache<'a> { .into_owned(); Ok(Self { decoded_representation, - cache, - phantom: PhantomData, + cache: bytes, }) } } @@ -82,21 +74,15 @@ impl<'a> ArrayPartialDecoderTraits for ArrayPartialDecoderCache<'a> { &self, decoded_regions: &[ArraySubset], _options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { let mut out = Vec::with_capacity(decoded_regions.len()); let array_shape = self.decoded_representation.shape_u64(); - let element_size = self.decoded_representation.element_size(); for array_subset in decoded_regions { - out.push(Cow::Owned( - array_subset - .extract_bytes(&self.cache, &array_shape, element_size) - .map_err(|_| { - IncompatibleArraySubsetAndShapeError::from(( - array_subset.clone(), - self.decoded_representation.shape_u64(), - )) - })?, - )); + out.push(self.cache.extract_array_subset( + array_subset, + &array_shape, + self.decoded_representation.data_type(), + )?); } Ok(out) } @@ -113,7 +99,7 @@ impl<'a> AsyncArrayPartialDecoderTraits for ArrayPartialDecoderCache<'a> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { ArrayPartialDecoderTraits::partial_decode_opt(self, decoded_regions, options) } } diff --git a/src/array/codec/array_to_array/bitround.rs b/src/array/codec/array_to_array/bitround.rs index 9da4292f..56f01e39 100644 --- a/src/array/codec/array_to_array/bitround.rs +++ b/src/array/codec/array_to_array/bitround.rs @@ -175,7 +175,7 @@ fn round_bytes(bytes: &mut [u8], data_type: &DataType, keepbits: u32) -> Result< #[cfg(test)] mod tests { - use std::{borrow::Cow, num::NonZeroU64}; + use std::num::NonZeroU64; use array_representation::ChunkRepresentation; use itertools::Itertools; @@ -183,10 +183,8 @@ mod tests { use crate::{ array::{ array_representation, - codec::{ - ArrayCodecTraits, ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, BytesCodec, - CodecOptions, - }, + codec::{ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, BytesCodec, CodecOptions}, + ArrayBytes, }, array_subset::ArraySubset, }; @@ -217,25 +215,24 @@ mod tests { 98765.43210, ]; let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes = ArrayBytes::from(bytes); let codec_configuration: BitroundCodecConfiguration = serde_json::from_str(JSON).unwrap(); let codec = BitroundCodec::new_with_configuration(&codec_configuration); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) .unwrap(); let decoded = codec - .decode( - Cow::Borrowed(&encoded), - &chunk_representation, - &CodecOptions::default(), - ) + .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - let decoded_elements = crate::array::transmute_from_bytes_vec::(decoded.to_vec()); + let decoded_elements = crate::array::transmute_from_bytes_vec::( + decoded.into_fixed().unwrap().into_owned(), + ); assert_eq!(decoded_elements, &[0.0f32, 1.25f32, -8.0f32, 98304.0f32]); } @@ -250,25 +247,24 @@ mod tests { .unwrap(); let elements: Vec = vec![0, 1024, 1280, 1664, 1685, 123145182, 4294967295]; let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes = ArrayBytes::from(bytes); let codec_configuration: BitroundCodecConfiguration = serde_json::from_str(JSON).unwrap(); let codec = BitroundCodec::new_with_configuration(&codec_configuration); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) .unwrap(); let decoded = codec - .decode( - Cow::Borrowed(&encoded), - &chunk_representation, - &CodecOptions::default(), - ) + .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - let decoded_elements = crate::array::transmute_from_bytes_vec::(decoded.to_vec()); + let decoded_elements = crate::array::transmute_from_bytes_vec::( + decoded.into_fixed().unwrap().into_owned(), + ); for element in &decoded_elements { println!("{element} -> {element:#b}"); } @@ -289,25 +285,24 @@ mod tests { .unwrap(); let elements: Vec = vec![0, 3, 7, 15, 17, 54, 89, 128, 255]; let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes = ArrayBytes::from(bytes); let codec_configuration: BitroundCodecConfiguration = serde_json::from_str(JSON).unwrap(); let codec = BitroundCodec::new_with_configuration(&codec_configuration); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) .unwrap(); let decoded = codec - .decode( - Cow::Borrowed(&encoded), - &chunk_representation, - &CodecOptions::default(), - ) + .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - let decoded_elements = crate::array::transmute_from_bytes_vec::(decoded.to_vec()); + let decoded_elements = crate::array::transmute_from_bytes_vec::( + decoded.into_fixed().unwrap().into_owned(), + ); for element in &decoded_elements { println!("{element} -> {element:#b}"); } @@ -327,20 +322,21 @@ mod tests { 0.0f32.into(), ) .unwrap(); - let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = crate::array::transmute_to_bytes_vec(elements).into(); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) - .unwrap(); + .unwrap() + .into_owned(); let decoded_regions = [ ArraySubset::new_with_ranges(&[3..5]), ArraySubset::new_with_ranges(&[17..21]), ]; - let input_handle = Box::new(std::io::Cursor::new(encoded)); + let input_handle = Box::new(std::io::Cursor::new(encoded.into_fixed().unwrap())); let bytes_codec = BytesCodec::default(); let input_handle = bytes_codec .partial_decoder( @@ -361,7 +357,11 @@ mod tests { .unwrap(); let decoded_partial_chunk = decoded_partial_chunk .into_iter() - .map(|bytes| crate::array::convert_from_bytes_slice::(&bytes)) + .map(|bytes| { + crate::array::transmute_from_bytes_vec::( + bytes.into_fixed().unwrap().into_owned(), + ) + }) .collect_vec(); let answer: &[Vec] = &[vec![3.0, 4.0], vec![16.0, 16.0, 20.0, 20.0]]; assert_eq!(answer, decoded_partial_chunk); @@ -382,10 +382,11 @@ mod tests { ) .unwrap(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes = ArrayBytes::from(bytes); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -394,7 +395,7 @@ mod tests { ArraySubset::new_with_ranges(&[3..5]), ArraySubset::new_with_ranges(&[17..21]), ]; - let input_handle = Box::new(std::io::Cursor::new(encoded)); + let input_handle = Box::new(std::io::Cursor::new(encoded.into_fixed().unwrap())); let bytes_codec = BytesCodec::default(); let input_handle = bytes_codec .async_partial_decoder( @@ -418,7 +419,11 @@ mod tests { .unwrap(); let decoded_partial_chunk = decoded_partial_chunk .into_iter() - .map(|bytes| crate::array::convert_from_bytes_slice::(&bytes)) + .map(|bytes| { + crate::array::transmute_from_bytes_vec::( + bytes.into_fixed().unwrap().into_owned(), + ) + }) .collect_vec(); let answer: &[Vec] = &[vec![3.0, 4.0], vec![16.0, 16.0, 20.0, 20.0]]; assert_eq!(answer, decoded_partial_chunk); diff --git a/src/array/codec/array_to_array/bitround/bitround_codec.rs b/src/array/codec/array_to_array/bitround/bitround_codec.rs index 31611eab..c467cbb4 100644 --- a/src/array/codec/array_to_array/bitround/bitround_codec.rs +++ b/src/array/codec/array_to_array/bitround/bitround_codec.rs @@ -1,9 +1,7 @@ -use std::borrow::Cow; - use crate::{ array::{ codec::{ - options::CodecOptions, ArrayCodecTraits, ArrayPartialDecoderTraits, + options::CodecOptions, ArrayBytes, ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToArrayCodecTraits, CodecError, CodecTraits, RecommendedConcurrency, }, ArrayMetadataOptions, ChunkRepresentation, DataType, @@ -76,33 +74,34 @@ impl ArrayCodecTraits for BitroundCodec { // TODO: bitround is well suited to multithread, when is it optimal to kick in? Ok(RecommendedConcurrency::new_maximum(1)) } +} +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToArrayCodecTraits for BitroundCodec { fn encode<'a>( &self, - mut decoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { + let mut bytes = bytes.into_fixed()?; round_bytes( - decoded_value.to_mut(), + bytes.to_mut(), decoded_representation.data_type(), self.keepbits, )?; - Ok(decoded_value) + Ok(ArrayBytes::from(bytes)) } fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, _decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { - Ok(encoded_value) + ) -> Result, CodecError> { + Ok(bytes) } -} -#[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToArrayCodecTraits for BitroundCodec { fn partial_decoder<'a>( &'a self, input_handle: Box, diff --git a/src/array/codec/array_to_array/bitround/bitround_partial_decoder.rs b/src/array/codec/array_to_array/bitround/bitround_partial_decoder.rs index 678abc99..1d520d27 100644 --- a/src/array/codec/array_to_array/bitround/bitround_partial_decoder.rs +++ b/src/array/codec/array_to_array/bitround/bitround_partial_decoder.rs @@ -1,8 +1,6 @@ -use std::borrow::Cow; - use crate::{ array::{ - codec::{ArrayPartialDecoderTraits, CodecError, CodecOptions}, + codec::{ArrayBytes, ArrayPartialDecoderTraits, CodecError, CodecOptions}, DataType, }, array_subset::ArraySubset, @@ -61,16 +59,19 @@ impl ArrayPartialDecoderTraits for BitroundPartialDecoder<'_> { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { - let mut bytes = self + ) -> Result>, CodecError> { + let bytes = self .input_handle .partial_decode_opt(array_subsets, options)?; - for bytes in &mut bytes { + let mut bytes_out = Vec::with_capacity(bytes.len()); + for bytes in bytes { + let mut bytes = bytes.into_fixed()?; round_bytes(bytes.to_mut(), &self.data_type, self.keepbits)?; + bytes_out.push(bytes.into()); } - Ok(bytes) + Ok(bytes_out) } } @@ -126,16 +127,19 @@ impl AsyncArrayPartialDecoderTraits for AsyncBitroundPartialDecoder<'_> { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { - let mut bytes = self + ) -> Result>, CodecError> { + let bytes = self .input_handle .partial_decode_opt(array_subsets, options) .await?; - for bytes in &mut bytes { + let mut bytes_out = Vec::with_capacity(bytes.len()); + for bytes in bytes { + let mut bytes = bytes.into_fixed()?; round_bytes(bytes.to_mut(), &self.data_type, self.keepbits)?; + bytes_out.push(bytes.into()); } - Ok(bytes) + Ok(bytes_out) } } diff --git a/src/array/codec/array_to_array/transpose.rs b/src/array/codec/array_to_array/transpose.rs index 89dee8ce..33706274 100644 --- a/src/array/codec/array_to_array/transpose.rs +++ b/src/array/codec/array_to_array/transpose.rs @@ -14,7 +14,11 @@ pub use crate::metadata::v3::codec::transpose::{ pub use transpose_codec::TransposeCodec; use crate::{ - array::codec::{Codec, CodecPlugin}, + array::{ + array_bytes::RawBytesOffsets, + codec::{Codec, CodecPlugin}, + ArrayBytes, RawBytes, + }, metadata::v3::{codec::transpose, MetadataV3}, plugin::{PluginCreateError, PluginMetadataInvalidError}, }; @@ -90,17 +94,41 @@ fn permute(v: &[T], order: &TransposeOrder) -> Vec { vec } +fn transpose_vlen<'a>( + bytes: &RawBytes, + offsets: &RawBytesOffsets, + shape: &[usize], + order: Vec, +) -> ArrayBytes<'a> { + debug_assert_eq!(shape.len(), order.len()); + + // Get the transposed element indices + let ndarray_indices = + ndarray::ArrayD::from_shape_vec(shape, (0..shape.iter().product()).collect()).unwrap(); + let ndarray_indices_transposed = ndarray_indices.permuted_axes(order); + + // Collect the new bytes/offsets + let mut bytes_new = Vec::with_capacity(bytes.len()); + let mut offsets_new = Vec::with_capacity(offsets.len()); + for idx in &ndarray_indices_transposed { + offsets_new.push(bytes_new.len()); + let curr = offsets[*idx]; + let next = offsets[idx + 1]; + bytes_new.extend_from_slice(&bytes[curr..next]); + } + offsets_new.push(bytes_new.len()); + + ArrayBytes::new_vlen(bytes_new, offsets_new) +} + #[cfg(test)] mod tests { - use std::{borrow::Cow, num::NonZeroU64}; + use std::num::NonZeroU64; use crate::{ array::{ - codec::{ - ArrayCodecTraits, ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, BytesCodec, - CodecOptions, - }, - ChunkRepresentation, DataType, FillValue, + codec::{ArrayToArrayCodecTraits, ArrayToBytesCodecTraits, BytesCodec, CodecOptions}, + ArrayBytes, ChunkRepresentation, DataType, FillValue, }, array_subset::ArraySubset, }; @@ -118,26 +146,25 @@ mod tests { fill_value, ) .unwrap(); - let bytes: Vec = (0..chunk_representation.size()).map(|s| s as u8).collect(); + let size = chunk_representation.num_elements_usize() + * chunk_representation.data_type().fixed_size().unwrap(); + let bytes: Vec = (0..size).map(|s| s as u8).collect(); + let bytes: ArrayBytes = bytes.into(); let configuration: TransposeCodecConfiguration = serde_json::from_str(json).unwrap(); let codec = TransposeCodec::new_with_configuration(&configuration).unwrap(); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) .unwrap(); let decoded = codec - .decode( - Cow::Borrowed(&encoded), - &chunk_representation, - &CodecOptions::default(), - ) + .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); // let array = ndarray::ArrayViewD::from_shape(array_representation.shape(), &bytes).unwrap(); // let array_representation_transpose = @@ -179,20 +206,17 @@ mod tests { ) .unwrap(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let encoded = codec - .encode( - Cow::Borrowed(&bytes), - &chunk_representation, - &CodecOptions::default(), - ) + .encode(bytes, &chunk_representation, &CodecOptions::default()) .unwrap(); let decoded_regions = [ ArraySubset::new_with_ranges(&[0..4, 0..4]), ArraySubset::new_with_ranges(&[1..3, 1..4]), ArraySubset::new_with_ranges(&[2..4, 0..2]), ]; - let input_handle = Box::new(std::io::Cursor::new(encoded)); + let input_handle = Box::new(std::io::Cursor::new(encoded.into_fixed().unwrap())); let bytes_codec = BytesCodec::default(); let input_handle = bytes_codec .partial_decoder( @@ -213,7 +237,9 @@ mod tests { .unwrap(); let decoded_partial_chunk = decoded_partial_chunk .into_iter() - .map(|bytes| crate::array::convert_from_bytes_slice::(&bytes)) + .map(|bytes| { + crate::array::convert_from_bytes_slice::(&bytes.into_fixed().unwrap()) + }) .collect::>(); let answer: &[Vec] = &[ vec![ @@ -239,10 +265,11 @@ mod tests { ) .unwrap(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -252,7 +279,7 @@ mod tests { ArraySubset::new_with_ranges(&[1..3, 1..4]), ArraySubset::new_with_ranges(&[2..4, 0..2]), ]; - let input_handle = Box::new(std::io::Cursor::new(encoded)); + let input_handle = Box::new(std::io::Cursor::new(encoded.into_fixed().unwrap())); let bytes_codec = BytesCodec::default(); let input_handle = bytes_codec .async_partial_decoder( @@ -276,7 +303,11 @@ mod tests { .unwrap(); let decoded_partial_chunk = decoded_partial_chunk .into_iter() - .map(|bytes| crate::array::convert_from_bytes_slice::(&bytes)) + .map(|bytes| { + crate::array::transmute_from_bytes_vec::( + bytes.into_fixed().unwrap().into_owned(), + ) + }) .collect::>(); let answer: &[Vec] = &[ vec![ diff --git a/src/array/codec/array_to_array/transpose/transpose_codec.rs b/src/array/codec/array_to_array/transpose/transpose_codec.rs index 69aca822..81b40308 100644 --- a/src/array/codec/array_to_array/transpose/transpose_codec.rs +++ b/src/array/codec/array_to_array/transpose/transpose_codec.rs @@ -1,14 +1,12 @@ -use std::borrow::Cow; - use crate::{ array::{ codec::{ - options::CodecOptions, ArrayCodecTraits, ArrayPartialDecoderTraits, + options::CodecOptions, ArrayBytes, ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToArrayCodecTraits, CodecError, CodecTraits, RecommendedConcurrency, }, ArrayMetadataOptions, ChunkRepresentation, }, - metadata::{v3::codec::transpose::TransposeCodecConfigurationV1, v3::MetadataV3}, + metadata::v3::{codec::transpose::TransposeCodecConfigurationV1, MetadataV3}, plugin::PluginCreateError, }; @@ -65,6 +63,90 @@ impl CodecTraits for TransposeCodec { #[cfg_attr(feature = "async", async_trait::async_trait)] impl ArrayToArrayCodecTraits for TransposeCodec { + fn encode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + + match bytes { + ArrayBytes::Variable(bytes, offsets) => { + let order_encode = self.order.0.clone(); + let shape = decoded_representation + .shape() + .iter() + .map(|s| usize::try_from(s.get()).unwrap()) + .collect::>(); + Ok(super::transpose_vlen( + &bytes, + &offsets, + &shape, + order_encode, + )) + } + ArrayBytes::Fixed(bytes) => { + let order_encode = + calculate_order_encode(&self.order, decoded_representation.shape().len()); + let data_type_size = decoded_representation.data_type().fixed_size().unwrap(); + let bytes = transpose_array( + &order_encode, + &decoded_representation.shape_u64(), + data_type_size, + &bytes, + ) + .map_err(|_| CodecError::Other("transpose_array invalid arguments?".to_string()))?; + Ok(ArrayBytes::from(bytes)) + } + } + } + + fn decode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + + match bytes { + ArrayBytes::Variable(bytes, offsets) => { + let mut order_decode = vec![0; decoded_representation.shape().len()]; + for (i, val) in self.order.0.iter().enumerate() { + order_decode[*val] = i; + } + let shape = decoded_representation + .shape() + .iter() + .map(|s| usize::try_from(s.get()).unwrap()) + .collect::>(); + Ok(super::transpose_vlen( + &bytes, + &offsets, + &shape, + order_decode, + )) + } + ArrayBytes::Fixed(bytes) => { + let order_decode = + calculate_order_decode(&self.order, decoded_representation.shape().len()); + let transposed_shape = permute(&decoded_representation.shape_u64(), &self.order); + let data_type_size = decoded_representation.data_type().fixed_size().unwrap(); + let bytes = + transpose_array(&order_decode, &transposed_shape, data_type_size, &bytes) + .map_err(|_| CodecError::Other("transpose_array error".to_string()))?; + Ok(ArrayBytes::from(bytes)) + } + } + } + fn partial_decoder<'a>( &'a self, input_handle: Box, @@ -119,60 +201,4 @@ impl ArrayCodecTraits for TransposeCodec { // TODO: This could be increased, need to implement `transpose_array` without ndarray Ok(RecommendedConcurrency::new_maximum(1)) } - - fn encode<'a>( - &self, - decoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - _options: &CodecOptions, - ) -> Result, CodecError> { - if decoded_value.len() as u64 != decoded_representation.size() { - return Err(CodecError::UnexpectedChunkDecodedSize( - decoded_value.len(), - decoded_representation.size(), - )); - } - - if self.order.0.iter().copied().eq(0..self.order.0.len()) { - // Fast path for identity transform - Ok(decoded_value) - } else { - let len = decoded_value.len(); - let order_encode = - calculate_order_encode(&self.order, decoded_representation.shape().len()); - transpose_array( - &order_encode, - &decoded_representation.shape_u64(), - decoded_representation.element_size(), - &decoded_value, - ) - .map_err(|_| CodecError::UnexpectedChunkDecodedSize(len, decoded_representation.size())) - .map(Cow::Owned) - } - } - - fn decode<'a>( - &self, - encoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - _options: &CodecOptions, - ) -> Result, CodecError> { - if self.order.0.iter().copied().eq(0..self.order.0.len()) { - // Fast path for identity transform - Ok(encoded_value) - } else { - let order_decode = - calculate_order_decode(&self.order, decoded_representation.shape().len()); - let transposed_shape = permute(&decoded_representation.shape_u64(), &self.order); - let len = encoded_value.len(); - transpose_array( - &order_decode, - &transposed_shape, - decoded_representation.element_size(), - &encoded_value, - ) - .map_err(|_| CodecError::UnexpectedChunkDecodedSize(len, decoded_representation.size())) - .map(Cow::Owned) - } - } } diff --git a/src/array/codec/array_to_array/transpose/transpose_partial_decoder.rs b/src/array/codec/array_to_array/transpose/transpose_partial_decoder.rs index 60874482..e7b0ba16 100644 --- a/src/array/codec/array_to_array/transpose/transpose_partial_decoder.rs +++ b/src/array/codec/array_to_array/transpose/transpose_partial_decoder.rs @@ -1,8 +1,6 @@ -use std::borrow::Cow; - use super::{calculate_order_decode, permute, transpose_array, TransposeOrder}; use crate::array::{ - codec::{ArrayPartialDecoderTraits, ArraySubset, CodecError, CodecOptions}, + codec::{ArrayBytes, ArrayPartialDecoderTraits, ArraySubset, CodecError, CodecOptions}, ChunkRepresentation, DataType, }; @@ -31,6 +29,77 @@ impl<'a> TransposePartialDecoder<'a> { } } +fn validate_regions( + decoded_regions: &[ArraySubset], + dimensionality: usize, +) -> Result<(), CodecError> { + for array_subset in decoded_regions { + if array_subset.dimensionality() != dimensionality { + return Err(CodecError::InvalidArraySubsetDimensionalityError( + array_subset.clone(), + dimensionality, + )); + } + } + Ok(()) +} + +fn get_decoded_regions_transposed( + order: &TransposeOrder, + decoded_regions: &[ArraySubset], +) -> Vec { + let mut decoded_regions_transposed = Vec::with_capacity(decoded_regions.len()); + for decoded_region in decoded_regions { + let start = permute(decoded_region.start(), order); + let size = permute(decoded_region.shape(), order); + let decoded_region_transpose = + unsafe { ArraySubset::new_with_start_shape_unchecked(start, size) }; + decoded_regions_transposed.push(decoded_region_transpose); + } + decoded_regions_transposed +} + +/// Reverse the transpose on each subset +fn do_transpose<'a>( + encoded_value: Vec>, + decoded_regions: &[ArraySubset], + order: &TransposeOrder, + decoded_representation: &ChunkRepresentation, +) -> Result>, CodecError> { + let order_decode = calculate_order_decode(order, decoded_representation.shape().len()); + let data_type_size = decoded_representation.data_type().size(); + std::iter::zip(decoded_regions, encoded_value) + .map(|(subset, bytes)| { + bytes.validate(subset.num_elements(), data_type_size)?; + match bytes { + ArrayBytes::Variable(bytes, offsets) => { + let mut order_decode = vec![0; decoded_representation.shape().len()]; + for (i, val) in order.0.iter().enumerate() { + order_decode[*val] = i; + } + Ok(super::transpose_vlen( + &bytes, + &offsets, + &subset.shape_usize(), + order_decode, + )) + } + ArrayBytes::Fixed(bytes) => { + let data_type_size = decoded_representation.data_type().fixed_size().unwrap(); + let bytes = transpose_array( + &order_decode, + &permute(subset.shape(), order), + data_type_size, + &bytes, + ) + .map_err(|_| CodecError::Other("transpose_array error".to_string()))?; + Ok(ArrayBytes::from(bytes)) + } + } + }) + .collect::, CodecError>>() +} + impl ArrayPartialDecoderTraits for TransposePartialDecoder<'_> { fn data_type(&self) -> &DataType { self.decoded_representation.data_type() @@ -40,57 +109,22 @@ impl ArrayPartialDecoderTraits for TransposePartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { - for array_subset in decoded_regions { - if array_subset.dimensionality() != self.decoded_representation.dimensionality() { - return Err(CodecError::InvalidArraySubsetDimensionalityError( - array_subset.clone(), - self.decoded_representation.dimensionality(), - )); - } - } - - // Get transposed array subsets - let mut decoded_regions_transposed = Vec::with_capacity(decoded_regions.len()); - for decoded_region in decoded_regions { - let start = permute(decoded_region.start(), &self.order); - let size = permute(decoded_region.shape(), &self.order); - let decoded_region_transpose = - unsafe { ArraySubset::new_with_start_shape_unchecked(start, size) }; - decoded_regions_transposed.push(decoded_region_transpose); - } + ) -> Result>, CodecError> { + validate_regions( + decoded_regions, + self.decoded_representation.dimensionality(), + )?; + let decoded_regions_transposed = + get_decoded_regions_transposed(&self.order, decoded_regions); let encoded_value = self .input_handle .partial_decode_opt(&decoded_regions_transposed, options)?; - - if self.order.0.iter().copied().eq(0..self.order.0.len()) { - // Fast path for identity transform - Ok(encoded_value) - } else { - // Reverse the transpose on each subset - let order_decode = - calculate_order_decode(&self.order, self.decoded_representation.shape().len()); - let decoded_value = std::iter::zip(decoded_regions, encoded_value) - .map(|(subset, bytes)| { - let len = bytes.len(); - transpose_array( - &order_decode, - &permute(subset.shape(), &self.order), - self.decoded_representation.element_size(), - &bytes, - ) - .map_err(|_| { - CodecError::UnexpectedChunkDecodedSize( - len, - subset.num_elements() - * self.decoded_representation.element_size() as u64, - ) - }) - .map(Cow::Owned) - }) - .collect::, _>>()?; - Ok(decoded_value) - } + do_transpose( + encoded_value, + decoded_regions, + &self.order, + &self.decoded_representation, + ) } } @@ -129,57 +163,22 @@ impl AsyncArrayPartialDecoderTraits for AsyncTransposePartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { - for array_subset in decoded_regions { - if array_subset.dimensionality() != self.decoded_representation.dimensionality() { - return Err(CodecError::InvalidArraySubsetDimensionalityError( - array_subset.clone(), - self.decoded_representation.dimensionality(), - )); - } - } - - // Get transposed array subsets - let mut decoded_regions_transposed = Vec::with_capacity(decoded_regions.len()); - for decoded_region in decoded_regions { - let start = permute(decoded_region.start(), &self.order); - let size = permute(decoded_region.shape(), &self.order); - let decoded_region_transpose = - unsafe { ArraySubset::new_with_start_shape_unchecked(start, size) }; - decoded_regions_transposed.push(decoded_region_transpose); - } + ) -> Result>, CodecError> { + validate_regions( + decoded_regions, + self.decoded_representation.dimensionality(), + )?; + let decoded_regions_transposed = + get_decoded_regions_transposed(&self.order, decoded_regions); let encoded_value = self .input_handle .partial_decode_opt(&decoded_regions_transposed, options) .await?; - - if self.order.0.iter().copied().eq(0..self.order.0.len()) { - // Fast path for identity transform - Ok(encoded_value) - } else { - // Reverse the transpose on each subset - let order_decode = - calculate_order_decode(&self.order, self.decoded_representation.shape().len()); - let decoded_value = std::iter::zip(decoded_regions, encoded_value) - .map(|(subset, bytes)| { - let len = bytes.len(); - transpose_array( - &order_decode, - &permute(subset.shape(), &self.order), - self.decoded_representation.element_size(), - &bytes, - ) - .map(Cow::Owned) - .map_err(|_| { - CodecError::UnexpectedChunkDecodedSize( - len, - subset.num_elements() - * self.decoded_representation.element_size() as u64, - ) - }) - }) - .collect::, _>>()?; - Ok(decoded_value) - } + do_transpose( + encoded_value, + decoded_regions, + &self.order, + &self.decoded_representation, + ) } } diff --git a/src/array/codec/array_to_bytes.rs b/src/array/codec/array_to_bytes.rs index 361df695..765b7544 100644 --- a/src/array/codec/array_to_bytes.rs +++ b/src/array/codec/array_to_bytes.rs @@ -2,6 +2,8 @@ pub mod bytes; pub mod codec_chain; +pub mod vlen; +pub mod vlen_interleaved; #[cfg(feature = "pcodec")] pub mod pcodec; diff --git a/src/array/codec/array_to_bytes/bytes.rs b/src/array/codec/array_to_bytes/bytes.rs index 09562fba..cd465a17 100644 --- a/src/array/codec/array_to_bytes/bytes.rs +++ b/src/array/codec/array_to_bytes/bytes.rs @@ -66,17 +66,19 @@ pub fn reverse_endianness(v: &mut [u8], data_type: &DataType) { }; v.chunks_exact_mut(8).for_each(swap); } + // Variable-sized data types are not supported and are rejected outside of this function + DataType::String | DataType::Binary => unreachable!(), } } #[cfg(test)] mod tests { - use std::{borrow::Cow, num::NonZeroU64}; + use std::num::NonZeroU64; use crate::{ array::{ - codec::{ArrayCodecTraits, ArrayToBytesCodecTraits, CodecOptions, CodecTraits}, - ChunkRepresentation, ChunkShape, Endianness, FillValue, + codec::{ArrayToBytesCodecTraits, CodecOptions, CodecTraits}, + ArrayBytes, ChunkRepresentation, ChunkShape, FillValue, }, array_subset::ArraySubset, }; @@ -126,19 +128,21 @@ mod tests { let chunk_shape = vec![NonZeroU64::new(10).unwrap(), NonZeroU64::new(10).unwrap()]; let chunk_representation = ChunkRepresentation::new(chunk_shape, data_type, fill_value).unwrap(); - let bytes: Vec = (0..chunk_representation.size()).map(|s| s as u8).collect(); + let size = chunk_representation.num_elements_usize() + * chunk_representation.data_type().fixed_size().unwrap(); + let bytes: ArrayBytes = (0..size).map(|s| s as u8).collect::>().into(); let codec = BytesCodec::new(endianness); let encoded = codec.encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), )?; let decoded = codec .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); Ok(()) } @@ -259,13 +263,13 @@ mod tests { ChunkRepresentation::new(chunk_shape.to_vec(), DataType::UInt8, FillValue::from(0u8)) .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u8).collect(); - let bytes = elements; + let bytes: ArrayBytes = elements.into(); let codec = BytesCodec::new(None); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -285,7 +289,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -303,13 +307,13 @@ mod tests { ChunkRepresentation::new(chunk_shape.to_vec(), DataType::UInt8, FillValue::from(0u8)) .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u8).collect(); - let bytes = elements; + let bytes: ArrayBytes = elements.into(); let codec = BytesCodec::new(None); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -331,7 +335,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) diff --git a/src/array/codec/array_to_bytes/bytes/bytes_codec.rs b/src/array/codec/array_to_bytes/bytes/bytes_codec.rs index eddd147c..936be8a2 100644 --- a/src/array/codec/array_to_bytes/bytes/bytes_codec.rs +++ b/src/array/codec/array_to_bytes/bytes/bytes_codec.rs @@ -1,7 +1,5 @@ // Note: No validation that this codec is created *without* a specified endianness for multi-byte data types. -use std::borrow::Cow; - use crate::{ array::{ codec::{ @@ -9,7 +7,8 @@ use crate::{ BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, + ArrayBytes, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, DataTypeSize, + RawBytes, }, metadata::v3::MetadataV3, }; @@ -19,7 +18,7 @@ use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecod use super::{ bytes_partial_decoder, reverse_endianness, BytesCodecConfiguration, BytesCodecConfigurationV1, - Endianness, IDENTIFIER, NATIVE_ENDIAN, + Endianness, NATIVE_ENDIAN, }; /// A `bytes` codec implementation. @@ -64,20 +63,30 @@ impl BytesCodec { fn do_encode_or_decode<'a>( &self, - mut value: Cow<'a, [u8]>, + mut value: RawBytes<'a>, decoded_representation: &ChunkRepresentation, - ) -> Result, CodecError> { - if value.len() as u64 != decoded_representation.size() { - return Err(CodecError::UnexpectedChunkDecodedSize( - value.len(), - decoded_representation.size(), - )); - } else if decoded_representation.element_size() > 1 && self.endian.is_none() { - return Err(CodecError::Other(format!( - "tried to encode an array with element size {} with endianness None", - decoded_representation.size() - ))); - } + ) -> Result, CodecError> { + match decoded_representation.data_type().size() { + DataTypeSize::Variable => { + return Err(CodecError::UnsupportedDataType( + decoded_representation.data_type().clone(), + super::IDENTIFIER.to_string(), + )) + } + DataTypeSize::Fixed(data_type_size) => { + let array_size = decoded_representation.num_elements() * data_type_size as u64; + if value.len() as u64 != array_size { + return Err(CodecError::UnexpectedChunkDecodedSize( + value.len(), + array_size, + )); + } else if data_type_size > 1 && self.endian.is_none() { + return Err(CodecError::Other(format!( + "tried to encode an array with element size {data_type_size} with endianness None" + ))); + } + } + }; if let Some(endian) = &self.endian { if !endian.is_native() { @@ -93,7 +102,10 @@ impl CodecTraits for BytesCodec { let configuration = BytesCodecConfigurationV1 { endian: self.endian, }; - Some(MetadataV3::new_with_serializable_configuration(IDENTIFIER, &configuration).unwrap()) + Some( + MetadataV3::new_with_serializable_configuration(super::IDENTIFIER, &configuration) + .unwrap(), + ) } fn partial_decoder_should_cache_input(&self) -> bool { @@ -124,28 +136,35 @@ impl ArrayCodecTraits for BytesCodec { // } Ok(RecommendedConcurrency::new_maximum(1)) } +} +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for BytesCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { - self.do_encode_or_decode(decoded_value, decoded_representation) + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + let bytes = bytes.into_fixed()?; + self.do_encode_or_decode(bytes, decoded_representation) } fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + bytes: RawBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { - self.do_encode_or_decode(encoded_value, decoded_representation) + ) -> Result, CodecError> { + Ok(ArrayBytes::from( + self.do_encode_or_decode(bytes, decoded_representation)?, + )) } -} -#[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToBytesCodecTraits for BytesCodec { fn partial_decoder<'a>( &self, input_handle: Box, @@ -179,8 +198,16 @@ impl ArrayToBytesCodecTraits for BytesCodec { &self, decoded_representation: &ChunkRepresentation, ) -> Result { - Ok(BytesRepresentation::FixedSize( - decoded_representation.num_elements() * decoded_representation.element_size() as u64, - )) + match decoded_representation.data_type().size() { + DataTypeSize::Variable => { + return Err(CodecError::UnsupportedDataType( + decoded_representation.data_type().clone(), + super::IDENTIFIER.to_string(), + )) + } + DataTypeSize::Fixed(data_type_size) => Ok(BytesRepresentation::FixedSize( + decoded_representation.num_elements() * data_type_size as u64, + )), + } } } diff --git a/src/array/codec/array_to_bytes/bytes/bytes_partial_decoder.rs b/src/array/codec/array_to_bytes/bytes/bytes_partial_decoder.rs index 75f08fb5..799cbc11 100644 --- a/src/array/codec/array_to_bytes/bytes/bytes_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/bytes/bytes_partial_decoder.rs @@ -6,7 +6,7 @@ use crate::{ ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, CodecOptions, }, - ChunkRepresentation, DataType, + ArrayBytes, ChunkRepresentation, DataType, DataTypeSize, }, array_subset::IncompatibleArraySubsetAndShapeError, }; @@ -47,47 +47,57 @@ impl ArrayPartialDecoderTraits for BytesPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { let mut bytes = Vec::with_capacity(decoded_regions.len()); let chunk_shape = self.decoded_representation.shape_u64(); for array_subset in decoded_regions { - // Get byte ranges - let byte_ranges = array_subset - .byte_ranges(&chunk_shape, self.decoded_representation.element_size()) - .map_err(|_| { - IncompatibleArraySubsetAndShapeError::from(( - array_subset.clone(), - self.decoded_representation.shape_u64(), + match self.decoded_representation.data_type().size() { + DataTypeSize::Variable => { + return Err(CodecError::UnsupportedDataType( + self.data_type().clone(), + super::IDENTIFIER.to_string(), )) - })?; - - // Decode - let decoded = self - .input_handle - .partial_decode_concat(&byte_ranges, options)? - .map_or_else( - || { - Cow::Owned( - self.decoded_representation - .fill_value() - .as_ne_bytes() - .repeat(array_subset.num_elements_usize()), - ) - }, - |mut decoded| { - if let Some(endian) = &self.endian { - if !endian.is_native() { - reverse_endianness( - decoded.to_mut(), - self.decoded_representation.data_type(), - ); - } - } - decoded - }, - ); - - bytes.push(decoded); + } + DataTypeSize::Fixed(data_type_size) => { + // Get byte ranges + let byte_ranges = array_subset + .byte_ranges(&chunk_shape, data_type_size) + .map_err(|_| { + IncompatibleArraySubsetAndShapeError::from(( + array_subset.clone(), + self.decoded_representation.shape_u64(), + )) + })?; + + // Decode + let decoded = self + .input_handle + .partial_decode_concat(&byte_ranges, options)? + .map_or_else( + || { + Cow::Owned( + self.decoded_representation + .fill_value() + .as_ne_bytes() + .repeat(array_subset.num_elements_usize()), + ) + }, + |mut decoded| { + if let Some(endian) = &self.endian { + if !endian.is_native() { + reverse_endianness( + decoded.to_mut(), + self.decoded_representation.data_type(), + ); + } + } + decoded + }, + ); + + bytes.push(ArrayBytes::from(decoded)); + } + } } Ok(bytes) } @@ -128,7 +138,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncBytesPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { for array_subset in decoded_regions { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( @@ -149,14 +159,22 @@ impl AsyncArrayPartialDecoderTraits for AsyncBytesPartialDecoder<'_> { } // Get byte ranges - let byte_ranges = array_subset - .byte_ranges(&chunk_shape, self.decoded_representation.element_size()) - .map_err(|_| { - IncompatibleArraySubsetAndShapeError::from(( - array_subset.clone(), - self.decoded_representation.shape_u64(), + let byte_ranges = match self.decoded_representation.element_size() { + DataTypeSize::Variable => { + return Err(CodecError::UnsupportedDataType( + self.data_type().clone(), + super::IDENTIFIER.to_string(), )) - })?; + } + DataTypeSize::Fixed(data_type_size) => array_subset + .byte_ranges(&chunk_shape, data_type_size) + .map_err(|_| { + IncompatibleArraySubsetAndShapeError::from(( + array_subset.clone(), + self.decoded_representation.shape_u64(), + )) + })?, + }; // Decode let decoded = self @@ -185,7 +203,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncBytesPartialDecoder<'_> { }, ); - bytes.push(decoded); + bytes.push(ArrayBytes::from(decoded)); } Ok(bytes) } diff --git a/src/array/codec/array_to_bytes/codec_chain.rs b/src/array/codec/array_to_bytes/codec_chain.rs index 36c6dae4..fb88ba44 100644 --- a/src/array/codec/array_to_bytes/codec_chain.rs +++ b/src/array/codec/array_to_bytes/codec_chain.rs @@ -1,7 +1,5 @@ //! An array to bytes codec formed by joining an array to array sequence, array to bytes, and bytes to bytes sequence of codecs. -use std::borrow::Cow; - use crate::{ array::{ codec::{ @@ -11,7 +9,8 @@ use crate::{ CodecTraits, }, concurrency::RecommendedConcurrency, - ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, + ArrayBytes, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, + RawBytes, }, metadata::v3::MetadataV3, plugin::PluginCreateError, @@ -225,6 +224,81 @@ impl CodecTraits for CodecChain { #[cfg_attr(feature = "async", async_trait::async_trait)] impl ArrayToBytesCodecTraits for CodecChain { + fn encode<'a>( + &self, + mut bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + + let mut decoded_representation = decoded_representation.clone(); + + // array->array + for codec in &self.array_to_array { + bytes = codec.encode(bytes, &decoded_representation, options)?; + decoded_representation = codec.compute_encoded_size(&decoded_representation)?; + } + + // array->bytes + let mut bytes = self + .array_to_bytes + .encode(bytes, &decoded_representation, options)?; + let mut decoded_representation = self + .array_to_bytes + .compute_encoded_size(&decoded_representation)?; + + // bytes->bytes + for codec in &self.bytes_to_bytes { + bytes = codec.encode(bytes, options)?; + decoded_representation = codec.compute_encoded_size(&decoded_representation); + } + + Ok(bytes) + } + + fn decode<'a>( + &self, + mut bytes: RawBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError> { + let array_representations = + self.get_array_representations(decoded_representation.clone())?; + let bytes_representations = + self.get_bytes_representations(array_representations.last().unwrap())?; + + // bytes->bytes + for (codec, bytes_representation) in std::iter::zip( + self.bytes_to_bytes.iter().rev(), + bytes_representations.iter().rev().skip(1), + ) { + bytes = codec.decode(bytes, bytes_representation, options)?; + } + + // bytes->array + let mut bytes = + self.array_to_bytes + .decode(bytes, array_representations.last().unwrap(), options)?; + + // array->array + for (codec, array_representation) in std::iter::zip( + self.array_to_array.iter().rev(), + array_representations.iter().rev().skip(1), + ) { + bytes = codec.decode(bytes, array_representation, options)?; + } + + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + Ok(bytes) + } + fn partial_decoder<'a>( &'a self, mut input_handle: Box, @@ -427,90 +501,6 @@ impl ArrayCodecTraits for CodecChain { Ok(recommended_concurrency) } - - fn encode<'a>( - &self, - decoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - options: &CodecOptions, - ) -> Result, CodecError> { - if decoded_value.len() as u64 != decoded_representation.size() { - return Err(CodecError::UnexpectedChunkDecodedSize( - decoded_value.len(), - decoded_representation.size(), - )); - } - - let mut decoded_representation = decoded_representation.clone(); - - let mut value = decoded_value; - // array->array - for codec in &self.array_to_array { - value = codec.encode(value, &decoded_representation, options)?; - decoded_representation = codec.compute_encoded_size(&decoded_representation)?; - } - - // array->bytes - value = self - .array_to_bytes - .encode(value, &decoded_representation, options)?; - let mut decoded_representation = self - .array_to_bytes - .compute_encoded_size(&decoded_representation)?; - - // bytes->bytes - for codec in &self.bytes_to_bytes { - value = codec.encode(value, options)?; - decoded_representation = codec.compute_encoded_size(&decoded_representation); - } - - Ok(value) - } - - fn decode<'a>( - &self, - mut encoded_value: Cow<'a, [u8]>, - decoded_representation: &ChunkRepresentation, - options: &CodecOptions, - ) -> Result, CodecError> { - let array_representations = - self.get_array_representations(decoded_representation.clone())?; - let bytes_representations = - self.get_bytes_representations(array_representations.last().unwrap())?; - - // bytes->bytes - for (codec, bytes_representation) in std::iter::zip( - self.bytes_to_bytes.iter().rev(), - bytes_representations.iter().rev().skip(1), - ) { - encoded_value = codec.decode(encoded_value, bytes_representation, options)?; - } - - // bytes->array - encoded_value = self.array_to_bytes.decode( - encoded_value, - array_representations.last().unwrap(), - options, - )?; - - // array->array - for (codec, array_representation) in std::iter::zip( - self.array_to_array.iter().rev(), - array_representations.iter().rev().skip(1), - ) { - encoded_value = codec.decode(encoded_value, array_representation, options)?; - } - - if encoded_value.len() as u64 != decoded_representation.size() { - return Err(CodecError::UnexpectedChunkDecodedSize( - encoded_value.len(), - decoded_representation.size(), - )); - } - - Ok(encoded_value) - } - fn partial_decode_granularity( &self, decoded_representation: &ChunkRepresentation, @@ -612,7 +602,7 @@ mod tests { decoded_regions: &[ArraySubset], decoded_partial_chunk_true: Vec, ) { - let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = crate::array::transmute_to_bytes_vec(elements).into(); let codec_configurations: Vec = vec![ #[cfg(feature = "transpose")] @@ -637,7 +627,7 @@ mod tests { let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -650,9 +640,9 @@ mod tests { ) .unwrap(); if not_just_bytes { - assert_ne!(encoded, decoded); + assert_ne!(encoded, decoded.clone().into_fixed().unwrap()); } - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); // let encoded = codec // .par_encode(bytes.clone(), &chunk_representation) @@ -679,7 +669,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) diff --git a/src/array/codec/array_to_bytes/pcodec.rs b/src/array/codec/array_to_bytes/pcodec.rs index 9c9d71eb..cfe03b86 100644 --- a/src/array/codec/array_to_bytes/pcodec.rs +++ b/src/array/codec/array_to_bytes/pcodec.rs @@ -47,12 +47,13 @@ pub(crate) fn create_codec_pcodec(metadata: &MetadataV3) -> Result = (0..chunk_representation.size()).map(|s| s as u8).collect(); + let size = chunk_representation.num_elements_usize() + * chunk_representation.data_type().fixed_size().unwrap(); + let bytes: Vec = (0..size).map(|s| s as u8).collect(); + let bytes: ArrayBytes = bytes.into(); let max_encoded_size = codec.compute_encoded_size(&chunk_representation)?; let encoded = codec.encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), )?; @@ -93,7 +97,7 @@ mod tests { let decoded = codec .decode(encoded, &chunk_representation, &CodecOptions::default()) .unwrap(); - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); Ok(()) } @@ -228,12 +232,13 @@ mod tests { .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u32).collect(); let bytes = transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let codec = PcodecCodec::new_with_configuration(&serde_json::from_str(JSON_VALID).unwrap()); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -253,7 +258,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().into_owned()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -275,12 +280,13 @@ mod tests { .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u32).collect(); let bytes = transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let codec = PcodecCodec::new_with_configuration(&serde_json::from_str(JSON_VALID).unwrap()); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -302,7 +308,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().into_owned()) .flatten() .collect::>() .chunks(std::mem::size_of::()) diff --git a/src/array/codec/array_to_bytes/pcodec/pcodec_codec.rs b/src/array/codec/array_to_bytes/pcodec/pcodec_codec.rs index 5d9be9f6..b3382d85 100644 --- a/src/array/codec/array_to_bytes/pcodec/pcodec_codec.rs +++ b/src/array/codec/array_to_bytes/pcodec/pcodec_codec.rs @@ -5,8 +5,8 @@ use pco::{standalone::guarantee::file_size, ChunkConfig, ModeSpec, PagingSpec}; use crate::{ array::{ codec::{ - ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, - BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, + ArrayBytes, ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, + BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, RawBytes, RecommendedConcurrency, }, convert_from_bytes_slice, transmute_to_bytes_vec, ArrayMetadataOptions, @@ -108,18 +108,22 @@ impl ArrayCodecTraits for PcodecCodec { // pcodec does not support parallel decode Ok(RecommendedConcurrency::new_maximum(1)) } +} +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for PcodecCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let data_type = decoded_representation.data_type(); + let bytes = bytes.into_fixed()?; macro_rules! pcodec_encode { ( $t:ty ) => { pco::standalone::simple_compress( - &convert_from_bytes_slice::<$t>(&decoded_value), + &convert_from_bytes_slice::<$t>(&bytes), &self.chunk_config, ) .map(Cow::Owned) @@ -164,20 +168,20 @@ impl ArrayCodecTraits for PcodecCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + bytes: RawBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let data_type = decoded_representation.data_type(); macro_rules! pcodec_decode { ( $t:ty ) => { - pco::standalone::simple_decompress(&encoded_value) + pco::standalone::simple_decompress(&bytes) .map(|bytes| Cow::Owned(transmute_to_bytes_vec::<$t>(bytes))) .map_err(|err| CodecError::Other(err.to_string())) }; } - match data_type { + let bytes = match data_type { DataType::UInt16 => { pcodec_decode!(u16) } @@ -209,12 +213,10 @@ impl ArrayCodecTraits for PcodecCodec { data_type.clone(), IDENTIFIER.to_string(), )), - } + }?; + Ok(ArrayBytes::from(bytes)) } -} -#[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToBytesCodecTraits for PcodecCodec { fn partial_decoder<'a>( &self, input_handle: Box, diff --git a/src/array/codec/array_to_bytes/pcodec/pcodec_partial_decoder.rs b/src/array/codec/array_to_bytes/pcodec/pcodec_partial_decoder.rs index 22a91a1e..a51fee5a 100644 --- a/src/array/codec/array_to_bytes/pcodec/pcodec_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/pcodec/pcodec_partial_decoder.rs @@ -1,14 +1,9 @@ -use std::borrow::Cow; - -use crate::{ - array::{ - codec::{ - ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, - CodecOptions, - }, - ChunkRepresentation, DataType, +use crate::array::{ + codec::{ + ArrayBytes, ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, + CodecOptions, RawBytes, }, - array_subset::IncompatibleArraySubsetAndShapeError, + ChunkRepresentation, DataType, }; #[cfg(feature = "async")] @@ -34,10 +29,10 @@ impl<'a> PcodecPartialDecoder<'a> { } fn do_partial_decode<'a>( - decoded: Option>, + decoded: Option>, decoded_regions: &[ArraySubset], decoded_representation: &ChunkRepresentation, -) -> Result>, CodecError> { +) -> Result>, CodecError> { let mut decoded_bytes = Vec::with_capacity(decoded_regions.len()); let chunk_shape = decoded_representation.shape_u64(); match decoded { @@ -47,7 +42,7 @@ fn do_partial_decode<'a>( .fill_value() .as_ne_bytes() .repeat(array_subset.num_elements_usize()); - decoded_bytes.push(Cow::Owned(bytes_subset)); + decoded_bytes.push(ArrayBytes::from(bytes_subset)); } } Some(decoded_value) => { @@ -56,20 +51,16 @@ fn do_partial_decode<'a>( let decoded_chunk = pco::standalone::simple_decompress(&decoded_value) .map(|bytes| crate::array::transmute_to_bytes_vec::<$t>(bytes)) .map_err(|err| CodecError::Other(err.to_string()))?; + let decoded_chunk: ArrayBytes = decoded_chunk.into(); for array_subset in decoded_regions { - let bytes_subset = array_subset - .extract_bytes( - decoded_chunk.as_slice(), + let bytes_subset = decoded_chunk + .extract_array_subset( + array_subset, &chunk_shape, - decoded_representation.element_size(), - ) - .map_err(|_| { - IncompatibleArraySubsetAndShapeError::from(( - array_subset.clone(), - decoded_representation.shape_u64(), - )) - })?; - decoded_bytes.push(Cow::Owned(bytes_subset)); + decoded_representation.data_type(), + )? + .into_owned(); + decoded_bytes.push(bytes_subset); } }; } @@ -115,7 +106,7 @@ impl ArrayPartialDecoderTraits for PcodecPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { let decoded = self.input_handle.decode(options)?; do_partial_decode(decoded, decoded_regions, &self.decoded_representation) } @@ -153,7 +144,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncPCodecPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { for array_subset in decoded_regions { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( diff --git a/src/array/codec/array_to_bytes/sharding.rs b/src/array/codec/array_to_bytes/sharding.rs index 28fde5ef..da416d5c 100644 --- a/src/array/codec/array_to_bytes/sharding.rs +++ b/src/array/codec/array_to_bytes/sharding.rs @@ -105,6 +105,7 @@ fn decode_shard_index( index_array_representation, options, )?; + let decoded_shard_index = decoded_shard_index.into_fixed()?; Ok(decoded_shard_index .chunks_exact(core::mem::size_of::()) .map(|v| u64::from_ne_bytes(v.try_into().unwrap() /* safe */)) @@ -114,9 +115,12 @@ fn decode_shard_index( #[cfg(test)] mod tests { use crate::{ - array::codec::{ - bytes_to_bytes::test_unbounded::TestUnboundedCodec, ArrayCodecTraits, - BytesToBytesCodecTraits, CodecOptionsBuilder, + array::{ + codec::{ + bytes_to_bytes::test_unbounded::TestUnboundedCodec, BytesToBytesCodecTraits, + CodecOptionsBuilder, + }, + ArrayBytes, }, array_subset::ArraySubset, config::global_config, @@ -199,6 +203,7 @@ mod tests { (0..chunk_representation.num_elements() as u16).collect() }; let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); if unbounded { bytes_to_bytes_codecs.push(Box::new(TestUnboundedCodec::new())) @@ -213,13 +218,13 @@ mod tests { .build(); let encoded = codec - .encode(Cow::Borrowed(&bytes), &chunk_representation, options) + .encode(bytes.clone(), &chunk_representation, options) .unwrap(); let decoded = codec .decode(encoded.clone(), &chunk_representation, options) .unwrap(); - assert_ne!(encoded, decoded); - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); + assert_ne!(encoded, decoded.into_fixed().unwrap()); } #[test] @@ -293,6 +298,7 @@ mod tests { (0..chunk_representation.num_elements() as u16).collect() }; let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); if unbounded { bytes_to_bytes_codecs.push(Box::new(TestUnboundedCodec::new())) @@ -307,13 +313,13 @@ mod tests { .build(); let encoded = codec - .encode(Cow::Borrowed(&bytes), &chunk_representation, options) + .encode(bytes.clone(), &chunk_representation, options) .unwrap(); let decoded = codec .decode(encoded.clone(), &chunk_representation, options) .unwrap(); - assert_ne!(encoded, decoded); - assert_eq!(bytes, decoded.to_vec()); + assert_eq!(bytes, decoded); + assert_ne!(encoded, decoded.into_fixed().unwrap()); } #[cfg(feature = "async")] @@ -361,7 +367,7 @@ mod tests { vec![4, 8] }; - let bytes = elements; + let bytes: ArrayBytes = elements.into(); let bytes_to_bytes_codecs: Vec> = if unbounded { vec![Box::new(TestUnboundedCodec::new())] @@ -378,7 +384,7 @@ mod tests { .build(); let encoded = codec - .encode(Cow::Borrowed(&bytes), &chunk_representation, options) + .encode(bytes.clone(), &chunk_representation, options) .unwrap(); let decoded_regions = [ArraySubset::new_with_ranges(&[1..3, 0..1])]; let input_handle = Box::new(std::io::Cursor::new(encoded)); @@ -391,7 +397,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -442,8 +448,7 @@ mod tests { } else { vec![4, 8] }; - - let bytes = elements; + let bytes: ArrayBytes = elements.into(); let bytes_to_bytes_codecs: Vec> = if unbounded { vec![Box::new(TestUnboundedCodec::new())] @@ -460,7 +465,7 @@ mod tests { .build(); let encoded = codec - .encode(Cow::Borrowed(&bytes), &chunk_representation, options) + .encode(bytes.clone(), &chunk_representation, options) .unwrap(); let decoded_regions = [ArraySubset::new_with_ranges(&[1..3, 0..1])]; let input_handle = Box::new(std::io::Cursor::new(encoded)); @@ -475,7 +480,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -511,8 +516,6 @@ mod tests { #[cfg(feature = "crc32c")] #[test] fn codec_sharding_partial_decode2() { - use crate::array::codec::ArrayCodecTraits; - let chunk_shape: ChunkShape = vec![2, 4, 4].try_into().unwrap(); let chunk_representation = ChunkRepresentation::new( chunk_shape.to_vec(), @@ -522,17 +525,14 @@ mod tests { .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u16).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let codec_configuration: ShardingCodecConfiguration = serde_json::from_str(JSON_VALID2).unwrap(); let codec = ShardingCodec::new_with_configuration(&codec_configuration).unwrap(); let encoded = codec - .encode( - Cow::Borrowed(&bytes), - &chunk_representation, - &CodecOptions::default(), - ) + .encode(bytes, &chunk_representation, &CodecOptions::default()) .unwrap(); let decoded_regions = [ArraySubset::new_with_ranges(&[1..2, 0..2, 0..3])]; let input_handle = Box::new(std::io::Cursor::new(encoded)); @@ -549,7 +549,7 @@ mod tests { println!("decoded_partial_chunk {decoded_partial_chunk:?}"); let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -567,18 +567,14 @@ mod tests { ChunkRepresentation::new(chunk_shape.to_vec(), DataType::UInt8, FillValue::from(0u8)) .unwrap(); let elements: Vec = (0..chunk_representation.num_elements() as u8).collect(); - let bytes = elements; + let bytes: ArrayBytes = elements.into(); let codec_configuration: ShardingCodecConfiguration = serde_json::from_str(JSON_VALID3).unwrap(); let codec = ShardingCodec::new_with_configuration(&codec_configuration).unwrap(); let encoded = codec - .encode( - Cow::Borrowed(&bytes), - &chunk_representation, - &CodecOptions::default(), - ) + .encode(bytes, &chunk_representation, &CodecOptions::default()) .unwrap(); let decoded_regions = [ArraySubset::new_with_ranges(&[1..3, 0..1])]; let input_handle = Box::new(std::io::Cursor::new(encoded)); @@ -595,7 +591,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) diff --git a/src/array/codec/array_to_bytes/sharding/sharding_codec.rs b/src/array/codec/array_to_bytes/sharding/sharding_codec.rs index ed71e36d..757894bf 100644 --- a/src/array/codec/array_to_bytes/sharding/sharding_codec.rs +++ b/src/array/codec/array_to_bytes/sharding/sharding_codec.rs @@ -2,6 +2,7 @@ use std::{borrow::Cow, num::NonZeroU64, sync::atomic::AtomicUsize}; use crate::{ array::{ + array_bytes::{merge_chunks_vlen, update_bytes_flen}, chunk_shape_to_array_shape, codec::{ ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, @@ -11,7 +12,8 @@ use crate::{ concurrency::calc_concurrency_outer_inner, transmute_to_bytes_vec, unravel_index, unsafe_cell_slice::UnsafeCellSlice, - ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, FillValue, + ArrayBytes, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, + DataTypeSize, FillValue, RawBytes, }, array_subset::ArraySubset, metadata::v3::MetadataV3, @@ -127,18 +129,23 @@ impl ArrayCodecTraits for ShardingCodec { Ok(RecommendedConcurrency::new_maximum(num_elements.into())) } + fn partial_decode_granularity( + &self, + _decoded_representation: &ChunkRepresentation, + ) -> ChunkShape { + self.chunk_shape.clone() + } +} + +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for ShardingCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, shard_rep: &ChunkRepresentation, options: &CodecOptions, - ) -> Result, CodecError> { - if decoded_value.len() as u64 != shard_rep.size() { - return Err(CodecError::UnexpectedChunkDecodedSize( - decoded_value.len(), - shard_rep.size(), - )); - } + ) -> Result, CodecError> { + bytes.validate(shard_rep.num_elements(), shard_rep.data_type().size())?; // Get chunk bytes representation, and choose implementation based on whether the size is unbounded or not let chunk_rep = unsafe { @@ -149,34 +156,26 @@ impl ArrayCodecTraits for ShardingCodec { ) }; let chunk_bytes_representation = self.inner_codecs.compute_encoded_size(&chunk_rep)?; - Ok(Cow::Owned(match chunk_bytes_representation { + + let bytes = match chunk_bytes_representation { BytesRepresentation::BoundedSize(size) | BytesRepresentation::FixedSize(size) => { - self.encode_bounded(&decoded_value, shard_rep, &chunk_rep, size, options) + self.encode_bounded(&bytes, shard_rep, &chunk_rep, size, options) } BytesRepresentation::UnboundedSize => { - self.encode_unbounded(&decoded_value, shard_rep, &chunk_rep, options) + self.encode_unbounded(&bytes, shard_rep, &chunk_rep, options) } - }?)) + }?; + Ok(RawBytes::from(bytes)) } #[allow(clippy::too_many_lines)] fn decode<'a>( &self, - encoded_shard: Cow<'a, [u8]>, + encoded_shard: RawBytes<'a>, shard_representation: &ChunkRepresentation, options: &CodecOptions, - ) -> Result, CodecError> { - // Allocate an array for the output - let len = shard_representation.size_usize(); - let mut decoded_shard = Vec::::with_capacity(len); - + ) -> Result, CodecError> { let shard_shape = shard_representation.shape_u64(); - let chunks_per_shard = - calculate_chunks_per_shard(shard_representation.shape(), self.chunk_shape.as_slice())?; - let shard_index = - self.decode_index(&encoded_shard, chunks_per_shard.as_slice(), options)?; - - // Decode chunks let chunk_representation = unsafe { ChunkRepresentation::new_unchecked( self.chunk_shape.as_slice().to_vec(), @@ -184,19 +183,20 @@ impl ArrayCodecTraits for ShardingCodec { shard_representation.fill_value().clone(), ) }; + let chunks_per_shard = + calculate_chunks_per_shard(shard_representation.shape(), chunk_representation.shape())?; + let num_chunks = chunks_per_shard + .as_slice() + .iter() + .map(|i| usize::try_from(i.get()).unwrap()) + .product::(); + + let shard_index = + self.decode_index(&encoded_shard, chunks_per_shard.as_slice(), options)?; let any_empty = shard_index .par_iter() .any(|offset_or_size| *offset_or_size == u64::MAX); - let contiguous_fill_value = if any_empty { - Some(get_contiguous_fill_value( - shard_representation.fill_value(), - &self.chunk_shape, - &shard_shape, - )) - } else { - None - }; // Calc self/internal concurrent limits let (shard_concurrent_limit, concurrency_limit_inner_chunks) = calc_concurrency_outer_inner( @@ -211,42 +211,20 @@ impl ArrayCodecTraits for ShardingCodec { .concurrent_target(concurrency_limit_inner_chunks) .build(); - let chunks_per_shard = - calculate_chunks_per_shard(shard_representation.shape(), chunk_representation.shape())?; - let num_chunks = chunks_per_shard - .as_slice() - .iter() - .map(|i| usize::try_from(i.get()).unwrap()) - .product::(); - let element_size = chunk_representation.element_size() as u64; - - { - let output = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut decoded_shard); - rayon_iter_concurrent_limit::iter_concurrent_limit!( - shard_concurrent_limit, - (0..num_chunks), - try_for_each, - |chunk_index: usize| { + match shard_representation.data_type().size() { + DataTypeSize::Variable => { + let decode_inner_chunk = |chunk_index: usize| { let chunk_subset = self.chunk_index_to_subset(chunk_index as u64, chunks_per_shard.as_slice()); - let output = unsafe { output.get() }; // Read the offset/size let offset = shard_index[chunk_index * 2]; let size = shard_index[chunk_index * 2 + 1]; - if offset == u64::MAX && size == u64::MAX { - if let Some(fv) = &contiguous_fill_value { - let contiguous_iterator = unsafe { - chunk_subset.contiguous_linearised_indices_unchecked(&shard_shape) - }; - for (index, elements) in &contiguous_iterator { - debug_assert_eq!(fv.len() as u64, elements * element_size); - let shard_offset = usize::try_from(index * element_size).unwrap(); - output[shard_offset..shard_offset + fv.len()].copy_from_slice(fv); - } - } else { - unreachable!(); - } + let chunk_bytes = if offset == u64::MAX && size == u64::MAX { + ArrayBytes::new_fill_value( + chunk_representation.num_elements_usize(), + chunk_representation.fill_value(), + ) } else if usize::try_from(offset + size).unwrap() > encoded_shard.len() { return Err(CodecError::Other( "The shard index references out-of-bounds bytes. The chunk may be corrupted." @@ -256,46 +234,112 @@ impl ArrayCodecTraits for ShardingCodec { let offset: usize = offset.try_into().unwrap(); let size: usize = size.try_into().unwrap(); let encoded_chunk = &encoded_shard[offset..offset + size]; - let decoded_chunk = self.inner_codecs.decode( + self.inner_codecs.decode( Cow::Borrowed(encoded_chunk), &chunk_representation, &options, - )?; - let contiguous_iterator = unsafe { - chunk_subset.contiguous_linearised_indices_unchecked(&shard_shape) + )? + }; + Ok((chunk_bytes, chunk_subset)) + }; + + // Decode the inner chunks + let chunk_bytes_and_subsets = rayon_iter_concurrent_limit::iter_concurrent_limit!( + shard_concurrent_limit, + (0..num_chunks), + map, + decode_inner_chunk + ) + .collect::, _>>()?; + + // Convert into an array + merge_chunks_vlen(chunk_bytes_and_subsets, &shard_representation.shape_u64()) + } + DataTypeSize::Fixed(data_type_size) => { + // Allocate an array for the output + let mut decoded_shard = Vec::::with_capacity( + shard_representation.num_elements_usize() * data_type_size, + ); + + let contiguous_fill_value = if any_empty { + Some(get_contiguous_fill_value( + shard_representation.fill_value(), + &self.chunk_shape, + &shard_shape, + )) + } else { + None + }; + + { + let output = + UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut decoded_shard); + let decode_chunk = |chunk_index: usize| { + let chunk_subset = self + .chunk_index_to_subset(chunk_index as u64, chunks_per_shard.as_slice()); + let output = unsafe { output.get() }; + + // Read the offset/size + let offset = shard_index[chunk_index * 2]; + let size = shard_index[chunk_index * 2 + 1]; + if offset == u64::MAX && size == u64::MAX { + if let Some(fv) = &contiguous_fill_value { + let contiguous_iterator = unsafe { + chunk_subset + .contiguous_linearised_indices_unchecked(&shard_shape) + }; + for (index, elements) in &contiguous_iterator { + debug_assert_eq!( + fv.len() as u64, + elements * data_type_size as u64 + ); + let shard_offset = + usize::try_from(index * data_type_size as u64).unwrap(); + output[shard_offset..shard_offset + fv.len()] + .copy_from_slice(fv); + } + } else { + unreachable!(); + } + } else if usize::try_from(offset + size).unwrap() > encoded_shard.len() { + return Err(CodecError::Other( + "The shard index references out-of-bounds bytes. The chunk may be corrupted." + .to_string(), + )); + } else { + let offset: usize = offset.try_into().unwrap(); + let size: usize = size.try_into().unwrap(); + let encoded_chunk = &encoded_shard[offset..offset + size]; + let decoded_chunk = self.inner_codecs.decode( + Cow::Borrowed(encoded_chunk), + &chunk_representation, + &options, + )?; + update_bytes_flen( + output, + &shard_representation.shape_u64(), + &decoded_chunk.into_fixed()?, + &chunk_subset, + data_type_size, + ); }; - let length = usize::try_from( - contiguous_iterator.contiguous_elements() * element_size, - ) - .unwrap(); - let mut data_idx = 0; - for (index, _) in &contiguous_iterator { - let shard_offset = usize::try_from(index * element_size).unwrap(); - output[shard_offset..shard_offset + length] - .copy_from_slice(&decoded_chunk[data_idx..data_idx + length]); - data_idx += length; - } + + Ok::<_, CodecError>(()) }; - Ok::<_, CodecError>(()) + rayon_iter_concurrent_limit::iter_concurrent_limit!( + shard_concurrent_limit, + (0..num_chunks), + try_for_each, + decode_chunk + )?; } - )?; + unsafe { decoded_shard.set_len(decoded_shard.capacity()) }; + Ok(ArrayBytes::from(decoded_shard)) + } } - - unsafe { decoded_shard.set_len(len) }; - Ok(Cow::Owned(decoded_shard)) } - fn partial_decode_granularity( - &self, - _decoded_representation: &ChunkRepresentation, - ) -> ChunkShape { - self.chunk_shape.clone() - } -} - -#[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToBytesCodecTraits for ShardingCodec { fn partial_decoder<'a>( &'a self, input_handle: Box, @@ -407,13 +451,16 @@ impl ShardingCodec { #[allow(clippy::too_many_lines)] fn encode_bounded( &self, - decoded_value: &[u8], + decoded_value: &ArrayBytes, shard_representation: &ChunkRepresentation, chunk_representation: &ChunkRepresentation, chunk_size_bounded: u64, options: &CodecOptions, ) -> Result, CodecError> { - debug_assert_eq!(decoded_value.len() as u64, shard_representation.size()); // already validated in par_encode + decoded_value.validate( + shard_representation.num_elements(), + shard_representation.data_type().size(), + )?; // Calculate maximum possible shard size let chunks_per_shard = @@ -453,7 +500,6 @@ impl ShardingCodec { .into_builder() .concurrent_target(concurrency_limit_inner_chunks) .build(); - // println!("{shard_concurrent_limit} {concurrency_limit_inner_chunks:?}"); // FIXME: log debug? // Encode the shards and update the shard index { @@ -472,19 +518,15 @@ impl ShardingCodec { |chunk_index: usize| { let chunk_subset = self.chunk_index_to_subset(chunk_index as u64, chunks_per_shard.as_slice()); - let bytes = unsafe { - chunk_subset.extract_bytes_unchecked( - decoded_value, - &shard_shape, - shard_representation.element_size(), - ) - }; - if !chunk_representation.fill_value().equals_all(&bytes) { - let chunk_encoded = self.inner_codecs.encode( - bytes.into(), - chunk_representation, - &options, - )?; + let bytes = decoded_value.extract_array_subset( + &chunk_subset, + &shard_shape, + chunk_representation.data_type(), + )?; + if !bytes.is_fill_value(chunk_representation.fill_value()) { + let chunk_encoded = + self.inner_codecs + .encode(bytes, chunk_representation, &options)?; let chunk_offset = encoded_shard_offset .fetch_add(chunk_encoded.len(), std::sync::atomic::Ordering::Relaxed); @@ -520,8 +562,9 @@ impl ShardingCodec { }; // Encode and write array index + let shard_index_bytes: RawBytes = transmute_to_bytes_vec(shard_index).into(); let encoded_array_index = self.index_codecs.encode( - Cow::Owned(transmute_to_bytes_vec(shard_index)), + shard_index_bytes.into(), &index_decoded_representation, &options, )?; @@ -549,12 +592,15 @@ impl ShardingCodec { #[allow(clippy::too_many_lines)] fn encode_unbounded( &self, - decoded_value: &[u8], + decoded_value: &ArrayBytes, shard_representation: &ChunkRepresentation, chunk_representation: &ChunkRepresentation, options: &CodecOptions, ) -> Result, CodecError> { - debug_assert_eq!(decoded_value.len() as u64, shard_representation.size()); // already validated in par_encode + decoded_value.validate( + shard_representation.num_elements(), + shard_representation.data_type().size(), + )?; let chunks_per_shard = calculate_chunks_per_shard(shard_representation.shape(), chunk_representation.shape())?; @@ -584,26 +630,28 @@ impl ShardingCodec { .into_builder() .concurrent_target(concurrency_limit_inner_chunks) .build(); - // println!("{shard_concurrent_limit} {concurrency_limit_inner_chunks:?}"); // FIXME: log debug? let encode_chunk = |chunk_index| { let chunk_subset = self.chunk_index_to_subset(chunk_index as u64, chunks_per_shard.as_slice()); - let bytes = unsafe { - chunk_subset.extract_bytes_unchecked( - decoded_value, - &shard_shape, - shard_representation.element_size(), - ) + + let bytes = decoded_value.extract_array_subset( + &chunk_subset, + &shard_shape, + chunk_representation.data_type(), + ); + let bytes = match bytes { + Ok(bytes) => bytes, + Err(err) => return Some(Err(err)), }; - if chunk_representation.fill_value().equals_all(&bytes) { + + let is_fill_value = bytes.is_fill_value(chunk_representation.fill_value()); + if is_fill_value { None } else { - let encoded_chunk = self.inner_codecs.encode( - Cow::Owned(bytes), - chunk_representation, - &options_inner, - ); + let encoded_chunk = + self.inner_codecs + .encode(bytes, chunk_representation, &options_inner); match encoded_chunk { Ok(encoded_chunk) => Some(Ok((chunk_index, encoded_chunk.to_vec()))), Err(err) => Some(Err(err)), @@ -662,7 +710,7 @@ impl ShardingCodec { // Write shard index let encoded_array_index = self.index_codecs.encode( - Cow::Owned(transmute_to_bytes_vec(shard_index)), + ArrayBytes::from(transmute_to_bytes_vec(shard_index)), &index_decoded_representation, options, )?; diff --git a/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs b/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs index a55e724d..17ce5bd2 100644 --- a/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs @@ -1,9 +1,10 @@ -use std::{borrow::Cow, num::NonZeroU64}; +use std::num::NonZeroU64; use rayon::prelude::*; use crate::{ array::{ + array_bytes::{merge_chunks_vlen, update_bytes_flen}, chunk_grid::RegularChunkGrid, chunk_shape_to_array_shape, codec::{ @@ -14,7 +15,7 @@ use crate::{ concurrency::{calc_concurrency_outer_inner, RecommendedConcurrency}, ravel_indices, unsafe_cell_slice::UnsafeCellSlice, - ChunkRepresentation, ChunkShape, DataType, + ArrayBytes, ChunkRepresentation, ChunkShape, DataType, DataTypeSize, }, byte_range::ByteRange, }; @@ -128,7 +129,7 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { for array_subset in array_subsets { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( @@ -142,7 +143,7 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { return Ok(array_subsets .iter() .map(|decoded_region| { - Cow::Owned( + ArrayBytes::from( self.decoded_representation .fill_value() .as_ne_bytes() @@ -167,9 +168,6 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { let chunks_per_shard = chunk_shape_to_array_shape(chunks_per_shard.as_slice()); let num_chunks = usize::try_from(chunks_per_shard.iter().product::()).unwrap(); - let element_size = self.decoded_representation.element_size(); - let fill_value = chunk_representation.fill_value().as_ne_bytes(); - // Calculate inner chunk/codec concurrency let (inner_chunk_concurrent_limit, concurrency_limit_codec) = calc_concurrency_outer_inner( options.concurrent_target(), @@ -188,79 +186,157 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { let mut out = Vec::with_capacity(array_subsets.len()); for array_subset in array_subsets { - let array_subset_size = array_subset.num_elements_usize() * element_size; - let mut out_array_subset = vec![0; array_subset_size]; - let out_array_subset_slice = UnsafeCellSlice::new(out_array_subset.as_mut_slice()); - let chunks = unsafe { array_subset.chunks_unchecked(chunk_representation.shape()) }; - rayon_iter_concurrent_limit::iter_concurrent_limit!( - inner_chunk_concurrent_limit, - chunks, - try_for_each, - |(chunk_indices, chunk_subset): (Vec, _)| { - let out_array_subset_slice = unsafe { out_array_subset_slice.get() }; - - let shard_index_idx: usize = - usize::try_from(ravel_indices(&chunk_indices, &chunks_per_shard) * 2) - .unwrap(); - let offset = shard_index[shard_index_idx]; - let size = shard_index[shard_index_idx + 1]; - - // Get the subset of bytes from the chunk which intersect the array - let overlap = unsafe { array_subset.overlap_unchecked(&chunk_subset) }; - let array_subset_in_chunk_subset = - unsafe { overlap.relative_to_unchecked(chunk_subset.start()) }; - - let decoded_bytes = if offset == u64::MAX && size == u64::MAX { - // The chunk is just the fill value - fill_value.repeat(array_subset_in_chunk_subset.num_elements_usize()) - } else { - // Partially decode the inner chunk - let partial_decoder = self.inner_codecs.partial_decoder( - Box::new(ByteIntervalPartialDecoder::new( - &*self.input_handle, - offset, - size, - )), - &chunk_representation, - &options, - ) - .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { - CodecError::Other( - "The shard index references out-of-bounds bytes. The chunk may be corrupted." - .to_string(), + + match self.decoded_representation.element_size() { + DataTypeSize::Variable => { + let decode_inner_chunk_subset = |(chunk_indices, chunk_subset): ( + Vec, + _, + )| { + let shard_index_idx: usize = + usize::try_from(ravel_indices(&chunk_indices, &chunks_per_shard) * 2) + .unwrap(); + let offset = shard_index[shard_index_idx]; + let size = shard_index[shard_index_idx + 1]; + + // Get the subset of bytes from the chunk which intersect the array + let chunk_subset_overlap = + unsafe { array_subset.overlap_unchecked(&chunk_subset) }; + + let chunk_subset_bytes = if offset == u64::MAX && size == u64::MAX { + ArrayBytes::new_fill_value( + chunk_subset_overlap.num_elements_usize(), + chunk_representation.fill_value(), ) } else { - err - })?; - let decoded_bytes = partial_decoder - .partial_decode_opt(&[array_subset_in_chunk_subset], &options)? - .remove(0); - decoded_bytes.to_vec() + // Partially decode the inner chunk + let partial_decoder = self.inner_codecs.partial_decoder( + Box::new(ByteIntervalPartialDecoder::new( + &*self.input_handle, + offset, + size, + )), + &chunk_representation, + &options, + ) + .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { + CodecError::Other( + "The shard index references out-of-bounds bytes. The chunk may be corrupted." + .to_string(), + ) + } else { + err + })?; + partial_decoder + .partial_decode_opt( + &[chunk_subset_overlap + .relative_to(chunk_subset.start()) + .unwrap()], + &options, + )? + .remove(0) + .into_owned() + }; + Ok::<_, CodecError>(( + chunk_subset_bytes, + chunk_subset_overlap + .relative_to(array_subset.start()) + .unwrap(), + )) }; - // Copy decoded bytes to the output - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - let mut decoded_offset = 0; - let contiguous_iterator = unsafe { - chunk_subset_in_array_subset - .contiguous_linearised_indices_unchecked(array_subset.shape()) + // Decode the inner chunk subsets + let chunk_bytes_and_subsets = + rayon_iter_concurrent_limit::iter_concurrent_limit!( + inner_chunk_concurrent_limit, + chunks, + map, + decode_inner_chunk_subset + ) + .collect::, _>>()?; + + // Convert into an array + let out_array_subset = + merge_chunks_vlen(chunk_bytes_and_subsets, array_subset.shape())?; + out.push(out_array_subset); + } + DataTypeSize::Fixed(data_type_size) => { + let array_subset_size = array_subset.num_elements_usize() * data_type_size; + let mut out_array_subset = vec![0; array_subset_size]; + let out_array_subset_slice = + UnsafeCellSlice::new(out_array_subset.as_mut_slice()); + + let decode_inner_chunk_subset_into_slice = |(chunk_indices, chunk_subset): ( + Vec, + _, + )| { + let shard_index_idx: usize = + usize::try_from(ravel_indices(&chunk_indices, &chunks_per_shard) * 2) + .unwrap(); + let offset = shard_index[shard_index_idx]; + let size = shard_index[shard_index_idx + 1]; + + // Get the subset of bytes from the chunk which intersect the array + let chunk_subset_overlap = + unsafe { array_subset.overlap_unchecked(&chunk_subset) }; + + let decoded_bytes = if offset == u64::MAX && size == u64::MAX { + ArrayBytes::new_fill_value( + chunk_subset_overlap.num_elements_usize(), + chunk_representation.fill_value(), + ) + } else { + // Partially decode the inner chunk + let partial_decoder = self.inner_codecs.partial_decoder( + Box::new(ByteIntervalPartialDecoder::new( + &*self.input_handle, + offset, + size, + )), + &chunk_representation, + &options, + ) + .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { + CodecError::Other( + "The shard index references out-of-bounds bytes. The chunk may be corrupted." + .to_string(), + ) + } else { + err + })?; + partial_decoder + .partial_decode_opt( + &[chunk_subset_overlap + .relative_to(chunk_subset.start()) + .unwrap()], + &options, + )? + .remove(0) + .into_owned() + }; + let decoded_bytes = decoded_bytes.into_fixed()?; + update_bytes_flen( + unsafe { out_array_subset_slice.get() }, + array_subset.shape(), + &decoded_bytes, + &chunk_subset_overlap + .relative_to(array_subset.start()) + .unwrap(), + data_type_size, + ); + Ok::<_, CodecError>(()) }; - let length = contiguous_iterator.contiguous_elements_usize() * element_size; - for (array_subset_element_index, _num_elements) in &contiguous_iterator { - let output_offset = - usize::try_from(array_subset_element_index).unwrap() * element_size; - out_array_subset_slice[output_offset..output_offset + length] - .copy_from_slice( - &decoded_bytes[decoded_offset..decoded_offset + length], - ); - decoded_offset += length; - } - Ok::<_, CodecError>(()) + + rayon_iter_concurrent_limit::iter_concurrent_limit!( + inner_chunk_concurrent_limit, + chunks, + try_for_each, + decode_inner_chunk_subset_into_slice + )?; + out.push(ArrayBytes::from(out_array_subset)); } - )?; - out.push(Cow::Owned(out_array_subset)); + } } Ok(out) } @@ -370,7 +446,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncShardingPartialDecoder<'_> { &self, array_subsets: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { for array_subset in array_subsets { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( @@ -384,7 +460,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncShardingPartialDecoder<'_> { return Ok(array_subsets .iter() .map(|decoded_region| { - Cow::Owned( + ArrayBytes::from( self.decoded_representation .fill_value() .as_ne_bytes() @@ -400,180 +476,242 @@ impl AsyncArrayPartialDecoderTraits for AsyncShardingPartialDecoder<'_> { )?; let chunks_per_shard = chunk_shape_to_array_shape(chunks_per_shard.as_slice()); - let element_size = self.decoded_representation.element_size(); + let chunk_representation = unsafe { + ChunkRepresentation::new_unchecked( + self.chunk_grid.chunk_shape().to_vec(), + self.decoded_representation.data_type().clone(), + self.decoded_representation.fill_value().clone(), + ) + }; + let mut out = Vec::with_capacity(array_subsets.len()); - // FIXME: Could go parallel here + // TODO: Could go parallel here? for array_subset in array_subsets { - // shard (subset) - let shard_size = array_subset.num_elements_usize() * element_size; - let mut shard = Vec::with_capacity(shard_size); - let shard_slice = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut shard); - - // Find filled / non filled chunks - let chunk_info = - unsafe { array_subset.chunks_unchecked(self.chunk_grid.chunk_shape()) } - .into_iter() - .map(|(chunk_indices, chunk_subset)| { - let chunk_index = ravel_indices(&chunk_indices, &chunks_per_shard); - let chunk_index = usize::try_from(chunk_index).unwrap(); - - // Read the offset/size - let offset = shard_index[chunk_index * 2]; - let size = shard_index[chunk_index * 2 + 1]; - if offset == u64::MAX && size == u64::MAX { - (chunk_subset, None) - } else { - let offset: usize = offset.try_into().unwrap(); - let size: usize = size.try_into().unwrap(); - (chunk_subset, Some((offset, size))) - } - }) - .collect::>(); - - // Decode unfilled chunks - let results = futures::future::join_all( - chunk_info - .iter() - .filter_map(|(chunk_subset, offset_size)| { - offset_size - .as_ref() - .map(|offset_size| (chunk_subset, offset_size)) - }) - .map(|(chunk_subset, (offset, size))| async move { - let chunk_representation = unsafe { - ChunkRepresentation::new_unchecked( - self.chunk_grid.chunk_shape().to_vec(), - self.decoded_representation.data_type().clone(), - self.decoded_representation.fill_value().clone(), - ) - }; - let partial_decoder = self - .inner_codecs - .async_partial_decoder( - Box::new(AsyncByteIntervalPartialDecoder::new( - &*self.input_handle, - u64::try_from(*offset).unwrap(), - u64::try_from(*size).unwrap(), - )), - &chunk_representation, - options, // FIXME: Adjust options for partial decoding - ) - .await - .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { - CodecError::Other( - "The shard index references out-of-bounds bytes. The chunk may be corrupted." - .to_string(), + match self.decoded_representation.element_size() { + DataTypeSize::Variable => { + let chunks = + unsafe { array_subset.chunks_unchecked(chunk_representation.shape()) }; + + let decode_inner_chunk_subset = |(chunk_indices, chunk_subset): ( + Vec, + _, + )| { + let shard_index_idx: usize = + usize::try_from(ravel_indices(&chunk_indices, &chunks_per_shard) * 2) + .unwrap(); + let chunk_representation = chunk_representation.clone(); + async move { + let offset = shard_index[shard_index_idx]; + let size = shard_index[shard_index_idx + 1]; + + // Get the subset of bytes from the chunk which intersect the array + let chunk_subset_overlap = + unsafe { array_subset.overlap_unchecked(&chunk_subset) }; + + let chunk_subset_bytes = if offset == u64::MAX && size == u64::MAX { + ArrayBytes::new_fill_value( + chunk_subset_overlap.num_elements_usize(), + chunk_representation.fill_value(), ) } else { - err - })?; - let overlap = unsafe { array_subset.overlap_unchecked(chunk_subset) }; - let array_subset_in_chunk_subset = - unsafe { overlap.relative_to_unchecked(chunk_subset.start()) }; - // Partial decoding is actually really slow with the blosc codec! Assume sharded chunks are small, and just decode the whole thing and extract bytes - // TODO: Investigate further - // let decoded_chunk = partial_decoder - // .partial_decode(&[array_subset_in_chunk_subset]) - // .await? - // .remove(0); - let decoded_chunk = partial_decoder - .partial_decode_opt( - &[ArraySubset::new_with_shape(chunk_subset.shape().to_vec())], - options, - ) // FIXME: Adjust options for partial decoding - .await? - .remove(0); - let decoded_chunk = array_subset_in_chunk_subset - .extract_bytes(&decoded_chunk, chunk_subset.shape(), element_size) - .unwrap(); - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - Ok::<_, CodecError>((chunk_subset_in_array_subset, decoded_chunk)) - }), - ) - .await; - // FIXME: Concurrency limit for futures - - if !results.is_empty() { - rayon_iter_concurrent_limit::iter_concurrent_limit!( - options.concurrent_target(), - results, - try_for_each, - |subset_and_decoded_chunk| { - let (chunk_subset_in_array_subset, decoded_chunk): (ArraySubset, Vec) = - subset_and_decoded_chunk?; - let mut data_idx = 0; - let element_size = element_size as u64; - let shard_slice = unsafe { shard_slice.get() }; - let contiguous_iterator = unsafe { - chunk_subset_in_array_subset - .contiguous_linearised_indices_unchecked(array_subset.shape()) - }; - let length = usize::try_from( - contiguous_iterator.contiguous_elements() * element_size, - ) - .unwrap(); - for (index, _num_elements) in &contiguous_iterator { - let shard_offset = usize::try_from(index * element_size).unwrap(); - shard_slice[shard_offset..shard_offset + length] - .copy_from_slice(&decoded_chunk[data_idx..data_idx + length]); - data_idx += length; + // Partially decode the inner chunk + let partial_decoder = self.inner_codecs.async_partial_decoder( + Box::new(AsyncByteIntervalPartialDecoder::new( + &*self.input_handle, + offset, + size, + )), + &chunk_representation, + options, + ).await + .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { + CodecError::Other( + "The shard index references out-of-bounds bytes. The chunk may be corrupted." + .to_string(), + ) + } else { + err + })?; + partial_decoder + .partial_decode_opt( + &[chunk_subset_overlap + .relative_to(chunk_subset.start()) + .unwrap()], + options, + ) + .await? + .remove(0) + .into_owned() + }; + Ok::<_, CodecError>(( + chunk_subset_bytes, + chunk_subset_overlap + .relative_to(array_subset.start()) + .unwrap(), + )) } - Ok::<_, CodecError>(()) - } - )?; - } + }; - // Write filled chunks - let filled_chunks = chunk_info - .iter() - .filter_map(|(chunk_subset, offset_size)| { - if offset_size.is_none() { - Some(chunk_subset) - } else { - None - } - }) - .collect::>(); - if !filled_chunks.is_empty() { - let chunk_array_ss = ArraySubset::new_with_shape(self.chunk_grid.chunk_shape_u64()); - let filled_chunk = self - .decoded_representation - .fill_value() - .as_ne_bytes() - .repeat(chunk_array_ss.num_elements_usize()); - - // Write filled chunks - rayon_iter_concurrent_limit::iter_concurrent_limit!( - options.concurrent_target(), - filled_chunks, - for_each, - |chunk_subset: &ArraySubset| { - let overlap = unsafe { array_subset.overlap_unchecked(chunk_subset) }; - let chunk_subset_in_array_subset = - unsafe { overlap.relative_to_unchecked(array_subset.start()) }; - let mut data_idx = 0; - let element_size = self.decoded_representation.element_size() as u64; - let shard_slice = unsafe { shard_slice.get() }; - let contiguous_iterator = unsafe { - chunk_subset_in_array_subset - .contiguous_linearised_indices_unchecked(array_subset.shape()) - }; - let length = usize::try_from( - contiguous_iterator.contiguous_elements() * element_size, + // Decode the inner chunk subsets + let futures = chunks.iter().map(decode_inner_chunk_subset); + let chunk_bytes_and_subsets = futures::future::try_join_all(futures).await?; + + // Convert into an array + let out_array_subset = + merge_chunks_vlen(chunk_bytes_and_subsets, array_subset.shape())?; + out.push(out_array_subset); + } + DataTypeSize::Fixed(data_type_size) => { + // Find filled / non filled chunks + let chunk_info = + unsafe { array_subset.chunks_unchecked(self.chunk_grid.chunk_shape()) } + .into_iter() + .map(|(chunk_indices, chunk_subset)| { + let chunk_index = ravel_indices(&chunk_indices, &chunks_per_shard); + let chunk_index = usize::try_from(chunk_index).unwrap(); + + // Read the offset/size + let offset = shard_index[chunk_index * 2]; + let size = shard_index[chunk_index * 2 + 1]; + if offset == u64::MAX && size == u64::MAX { + (chunk_subset, None) + } else { + let offset: usize = offset.try_into().unwrap(); + let size: usize = size.try_into().unwrap(); + (chunk_subset, Some((offset, size))) + } + }) + .collect::>(); + + let shard_size = array_subset.num_elements_usize() * data_type_size; + let mut shard = Vec::with_capacity(shard_size); + let shard_slice = UnsafeCellSlice::new_from_vec_with_spare_capacity(&mut shard); + + // Decode unfilled chunks + let results = futures::future::join_all( + chunk_info + .iter() + .filter_map(|(chunk_subset, offset_size)| { + offset_size + .as_ref() + .map(|offset_size| (chunk_subset, offset_size)) + }) + .map(|(chunk_subset, (offset, size))| { + let chunk_representation = chunk_representation.clone(); + async move { + let partial_decoder = self + .inner_codecs + .async_partial_decoder( + Box::new(AsyncByteIntervalPartialDecoder::new( + &*self.input_handle, + u64::try_from(*offset).unwrap(), + u64::try_from(*size).unwrap(), + )), + &chunk_representation, + options, // TODO: Adjust options for partial decoding? + ) + .await + .map_err(|err| if let CodecError::InvalidByteRangeError(_) = err { + CodecError::Other( + "The shard index references out-of-bounds bytes. The chunk may be corrupted." + .to_string(), + ) + } else { + err + })?; + let chunk_subset_overlap = unsafe { array_subset.overlap_unchecked(chunk_subset) }; + // Partial decoding is actually really slow with the blosc codec! Assume sharded chunks are small, and just decode the whole thing and extract bytes + // TODO: Investigate further + // let decoded_chunk = partial_decoder + // .partial_decode(&[chunk_subset_overlap.relative_to(chunk_subset.start())?]) + // .await? + // .remove(0); + let decoded_chunk = partial_decoder + .partial_decode_opt( + &[ArraySubset::new_with_shape(chunk_subset.shape().to_vec())], + options, + ) // TODO: Adjust options for partial decoding + .await? + .remove(0).into_owned(); + let decoded_chunk = decoded_chunk + .extract_array_subset( + &chunk_subset_overlap.relative_to(chunk_subset.start()).unwrap(), + chunk_subset.shape(), + self.decoded_representation.data_type() + )? + .into_fixed()? + .into_owned(); + Ok::<_, CodecError>((decoded_chunk, chunk_subset_overlap)) + }}), ) - .unwrap(); - for (index, _num_elements) in &contiguous_iterator { - let shard_offset = usize::try_from(index * element_size).unwrap(); - shard_slice[shard_offset..shard_offset + length] - .copy_from_slice(&filled_chunk[data_idx..data_idx + length]); - data_idx += length; - } + .await; + // FIXME: Concurrency limit for futures + + if !results.is_empty() { + rayon_iter_concurrent_limit::iter_concurrent_limit!( + options.concurrent_target(), + results, + try_for_each, + |subset_and_decoded_chunk| { + let (chunk_subset_bytes, chunk_subset_overlap): ( + Vec, + ArraySubset, + ) = subset_and_decoded_chunk?; + update_bytes_flen( + unsafe { shard_slice.get() }, + array_subset.shape(), + &chunk_subset_bytes.into(), + &chunk_subset_overlap + .relative_to(array_subset.start()) + .unwrap(), + data_type_size, + ); + Ok::<_, CodecError>(()) + } + )?; } - ); - }; - unsafe { shard.set_len(shard_size) }; - out.push(Cow::Owned(shard)); + + // Write filled chunks + let filled_chunks = chunk_info + .iter() + .filter_map(|(chunk_subset, offset_size)| { + if offset_size.is_none() { + Some(chunk_subset) + } else { + None + } + }) + .collect::>(); + if !filled_chunks.is_empty() { + // Write filled chunks + rayon_iter_concurrent_limit::iter_concurrent_limit!( + options.concurrent_target(), + filled_chunks, + for_each, + |chunk_subset: &ArraySubset| { + let chunk_subset_overlap = + unsafe { array_subset.overlap_unchecked(chunk_subset) }; + let filled_chunk = self + .decoded_representation + .fill_value() + .as_ne_bytes() + .repeat(chunk_subset_overlap.num_elements_usize()); + update_bytes_flen( + unsafe { shard_slice.get() }, + array_subset.shape(), + &filled_chunk.into(), + &chunk_subset_overlap + .relative_to(array_subset.start()) + .unwrap(), + data_type_size, + ); + } + ); + }; + unsafe { shard.set_len(shard_size) }; + out.push(ArrayBytes::from(shard)); + } + } } Ok(out) } diff --git a/src/array/codec/array_to_bytes/vlen.rs b/src/array/codec/array_to_bytes/vlen.rs new file mode 100644 index 00000000..07213411 --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen.rs @@ -0,0 +1,198 @@ +//! The `vlen` array to bytes codec. + +mod vlen_codec; +mod vlen_partial_decoder; + +use std::{mem::size_of, num::NonZeroU64}; + +use itertools::Itertools; +pub use vlen::IDENTIFIER; + +pub use crate::metadata::v3::codec::vlen::{VlenCodecConfiguration, VlenCodecConfigurationV1}; +use crate::{ + array::{ + codec::{ArrayToBytesCodecTraits, CodecError, CodecOptions}, + convert_from_bytes_slice, ChunkRepresentation, CodecChain, DataType, Endianness, FillValue, + RawBytes, NATIVE_ENDIAN, + }, + metadata::v3::codec::vlen, +}; + +pub use vlen_codec::VlenCodec; + +use crate::{ + array::codec::{Codec, CodecPlugin}, + metadata::MetadataV3, + plugin::{PluginCreateError, PluginMetadataInvalidError}, +}; + +use super::bytes::reverse_endianness; + +// Register the codec. +inventory::submit! { + CodecPlugin::new(IDENTIFIER, is_name_vlen, create_codec_vlen) +} + +fn is_name_vlen(name: &str) -> bool { + name.eq(IDENTIFIER) +} + +pub(crate) fn create_codec_vlen(metadata: &MetadataV3) -> Result { + let configuration: VlenCodecConfiguration = metadata + .to_configuration() + .map_err(|_| PluginMetadataInvalidError::new(IDENTIFIER, "codec", metadata.clone()))?; + let codec = Box::new(VlenCodec::new_with_configuration(&configuration)?); + Ok(Codec::ArrayToBytes(codec)) +} + +fn get_vlen_bytes_and_offsets( + index_chunk_representation: &ChunkRepresentation, + bytes: &RawBytes, + index_codecs: &CodecChain, + data_codecs: &CodecChain, + options: &CodecOptions, +) -> Result<(Vec, Vec), CodecError> { + // Get the index length and data start + if bytes.len() < size_of::() { + return Err(CodecError::UnexpectedChunkDecodedSize( + bytes.len(), + size_of::() as u64, + )); + } + let index_len = u64::from_le_bytes(bytes[0..size_of::()].try_into().unwrap()); + let index_len = usize::try_from(index_len) + .map_err(|_| CodecError::Other("index length exceeds usize::MAX".to_string()))?; + let data_start = size_of::() + index_len; + let data_compressed_len = bytes.len() - data_start; + + // Decode the index + let index = &bytes[size_of::()..data_start]; + let mut index_bytes = index_codecs + .decode(index.into(), index_chunk_representation, options)? + .into_fixed()?; + if NATIVE_ENDIAN == Endianness::Big { + reverse_endianness(index_bytes.to_mut(), &DataType::UInt64); + } + let index = match index_chunk_representation.data_type() { + // DataType::UInt8 => { + // let index = convert_from_bytes_slice::(&index_bytes); + // offsets_u8_to_usize(index) + // } + // DataType::UInt16 => { + // let index = convert_from_bytes_slice::(&index_bytes); + // offsets_u16_to_usize(index) + // } + DataType::UInt32 => { + let index = convert_from_bytes_slice::(&index_bytes); + offsets_u32_to_usize(index) + } + DataType::UInt64 => { + let index = convert_from_bytes_slice::(&index_bytes); + offsets_u64_to_usize(index) + } + _ => unreachable!("other data types are not part of VlenIndexDataType"), + }; + + // Get the data length + let Some(&data_len_expected) = index.last() else { + return Err(CodecError::Other( + "Index is empty? It should have at least one element".to_string(), + )); + }; + + // Decode the data + let data = &bytes[data_start..data_start + data_compressed_len]; + let data = if let Ok(data_len_expected) = NonZeroU64::try_from(data_len_expected as u64) { + data_codecs.decode( + data.into(), + &unsafe { + // SAFETY: data type and fill value are compatible + ChunkRepresentation::new_unchecked( + vec![data_len_expected], + DataType::UInt8, + FillValue::from(0u8), + ) + }, + options, + )? + } else { + vec![].into() + } + .into_fixed()? + .into_owned(); + let data_len = data.len(); + + // Check the data length is as expected + if data_len != data_len_expected { + return Err(CodecError::Other(format!( + "Expected data length {data_len_expected} does not match data length {data_len}" + ))); + } + + // Validate the offsets + for (curr, next) in index.iter().tuple_windows() { + if next < curr || *next > data_len { + return Err(CodecError::Other( + "Invalid bytes offsets in vlen Offset64 encoded chunk".to_string(), + )); + } + } + + Ok((data, index)) +} + +// /// Convert u8 offsets to usize +// /// +// /// # Panics if the offsets exceed [`usize::MAX`]. +// fn offsets_u8_to_usize(offsets: Vec) -> Vec { +// if size_of::() == size_of::() { +// bytemuck::allocation::cast_vec(offsets) +// } else { +// offsets +// .into_iter() +// .map(|offset| usize::from(offset)) +// .collect() +// } +// } + +// /// Convert u16 offsets to usize +// /// +// /// # Panics if the offsets exceed [`usize::MAX`]. +// fn offsets_u16_to_usize(offsets: Vec) -> Vec { +// if size_of::() == size_of::() { +// bytemuck::allocation::cast_vec(offsets) +// } else { +// offsets +// .into_iter() +// .map(|offset| usize::from(offset)) +// .collect() +// } +// } + +/// Convert u32 offsets to usize +/// +/// # Panics if the offsets exceed [`usize::MAX`]. +fn offsets_u32_to_usize(offsets: Vec) -> Vec { + if size_of::() == size_of::() { + bytemuck::allocation::cast_vec(offsets) + } else { + offsets + .into_iter() + .map(|offset| usize::try_from(offset).unwrap()) + .collect() + } +} + +/// Convert u64 offsets to usize +/// +/// # Panics if the offsets exceed [`usize::MAX`]. +fn offsets_u64_to_usize(offsets: Vec) -> Vec { + if size_of::() == size_of::() { + bytemuck::allocation::cast_vec(offsets) + } else { + offsets + .into_iter() + .map(|offset| usize::try_from(offset).unwrap()) + .collect() + } +} diff --git a/src/array/codec/array_to_bytes/vlen/vlen_codec.rs b/src/array/codec/array_to_bytes/vlen/vlen_codec.rs new file mode 100644 index 00000000..fc2e6004 --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen/vlen_codec.rs @@ -0,0 +1,305 @@ +use std::{mem::size_of, num::NonZeroU64}; + +use crate::{ + array::{ + codec::{ + ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, BytesCodec, + BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, + RecommendedConcurrency, + }, + transmute_to_bytes_vec, ArrayBytes, ArrayMetadataOptions, BytesRepresentation, + ChunkRepresentation, CodecChain, DataType, DataTypeSize, Endianness, FillValue, RawBytes, + }, + metadata::v3::{codec::vlen::VlenIndexDataType, MetadataV3}, + plugin::PluginCreateError, +}; + +#[cfg(feature = "async")] +use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; + +use super::{vlen_partial_decoder, VlenCodecConfiguration, VlenCodecConfigurationV1}; + +/// A `bytes` codec implementation. +#[derive(Debug, Clone)] +pub struct VlenCodec { + index_codecs: CodecChain, + data_codecs: CodecChain, + index_data_type: VlenIndexDataType, +} + +impl Default for VlenCodec { + fn default() -> Self { + let index_codecs = CodecChain::new( + vec![], + Box::new(BytesCodec::new(Some(Endianness::Little))), + vec![], + ); + let data_codecs = CodecChain::new(vec![], Box::new(BytesCodec::new(None)), vec![]); + Self { + index_codecs, + data_codecs, + index_data_type: VlenIndexDataType::UInt64, + } + } +} + +impl VlenCodec { + /// Create a new `vlen` codec. + #[must_use] + pub fn new( + index_codecs: CodecChain, + data_codecs: CodecChain, + index_data_type: VlenIndexDataType, + ) -> Self { + Self { + index_codecs, + data_codecs, + index_data_type, + } + } + + /// Create a new `vlen` codec from configuration. + /// + /// # Errors + /// Returns a [`PluginCreateError`] if the codecs cannot be constructed from the codec metadata. + pub fn new_with_configuration( + configuration: &VlenCodecConfiguration, + ) -> Result { + let VlenCodecConfiguration::V1(configuration) = configuration; + let index_codecs = CodecChain::from_metadata(&configuration.index_codecs)?; + let data_codecs = CodecChain::from_metadata(&configuration.data_codecs)?; + Ok(Self::new( + index_codecs, + data_codecs, + configuration.index_data_type, + )) + } +} + +impl CodecTraits for VlenCodec { + fn create_metadata_opt(&self, _options: &ArrayMetadataOptions) -> Option { + let configuration = VlenCodecConfigurationV1 { + index_codecs: self.index_codecs.create_metadatas(), + data_codecs: self.data_codecs.create_metadatas(), + index_data_type: self.index_data_type, + }; + Some( + MetadataV3::new_with_serializable_configuration(super::IDENTIFIER, &configuration) + .unwrap(), + ) + } + + fn partial_decoder_should_cache_input(&self) -> bool { + false + } + + fn partial_decoder_decodes_all(&self) -> bool { + true // TODO: Vlen could do partial decoding, but needs coalescing etc + } +} + +impl ArrayCodecTraits for VlenCodec { + fn recommended_concurrency( + &self, + _decoded_representation: &ChunkRepresentation, + ) -> Result { + Ok(RecommendedConcurrency::new_maximum(1)) + } +} + +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for VlenCodec { + fn encode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + let (data, offsets) = bytes.into_variable()?; + + // Encode offsets + let num_offsets = + NonZeroU64::try_from(decoded_representation.num_elements_usize() as u64 + 1).unwrap(); + let offsets = match self.index_data_type { + // VlenIndexDataType::UInt8 => { + // let offsets = offsets + // .iter() + // .map(|offset| u8::try_from(*offset)) + // .collect::, _>>() + // .map_err(|_| { + // CodecError::Other( + // "index offsets are too large for a uint8 index_data_type".to_string(), + // ) + // })?; + // let offsets = transmute_to_bytes_vec(offsets); + // let index_chunk_rep = ChunkRepresentation::new( + // vec![num_offsets], + // DataType::UInt8, + // FillValue::from(0u8), + // ) + // .unwrap(); + // self.index_codecs + // .encode(offsets.into(), &index_chunk_rep, options)? + // } + // VlenIndexDataType::UInt16 => { + // let offsets = offsets + // .iter() + // .map(|offset| u16::try_from(*offset)) + // .collect::, _>>() + // .map_err(|_| { + // CodecError::Other( + // "index offsets are too large for a uint16 index_data_type".to_string(), + // ) + // })?; + // let offsets = transmute_to_bytes_vec(offsets); + // let index_chunk_rep = ChunkRepresentation::new( + // vec![num_offsets], + // DataType::UInt16, + // FillValue::from(0u16), + // ) + // .unwrap(); + // self.index_codecs + // .encode(offsets.into(), &index_chunk_rep, options)? + // } + VlenIndexDataType::UInt32 => { + let offsets = offsets + .iter() + .map(|offset| u32::try_from(*offset)) + .collect::, _>>() + .map_err(|_| { + CodecError::Other( + "index offsets are too large for a uint32 index_data_type".to_string(), + ) + })?; + let offsets = transmute_to_bytes_vec(offsets); + let index_chunk_rep = ChunkRepresentation::new( + vec![num_offsets], + DataType::UInt32, + FillValue::from(0u32), + ) + .unwrap(); + self.index_codecs + .encode(offsets.into(), &index_chunk_rep, options)? + } + VlenIndexDataType::UInt64 => { + let offsets = offsets + .iter() + .map(|offset| u64::try_from(*offset).unwrap()) + .collect::>(); + let offsets = transmute_to_bytes_vec(offsets); + let index_chunk_rep = ChunkRepresentation::new( + vec![num_offsets], + DataType::UInt64, + FillValue::from(0u64), + ) + .unwrap(); + self.index_codecs + .encode(offsets.into(), &index_chunk_rep, options)? + } + }; + + // Encode data + let data = if let Ok(data_len) = NonZeroU64::try_from(data.len() as u64) { + self.data_codecs.encode( + data.into(), + &ChunkRepresentation::new(vec![data_len], DataType::UInt8, FillValue::from(0u8)) + .unwrap(), + options, + )? + } else { + vec![].into() + }; + + // Pack encoded offsets length, encoded offsets, and encoded data + let mut bytes = Vec::with_capacity(size_of::() + offsets.len() + data.len()); + bytes.extend_from_slice(&u64::try_from(offsets.len()).unwrap().to_le_bytes()); // offsets length as u64 little endian + bytes.extend_from_slice(&offsets); + bytes.extend_from_slice(&data); + Ok(bytes.into()) + } + + fn decode<'a>( + &self, + bytes: RawBytes<'a>, + decoded_representation: &ChunkRepresentation, + options: &CodecOptions, + ) -> Result, CodecError> { + let num_elements = decoded_representation.num_elements_usize(); + let index_shape = vec![NonZeroU64::try_from(num_elements as u64 + 1).unwrap()]; + let index_chunk_rep = match self.index_data_type { + // VlenIndexDataType::UInt8 => { + // ChunkRepresentation::new(index_shape, DataType::UInt8, FillValue::from(0u8)) + // } + // VlenIndexDataType::UInt16 => { + // ChunkRepresentation::new(index_shape, DataType::UInt16, FillValue::from(0u16)) + // } + VlenIndexDataType::UInt32 => { + ChunkRepresentation::new(index_shape, DataType::UInt32, FillValue::from(0u32)) + } + VlenIndexDataType::UInt64 => { + ChunkRepresentation::new(index_shape, DataType::UInt64, FillValue::from(0u64)) + } + } + .unwrap(); + let (data, index) = super::get_vlen_bytes_and_offsets( + &index_chunk_rep, + &bytes, + &self.index_codecs, + &self.data_codecs, + options, + )?; + Ok(ArrayBytes::new_vlen(data, index)) + } + + fn partial_decoder<'a>( + &'a self, + input_handle: Box, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + Ok(Box::new(vlen_partial_decoder::VlenPartialDecoder::new( + input_handle, + decoded_representation.clone(), + &self.index_codecs, + &self.data_codecs, + self.index_data_type, + ))) + } + + #[cfg(feature = "async")] + async fn async_partial_decoder<'a>( + &'a self, + input_handle: Box, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + Ok(Box::new( + vlen_partial_decoder::AsyncVlenPartialDecoder::new( + input_handle, + decoded_representation.clone(), + &self.index_codecs, + &self.data_codecs, + self.index_data_type, + ), + )) + } + + fn compute_encoded_size( + &self, + decoded_representation: &ChunkRepresentation, + ) -> Result { + match decoded_representation.data_type().size() { + DataTypeSize::Variable => Ok(BytesRepresentation::UnboundedSize), + DataTypeSize::Fixed(_) => { + return Err(CodecError::UnsupportedDataType( + decoded_representation.data_type().clone(), + super::IDENTIFIER.to_string(), + )) + } + } + } +} diff --git a/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs b/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs new file mode 100644 index 00000000..d142a8df --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs @@ -0,0 +1,178 @@ +// TODO: Support actual partial decoding, coalescing required + +use std::num::NonZeroU64; + +use crate::{ + array::{ + array_bytes::extract_decoded_regions_vlen, + codec::{ + ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, + CodecOptions, + }, + ArrayBytes, ChunkRepresentation, CodecChain, DataType, FillValue, RawBytes, + }, + metadata::v3::codec::vlen::VlenIndexDataType, +}; + +#[cfg(feature = "async")] +use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; + +/// Partial decoder for the `bytes` codec. +pub struct VlenPartialDecoder<'a> { + input_handle: Box, + decoded_representation: ChunkRepresentation, + index_codecs: &'a CodecChain, + data_codecs: &'a CodecChain, + index_data_type: VlenIndexDataType, +} + +impl<'a> VlenPartialDecoder<'a> { + /// Create a new partial decoder for the `bytes` codec. + pub fn new( + input_handle: Box, + decoded_representation: ChunkRepresentation, + index_codecs: &'a CodecChain, + data_codecs: &'a CodecChain, + index_data_type: VlenIndexDataType, + ) -> Self { + Self { + input_handle, + decoded_representation, + index_codecs, + data_codecs, + index_data_type, + } + } +} + +#[allow(clippy::too_many_arguments)] +fn decode_vlen_bytes<'a>( + index_codecs: &CodecChain, + data_codecs: &CodecChain, + index_data_type: VlenIndexDataType, + bytes: Option, + decoded_regions: &[ArraySubset], + fill_value: &FillValue, + shape: &[u64], + options: &CodecOptions, +) -> Result>, CodecError> { + if let Some(bytes) = bytes { + let num_elements = usize::try_from(shape.iter().product::()).unwrap(); + let index_shape = vec![unsafe { NonZeroU64::new_unchecked(1 + num_elements as u64) }]; + let index_chunk_representation = match index_data_type { + // VlenIndexDataType::UInt8 => { + // ChunkRepresentation::new(index_shape, DataType::UInt8, FillValue::from(0u8)) + // } + // VlenIndexDataType::UInt16 => { + // ChunkRepresentation::new(index_shape, DataType::UInt16, FillValue::from(0u16)) + // } + VlenIndexDataType::UInt32 => { + ChunkRepresentation::new(index_shape, DataType::UInt32, FillValue::from(0u32)) + } + VlenIndexDataType::UInt64 => { + ChunkRepresentation::new(index_shape, DataType::UInt64, FillValue::from(0u64)) + } + } + .expect("all data types/fill values are compatible"); + let (data, index) = super::get_vlen_bytes_and_offsets( + &index_chunk_representation, + &bytes, + index_codecs, + data_codecs, + options, + )?; + extract_decoded_regions_vlen(&data, &index, decoded_regions, shape) + } else { + // Chunk is empty, all decoded regions are empty + let mut output = Vec::with_capacity(decoded_regions.len()); + for decoded_region in decoded_regions { + output.push(ArrayBytes::new_fill_value( + decoded_region.num_elements_usize(), + fill_value, + )); + } + Ok(output) + } +} + +impl ArrayPartialDecoderTraits for VlenPartialDecoder<'_> { + fn data_type(&self) -> &DataType { + self.decoded_representation.data_type() + } + + fn partial_decode_opt( + &self, + decoded_regions: &[ArraySubset], + options: &CodecOptions, + ) -> Result>, CodecError> { + // Get all of the input bytes (cached due to CodecTraits::partial_decoder_decodes_all() == true) + let bytes = self.input_handle.decode(options)?; + decode_vlen_bytes( + self.index_codecs, + self.data_codecs, + self.index_data_type, + bytes, + decoded_regions, + self.decoded_representation.fill_value(), + &self.decoded_representation.shape_u64(), + options, + ) + } +} + +#[cfg(feature = "async")] +/// Asynchronous partial decoder for the `bytes` codec. +pub struct AsyncVlenPartialDecoder<'a> { + input_handle: Box, + decoded_representation: ChunkRepresentation, + index_codecs: &'a CodecChain, + data_codecs: &'a CodecChain, + index_data_type: VlenIndexDataType, +} + +#[cfg(feature = "async")] +impl<'a> AsyncVlenPartialDecoder<'a> { + /// Create a new partial decoder for the `bytes` codec. + pub fn new( + input_handle: Box, + decoded_representation: ChunkRepresentation, + index_codecs: &'a CodecChain, + data_codecs: &'a CodecChain, + index_data_type: VlenIndexDataType, + ) -> Self { + Self { + input_handle, + decoded_representation, + index_codecs, + data_codecs, + index_data_type, + } + } +} + +#[cfg(feature = "async")] +#[async_trait::async_trait] +impl AsyncArrayPartialDecoderTraits for AsyncVlenPartialDecoder<'_> { + fn data_type(&self) -> &DataType { + self.decoded_representation.data_type() + } + + async fn partial_decode_opt( + &self, + decoded_regions: &[ArraySubset], + options: &CodecOptions, + ) -> Result>, CodecError> { + // Get all of the input bytes (cached due to CodecTraits::partial_decoder_decodes_all() == true) + let bytes = self.input_handle.decode(options).await?; + decode_vlen_bytes( + self.index_codecs, + self.data_codecs, + self.index_data_type, + bytes, + decoded_regions, + self.decoded_representation.fill_value(), + &self.decoded_representation.shape_u64(), + options, + ) + } +} diff --git a/src/array/codec/array_to_bytes/vlen_interleaved.rs b/src/array/codec/array_to_bytes/vlen_interleaved.rs new file mode 100644 index 00000000..06d1164d --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen_interleaved.rs @@ -0,0 +1,83 @@ +//! The `vlen_interleaved` array to bytes codec. + +mod vlen_interleaved_codec; +mod vlen_interleaved_partial_decoder; + +use std::mem::size_of; + +pub use vlen_interleaved::IDENTIFIER; + +pub use crate::metadata::v3::codec::vlen_interleaved::{ + VlenInterleavedCodecConfiguration, VlenInterleavedCodecConfigurationV1, +}; +use crate::{ + array::{codec::CodecError, RawBytes}, + metadata::v3::codec::vlen_interleaved, +}; + +pub use vlen_interleaved_codec::VlenInterleavedCodec; + +use crate::{ + array::codec::{Codec, CodecPlugin}, + metadata::MetadataV3, + plugin::{PluginCreateError, PluginMetadataInvalidError}, +}; + +// Register the codec. +inventory::submit! { + CodecPlugin::new(IDENTIFIER, is_name_vlen_interleaved, create_codec_vlen_interleaved) +} + +fn is_name_vlen_interleaved(name: &str) -> bool { + name.eq(IDENTIFIER) +} + +pub(crate) fn create_codec_vlen_interleaved( + metadata: &MetadataV3, +) -> Result { + let configuration: VlenInterleavedCodecConfiguration = metadata + .to_configuration() + .map_err(|_| PluginMetadataInvalidError::new(IDENTIFIER, "codec", metadata.clone()))?; + let codec = Box::new(VlenInterleavedCodec::new_with_configuration(&configuration)); + Ok(Codec::ArrayToBytes(codec)) +} + +fn get_interleaved_bytes_and_offsets( + num_elements: usize, + bytes: &RawBytes, +) -> Result<(Vec, Vec), CodecError> { + // Validate the bytes is long enough to contain header and element lengths + let header_length = size_of::() * (1 + num_elements); + if bytes.len() < header_length { + return Err(CodecError::UnexpectedChunkDecodedSize( + bytes.len(), + header_length as u64, + )); + } + + // Validate the number of elements from the header + let header_num_elements = u32::from_le_bytes((&bytes[0..size_of::()]).try_into().unwrap()); + if u32::try_from(num_elements).unwrap() != header_num_elements { + return Err(CodecError::Other(format!( + "Expected header with {num_elements} elements, got {header_num_elements}" + ))); + } + + let bytes_len = bytes.len() - header_length; + let mut bytes_out = Vec::with_capacity(bytes_len); + let mut offsets_out = Vec::with_capacity(num_elements + 1); + let mut offset = size_of::(); + for _element in 0..num_elements { + let length = + u32::from_le_bytes(bytes[offset..offset + size_of::()].try_into().unwrap()); + offset += size_of::(); + offsets_out.push(bytes_out.len()); + if length != 0 { + bytes_out.extend_from_slice(&bytes[offset..offset + length as usize]); + offset += length as usize; + } + } + offsets_out.push(bytes_out.len()); + + Ok((bytes_out, offsets_out)) +} diff --git a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs new file mode 100644 index 00000000..db610d77 --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs @@ -0,0 +1,157 @@ +use std::mem::size_of; + +use itertools::Itertools; + +use crate::{ + array::{ + codec::{ + ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, + BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, + RecommendedConcurrency, + }, + ArrayBytes, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, DataTypeSize, + RawBytes, + }, + metadata::v3::MetadataV3, +}; + +#[cfg(feature = "async")] +use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; + +use super::{VlenInterleavedCodecConfiguration, VlenInterleavedCodecConfigurationV1}; + +/// The `vlen_interleaved` codec implementation. +#[derive(Debug, Clone, Default)] +pub struct VlenInterleavedCodec {} + +impl VlenInterleavedCodec { + /// Create a new `vlen` codec. + #[must_use] + pub fn new() -> Self { + Self {} + } + + /// Create a new `vlen` codec from configuration. + #[must_use] + pub fn new_with_configuration(_configuration: &VlenInterleavedCodecConfiguration) -> Self { + // let VlenInterleavedCodecConfiguration::V1(configuration) = configuration; + Self {} + } +} + +impl CodecTraits for VlenInterleavedCodec { + fn create_metadata_opt(&self, _options: &ArrayMetadataOptions) -> Option { + let configuration = VlenInterleavedCodecConfigurationV1 {}; + Some( + MetadataV3::new_with_serializable_configuration(super::IDENTIFIER, &configuration) + .unwrap(), + ) + } + + fn partial_decoder_should_cache_input(&self) -> bool { + false + } + + fn partial_decoder_decodes_all(&self) -> bool { + true // TODO: Vlen could do partial decoding, but needs coalescing etc + } +} + +impl ArrayCodecTraits for VlenInterleavedCodec { + fn recommended_concurrency( + &self, + _decoded_representation: &ChunkRepresentation, + ) -> Result { + Ok(RecommendedConcurrency::new_maximum(1)) + } +} + +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for VlenInterleavedCodec { + fn encode<'a>( + &self, + bytes: ArrayBytes<'a>, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + bytes.validate( + decoded_representation.num_elements(), + decoded_representation.data_type().size(), + )?; + let (bytes, offsets) = bytes.into_variable()?; + + let num_elements = decoded_representation.num_elements(); + debug_assert_eq!(1 + num_elements, offsets.len() as u64); + + let mut data: Vec = Vec::with_capacity(offsets.len() * size_of::() + bytes.len()); + // Number of elements + let num_elements = u32::try_from(num_elements).map_err(|_| { + CodecError::Other("num_elements exceeds u32::MAX in vlen codec".to_string()) + })?; + data.extend_from_slice(num_elements.to_le_bytes().as_slice()); + // Interleaved length (u32, little endian) and element bytes + for (&curr, &next) in offsets.iter().tuple_windows() { + let element_bytes = &bytes[curr..next]; + let element_bytes_len = u32::try_from(element_bytes.len()).unwrap(); + data.extend_from_slice(&element_bytes_len.to_le_bytes()); + data.extend_from_slice(element_bytes); + } + + Ok(data.into()) + } + + fn decode<'a>( + &self, + bytes: RawBytes<'a>, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + let num_elements = decoded_representation.num_elements_usize(); + let (bytes, offsets) = super::get_interleaved_bytes_and_offsets(num_elements, &bytes)?; + Ok(ArrayBytes::new_vlen(bytes, offsets)) + } + + fn partial_decoder<'a>( + &self, + input_handle: Box, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + Ok(Box::new( + super::vlen_interleaved_partial_decoder::VlenInterleavedPartialDecoder::new( + input_handle, + decoded_representation.clone(), + ), + )) + } + + #[cfg(feature = "async")] + async fn async_partial_decoder<'a>( + &'a self, + input_handle: Box, + decoded_representation: &ChunkRepresentation, + _options: &CodecOptions, + ) -> Result, CodecError> { + Ok(Box::new( + super::vlen_interleaved_partial_decoder::AsyncVlenInterleavedPartialDecoder::new( + input_handle, + decoded_representation.clone(), + ), + )) + } + + fn compute_encoded_size( + &self, + decoded_representation: &ChunkRepresentation, + ) -> Result { + match decoded_representation.data_type().size() { + DataTypeSize::Variable => Ok(BytesRepresentation::UnboundedSize), + DataTypeSize::Fixed(_) => { + return Err(CodecError::UnsupportedDataType( + decoded_representation.data_type().clone(), + super::IDENTIFIER.to_string(), + )) + } + } + } +} diff --git a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs new file mode 100644 index 00000000..bb707fb8 --- /dev/null +++ b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs @@ -0,0 +1,119 @@ +// TODO: Support actual partial decoding, coalescing required + +use crate::array::{ + array_bytes::extract_decoded_regions_vlen, + codec::{ + ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, CodecOptions, + }, + ArrayBytes, ChunkRepresentation, DataType, FillValue, RawBytes, +}; + +#[cfg(feature = "async")] +use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; + +/// Partial decoder for the `bytes` codec. +pub struct VlenInterleavedPartialDecoder<'a> { + input_handle: Box, + decoded_representation: ChunkRepresentation, +} + +impl<'a> VlenInterleavedPartialDecoder<'a> { + /// Create a new partial decoder for the `bytes` codec. + pub fn new( + input_handle: Box, + decoded_representation: ChunkRepresentation, + ) -> Self { + Self { + input_handle, + decoded_representation, + } + } +} + +fn decode_vlen_bytes<'a>( + bytes: Option, + decoded_regions: &[ArraySubset], + fill_value: &FillValue, + shape: &[u64], +) -> Result>, CodecError> { + if let Some(bytes) = bytes { + let num_elements = usize::try_from(shape.iter().product::()).unwrap(); + let (bytes, offsets) = super::get_interleaved_bytes_and_offsets(num_elements, &bytes)?; + extract_decoded_regions_vlen(&bytes, &offsets, decoded_regions, shape) + } else { + // Chunk is empty, all decoded regions are empty + let mut output = Vec::with_capacity(decoded_regions.len()); + for decoded_region in decoded_regions { + output.push(ArrayBytes::new_fill_value( + decoded_region.num_elements_usize(), + fill_value, + )); + } + Ok(output) + } +} + +impl ArrayPartialDecoderTraits for VlenInterleavedPartialDecoder<'_> { + fn data_type(&self) -> &DataType { + self.decoded_representation.data_type() + } + + fn partial_decode_opt( + &self, + decoded_regions: &[ArraySubset], + options: &CodecOptions, + ) -> Result>, CodecError> { + // Get all of the input bytes (cached due to CodecTraits::partial_decoder_decodes_all() == true) + let bytes = self.input_handle.decode(options)?; + decode_vlen_bytes( + bytes, + decoded_regions, + self.decoded_representation.fill_value(), + &self.decoded_representation.shape_u64(), + ) + } +} + +#[cfg(feature = "async")] +/// Asynchronous partial decoder for the `bytes` codec. +pub struct AsyncVlenInterleavedPartialDecoder<'a> { + input_handle: Box, + decoded_representation: ChunkRepresentation, +} + +#[cfg(feature = "async")] +impl<'a> AsyncVlenInterleavedPartialDecoder<'a> { + /// Create a new partial decoder for the `bytes` codec. + pub fn new( + input_handle: Box, + decoded_representation: ChunkRepresentation, + ) -> Self { + Self { + input_handle, + decoded_representation, + } + } +} + +#[cfg(feature = "async")] +#[async_trait::async_trait] +impl AsyncArrayPartialDecoderTraits for AsyncVlenInterleavedPartialDecoder<'_> { + fn data_type(&self) -> &DataType { + self.decoded_representation.data_type() + } + + async fn partial_decode_opt( + &self, + decoded_regions: &[ArraySubset], + options: &CodecOptions, + ) -> Result>, CodecError> { + // Get all of the input bytes (cached due to CodecTraits::partial_decoder_decodes_all() == true) + let bytes = self.input_handle.decode(options).await?; + decode_vlen_bytes( + bytes, + decoded_regions, + self.decoded_representation.fill_value(), + &self.decoded_representation.shape_u64(), + ) + } +} diff --git a/src/array/codec/array_to_bytes/zfp.rs b/src/array/codec/array_to_bytes/zfp.rs index 7c461c89..8a72adf1 100644 --- a/src/array/codec/array_to_bytes/zfp.rs +++ b/src/array/codec/array_to_bytes/zfp.rs @@ -271,10 +271,14 @@ fn zfp_decode( #[cfg(test)] mod tests { use num::traits::AsPrimitive; - use std::{borrow::Cow, num::NonZeroU64}; + use std::num::NonZeroU64; use crate::{ - array::codec::{ArrayCodecTraits, ArrayToBytesCodecTraits, CodecOptions}, + array::{ + codec::{ArrayToBytesCodecTraits, CodecOptions}, + element::ElementOwned, + ArrayBytes, + }, array_subset::ArraySubset, }; @@ -304,21 +308,23 @@ mod tests { ] } - fn codec_zfp_round_trip( + fn codec_zfp_round_trip< + T: core::fmt::Debug + std::cmp::PartialEq + ElementOwned + Copy + 'static, + >( chunk_representation: &ChunkRepresentation, configuration: &str, ) where i32: num::traits::AsPrimitive, { let elements: Vec = (0..27).map(|i: i32| i.as_()).collect(); - let bytes = crate::array::transmute_to_bytes_vec(elements.clone()); + let bytes = T::into_array_bytes(chunk_representation.data_type(), &elements).unwrap(); let configuration: ZfpCodecConfiguration = serde_json::from_str(configuration).unwrap(); let codec = ZfpCodec::new_with_configuration(&configuration); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -329,9 +335,10 @@ mod tests { &chunk_representation, &CodecOptions::default(), ) - .unwrap(); - - let decoded_elements = crate::array::convert_from_bytes_slice::(&decoded); + .unwrap() + .into_owned(); + let decoded_elements = + T::from_array_bytes(chunk_representation.data_type(), decoded).unwrap(); assert_eq!(elements, decoded_elements); } @@ -493,13 +500,14 @@ mod tests { ChunkRepresentation::new(chunk_shape, DataType::Float32, 0.0f32.into()).unwrap(); let elements: Vec = (0..27).map(|i| i as f32).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let configuration: ZfpCodecConfiguration = serde_json::from_str(JSON_REVERSIBLE).unwrap(); let codec = ZfpCodec::new_with_configuration(&configuration); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -523,7 +531,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) @@ -548,6 +556,7 @@ mod tests { ChunkRepresentation::new(chunk_shape, DataType::Float32, 0.0f32.into()).unwrap(); let elements: Vec = (0..27).map(|i| i as f32).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); + let bytes: ArrayBytes = bytes.into(); let configuration: ZfpCodecConfiguration = serde_json::from_str(JSON_REVERSIBLE).unwrap(); let codec = ZfpCodec::new_with_configuration(&configuration); @@ -555,7 +564,7 @@ mod tests { let max_encoded_size = codec.compute_encoded_size(&chunk_representation).unwrap(); let encoded = codec .encode( - Cow::Borrowed(&bytes), + bytes.clone(), &chunk_representation, &CodecOptions::default(), ) @@ -582,7 +591,7 @@ mod tests { let decoded_partial_chunk: Vec = decoded_partial_chunk .into_iter() - .map(|v| v.to_vec()) + .map(|bytes| bytes.into_fixed().unwrap().to_vec()) .flatten() .collect::>() .chunks(std::mem::size_of::()) diff --git a/src/array/codec/array_to_bytes/zfp/zfp_codec.rs b/src/array/codec/array_to_bytes/zfp/zfp_codec.rs index 3ea792fd..f98d7c81 100644 --- a/src/array/codec/array_to_bytes/zfp/zfp_codec.rs +++ b/src/array/codec/array_to_bytes/zfp/zfp_codec.rs @@ -11,8 +11,8 @@ use zfp_sys::{ use crate::{ array::{ codec::{ - ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, - BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, + ArrayBytes, ArrayCodecTraits, ArrayPartialDecoderTraits, ArrayToBytesCodecTraits, + BytesPartialDecoderTraits, CodecError, CodecOptions, CodecTraits, RawBytes, RecommendedConcurrency, }, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, DataType, @@ -129,18 +129,21 @@ impl ArrayCodecTraits for ZfpCodec { // TODO: zfp supports multi thread, when is it optimal to kick in? Ok(RecommendedConcurrency::new_maximum(1)) } +} +#[cfg_attr(feature = "async", async_trait::async_trait)] +impl ArrayToBytesCodecTraits for ZfpCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + bytes: ArrayBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { - let mut decoded_value_promoted = - promote_before_zfp_encoding(&decoded_value, decoded_representation)?; - let zfp_type = decoded_value_promoted.zfp_type(); + ) -> Result, CodecError> { + let bytes = bytes.into_fixed()?; + let mut bytes_promoted = promote_before_zfp_encoding(&bytes, decoded_representation)?; + let zfp_type = bytes_promoted.zfp_type(); let Some(field) = ZfpField::new( - &mut decoded_value_promoted, + &mut bytes_promoted, &decoded_representation .shape() .iter() @@ -185,22 +188,19 @@ impl ArrayCodecTraits for ZfpCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + bytes: RawBytes<'a>, decoded_representation: &ChunkRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { zfp_decode( &self.mode, - &mut encoded_value.to_vec(), // FIXME: Does zfp **really** need the encoded value as mutable? + &mut bytes.to_vec(), // FIXME: Does zfp **really** need the encoded value as mutable? decoded_representation, false, // FIXME ) - .map(Cow::Owned) + .map(ArrayBytes::from) } -} -#[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToBytesCodecTraits for ZfpCodec { fn partial_decoder<'a>( &'a self, input_handle: Box, diff --git a/src/array/codec/array_to_bytes/zfp/zfp_partial_decoder.rs b/src/array/codec/array_to_bytes/zfp/zfp_partial_decoder.rs index ac5179ac..7f7103f7 100644 --- a/src/array/codec/array_to_bytes/zfp/zfp_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/zfp/zfp_partial_decoder.rs @@ -1,8 +1,9 @@ -use std::borrow::Cow; - use crate::{ array::{ - codec::{ArrayPartialDecoderTraits, BytesPartialDecoderTraits, CodecError, CodecOptions}, + codec::{ + ArrayBytes, ArrayPartialDecoderTraits, BytesPartialDecoderTraits, CodecError, + CodecOptions, + }, ChunkRepresentation, DataType, }, array_subset::ArraySubset, @@ -51,7 +52,10 @@ impl ArrayPartialDecoderTraits for ZfpPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { + let data_type_size = self.data_type().fixed_size().ok_or_else(|| { + CodecError::UnsupportedDataType(self.data_type().clone(), super::IDENTIFIER.to_string()) + })?; for array_subset in decoded_regions { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( @@ -73,13 +77,9 @@ impl ArrayPartialDecoderTraits for ZfpPartialDecoder<'_> { false, // FIXME )?; for array_subset in decoded_regions { - let byte_ranges = unsafe { - array_subset.byte_ranges_unchecked( - &chunk_shape, - self.decoded_representation.element_size(), - ) - }; - out.push(Cow::Owned(extract_byte_ranges_concat( + let byte_ranges = + unsafe { array_subset.byte_ranges_unchecked(&chunk_shape, data_type_size) }; + out.push(ArrayBytes::from(extract_byte_ranges_concat( &decoded_value, &byte_ranges, )?)); @@ -87,7 +87,7 @@ impl ArrayPartialDecoderTraits for ZfpPartialDecoder<'_> { } None => { for decoded_region in decoded_regions { - out.push(Cow::Owned( + out.push(ArrayBytes::from( self.decoded_representation .fill_value() .as_ne_bytes() @@ -141,7 +141,10 @@ impl AsyncArrayPartialDecoderTraits for AsyncZfpPartialDecoder<'_> { &self, decoded_regions: &[ArraySubset], options: &CodecOptions, - ) -> Result>, CodecError> { + ) -> Result>, CodecError> { + let data_type_size = self.data_type().fixed_size().ok_or_else(|| { + CodecError::UnsupportedDataType(self.data_type().clone(), super::IDENTIFIER.to_string()) + })?; for array_subset in decoded_regions { if array_subset.dimensionality() != self.decoded_representation.dimensionality() { return Err(CodecError::InvalidArraySubsetDimensionalityError( @@ -163,13 +166,9 @@ impl AsyncArrayPartialDecoderTraits for AsyncZfpPartialDecoder<'_> { false, // FIXME )?; for array_subset in decoded_regions { - let byte_ranges = unsafe { - array_subset.byte_ranges_unchecked( - &chunk_shape, - self.decoded_representation.element_size(), - ) - }; - out.push(Cow::Owned(extract_byte_ranges_concat( + let byte_ranges = + unsafe { array_subset.byte_ranges_unchecked(&chunk_shape, data_type_size) }; + out.push(ArrayBytes::from(extract_byte_ranges_concat( &decoded_value, &byte_ranges, )?)); @@ -177,7 +176,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncZfpPartialDecoder<'_> { } None => { for decoded_region in decoded_regions { - out.push(Cow::Owned( + out.push(ArrayBytes::from( self.decoded_representation .fill_value() .as_ne_bytes() diff --git a/src/array/codec/byte_interval_partial_decoder.rs b/src/array/codec/byte_interval_partial_decoder.rs index e0e95eca..33fcffa7 100644 --- a/src/array/codec/byte_interval_partial_decoder.rs +++ b/src/array/codec/byte_interval_partial_decoder.rs @@ -1,6 +1,7 @@ -use std::borrow::Cow; - -use crate::byte_range::{ByteLength, ByteOffset, ByteRange}; +use crate::{ + array::RawBytes, + byte_range::{ByteLength, ByteOffset, ByteRange}, +}; use super::{BytesPartialDecoderTraits, CodecError, CodecOptions}; @@ -36,7 +37,7 @@ impl<'a> BytesPartialDecoderTraits for ByteIntervalPartialDecoder<'a> { &self, byte_ranges: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let byte_ranges: Vec = byte_ranges .iter() .map(|byte_range| match byte_range { @@ -92,7 +93,7 @@ impl<'a> AsyncBytesPartialDecoderTraits for AsyncByteIntervalPartialDecoder<'a> &self, byte_ranges: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let byte_ranges: Vec = byte_ranges .iter() .map(|byte_range| match byte_range { diff --git a/src/array/codec/bytes_partial_decoder_cache.rs b/src/array/codec/bytes_partial_decoder_cache.rs index de42f45a..634866ea 100644 --- a/src/array/codec/bytes_partial_decoder_cache.rs +++ b/src/array/codec/bytes_partial_decoder_cache.rs @@ -2,7 +2,10 @@ use std::{borrow::Cow, marker::PhantomData}; -use crate::byte_range::{extract_byte_ranges, ByteRange}; +use crate::{ + array::RawBytes, + byte_range::{extract_byte_ranges, ByteRange}, +}; use super::{BytesPartialDecoderTraits, CodecError, CodecOptions}; @@ -58,7 +61,7 @@ impl BytesPartialDecoderTraits for BytesPartialDecoderCache<'_> { &self, decoded_regions: &[ByteRange], _options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { Ok(match &self.cache { Some(bytes) => Some( extract_byte_ranges(bytes, decoded_regions) @@ -79,7 +82,7 @@ impl AsyncBytesPartialDecoderTraits for BytesPartialDecoderCache<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { BytesPartialDecoderTraits::partial_decode(self, decoded_regions, options) } } diff --git a/src/array/codec/bytes_to_bytes/blosc.rs b/src/array/codec/bytes_to_bytes/blosc.rs index ef8287b2..16bdc8b7 100644 --- a/src/array/codec/bytes_to_bytes/blosc.rs +++ b/src/array/codec/bytes_to_bytes/blosc.rs @@ -336,7 +336,9 @@ mod tests { let array_representation = ArrayRepresentation::new(vec![2, 2, 2], DataType::UInt16, FillValue::from(0u16)) .unwrap(); - let bytes_representation = BytesRepresentation::FixedSize(array_representation.size()); + let data_type_size = array_representation.data_type().fixed_size().unwrap(); + let array_size = array_representation.num_elements_usize() * data_type_size; + let bytes_representation = BytesRepresentation::FixedSize(array_size as u64); let elements: Vec = (0..array_representation.num_elements() as u16).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); @@ -349,10 +351,7 @@ mod tests { .encode(Cow::Borrowed(&bytes), &CodecOptions::default()) .unwrap(); let decoded_regions: Vec = ArraySubset::new_with_ranges(&[0..2, 1..2, 0..1]) - .byte_ranges( - array_representation.shape(), - array_representation.element_size(), - ) + .byte_ranges(array_representation.shape(), data_type_size) .unwrap(); let input_handle = Box::new(std::io::Cursor::new(encoded)); let partial_decoder = codec @@ -384,7 +383,9 @@ mod tests { let array_representation = ArrayRepresentation::new(vec![2, 2, 2], DataType::UInt16, FillValue::from(0u16)) .unwrap(); - let bytes_representation = BytesRepresentation::FixedSize(array_representation.size()); + let data_type_size = array_representation.data_type().fixed_size().unwrap(); + let array_size = array_representation.num_elements_usize() * data_type_size; + let bytes_representation = BytesRepresentation::FixedSize(array_size as u64); let elements: Vec = (0..array_representation.num_elements() as u16).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); @@ -397,10 +398,7 @@ mod tests { .encode(Cow::Borrowed(&bytes), &CodecOptions::default()) .unwrap(); let decoded_regions: Vec = ArraySubset::new_with_ranges(&[0..2, 1..2, 0..1]) - .byte_ranges( - array_representation.shape(), - array_representation.element_size(), - ) + .byte_ranges(array_representation.shape(), data_type_size) .unwrap(); let input_handle = Box::new(std::io::Cursor::new(encoded)); let partial_decoder = codec diff --git a/src/array/codec/bytes_to_bytes/blosc/blosc_codec.rs b/src/array/codec/bytes_to_bytes/blosc/blosc_codec.rs index f868d30f..c2a79046 100644 --- a/src/array/codec/bytes_to_bytes/blosc/blosc_codec.rs +++ b/src/array/codec/bytes_to_bytes/blosc/blosc_codec.rs @@ -8,7 +8,7 @@ use crate::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, plugin::PluginCreateError, @@ -136,7 +136,6 @@ impl CodecTraits for BloscCodec { cname: self.cname, clevel: self.clevel, shuffle: self.shuffle_mode.unwrap_or_else(|| { - // FIXME: If type size is not known... it must be if self.typesize.unwrap_or_default() > 0 { BloscShuffleMode::BitShuffle } else { @@ -170,9 +169,9 @@ impl BytesToBytesCodecTraits for BloscCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { // let n_threads = std::cmp::min( // options.concurrent_limit(), // std::thread::available_parallelism().unwrap(), @@ -184,10 +183,10 @@ impl BytesToBytesCodecTraits for BloscCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { // let n_threads = std::cmp::min( // options.concurrent_limit(), // std::thread::available_parallelism().unwrap(), diff --git a/src/array/codec/bytes_to_bytes/blosc/blosc_partial_decoder.rs b/src/array/codec/bytes_to_bytes/blosc/blosc_partial_decoder.rs index aa9fd701..c4779b99 100644 --- a/src/array/codec/bytes_to_bytes/blosc/blosc_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/blosc/blosc_partial_decoder.rs @@ -1,8 +1,12 @@ use std::borrow::Cow; use crate::{ - array::codec::{ - bytes_to_bytes::blosc::blosc_nbytes, BytesPartialDecoderTraits, CodecError, CodecOptions, + array::{ + codec::{ + bytes_to_bytes::blosc::blosc_nbytes, BytesPartialDecoderTraits, CodecError, + CodecOptions, + }, + RawBytes, }, byte_range::ByteRange, }; @@ -28,7 +32,7 @@ impl BytesPartialDecoderTraits for BloscPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options)?; let Some(encoded_value) = encoded_value else { return Ok(None); @@ -38,7 +42,6 @@ impl BytesPartialDecoderTraits for BloscPartialDecoder<'_> { let nbytes = blosc_nbytes(&encoded_value); let typesize = blosc_typesize(&encoded_value); if let (Some(nbytes), Some(typesize)) = (nbytes, typesize) { - // FIXME: This needs coalescing to be efficient, for now CodecTraits::partial_decoder_decodes_all is set to true let mut decoded_byte_ranges = Vec::with_capacity(decoded_regions.len()); for byte_range in decoded_regions { let start = usize::try_from(byte_range.start(nbytes as u64)).unwrap(); @@ -81,7 +84,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncBloscPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options).await?; let Some(encoded_value) = encoded_value else { return Ok(None); diff --git a/src/array/codec/bytes_to_bytes/bz2.rs b/src/array/codec/bytes_to_bytes/bz2.rs index 87717eca..09a49182 100644 --- a/src/array/codec/bytes_to_bytes/bz2.rs +++ b/src/array/codec/bytes_to_bytes/bz2.rs @@ -100,7 +100,9 @@ mod tests { let array_representation = ArrayRepresentation::new(vec![2, 2, 2], DataType::UInt16, FillValue::from(0u16)) .unwrap(); - let bytes_representation = BytesRepresentation::FixedSize(array_representation.size()); + let data_type_size = array_representation.data_type().fixed_size().unwrap(); + let array_size = array_representation.num_elements_usize() * data_type_size; + let bytes_representation = BytesRepresentation::FixedSize(array_size as u64); let elements: Vec = (0..array_representation.num_elements() as u16).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); @@ -112,10 +114,7 @@ mod tests { .encode(Cow::Borrowed(&bytes), &CodecOptions::default()) .unwrap(); let decoded_regions: Vec = ArraySubset::new_with_ranges(&[0..2, 1..2, 0..1]) - .byte_ranges( - array_representation.shape(), - array_representation.element_size(), - ) + .byte_ranges(array_representation.shape(), data_type_size) .unwrap(); let input_handle = Box::new(std::io::Cursor::new(encoded)); let partial_decoder = codec @@ -147,7 +146,9 @@ mod tests { let array_representation = ArrayRepresentation::new(vec![2, 2, 2], DataType::UInt16, FillValue::from(0u16)) .unwrap(); - let bytes_representation = BytesRepresentation::FixedSize(array_representation.size()); + let data_type_size = array_representation.data_type().fixed_size().unwrap(); + let array_size = array_representation.num_elements_usize() * data_type_size; + let bytes_representation = BytesRepresentation::FixedSize(array_size as u64); let elements: Vec = (0..array_representation.num_elements() as u16).collect(); let bytes = crate::array::transmute_to_bytes_vec(elements); @@ -159,10 +160,7 @@ mod tests { .encode(Cow::Borrowed(&bytes), &CodecOptions::default()) .unwrap(); let decoded_regions: Vec = ArraySubset::new_with_ranges(&[0..2, 1..2, 0..1]) - .byte_ranges( - array_representation.shape(), - array_representation.element_size(), - ) + .byte_ranges(array_representation.shape(), data_type_size) .unwrap(); let input_handle = Box::new(std::io::Cursor::new(encoded)); let partial_decoder = codec diff --git a/src/array/codec/bytes_to_bytes/bz2/bz2_codec.rs b/src/array/codec/bytes_to_bytes/bz2/bz2_codec.rs index 6bba2f1b..e55a81e2 100644 --- a/src/array/codec/bytes_to_bytes/bz2/bz2_codec.rs +++ b/src/array/codec/bytes_to_bytes/bz2/bz2_codec.rs @@ -9,7 +9,7 @@ use crate::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, }; @@ -74,9 +74,9 @@ impl BytesToBytesCodecTraits for Bz2Codec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let mut encoder = bzip2::read::BzEncoder::new(Cursor::new(decoded_value), self.compression); let mut out: Vec = Vec::new(); encoder.read_to_end(&mut out)?; @@ -85,10 +85,10 @@ impl BytesToBytesCodecTraits for Bz2Codec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let mut decoder = bzip2::read::BzDecoder::new(Cursor::new(encoded_value)); let mut out: Vec = Vec::new(); decoder.read_to_end(&mut out)?; diff --git a/src/array/codec/bytes_to_bytes/bz2/bz2_partial_decoder.rs b/src/array/codec/bytes_to_bytes/bz2/bz2_partial_decoder.rs index c3d7bf89..d0582923 100644 --- a/src/array/codec/bytes_to_bytes/bz2/bz2_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/bz2/bz2_partial_decoder.rs @@ -3,7 +3,10 @@ use std::{borrow::Cow, io::Read}; use bytes::Buf; use crate::{ - array::codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + array::{ + codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + RawBytes, + }, byte_range::{extract_byte_ranges, ByteRange}, }; @@ -26,7 +29,7 @@ impl BytesPartialDecoderTraits for Bz2PartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options)?; let Some(encoded_value) = encoded_value else { return Ok(None); @@ -66,7 +69,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncBz2PartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options).await?; let Some(encoded_value) = encoded_value else { return Ok(None); diff --git a/src/array/codec/bytes_to_bytes/crc32c/crc32c_codec.rs b/src/array/codec/bytes_to_bytes/crc32c/crc32c_codec.rs index 0e93b295..0cf0cfbe 100644 --- a/src/array/codec/bytes_to_bytes/crc32c/crc32c_codec.rs +++ b/src/array/codec/bytes_to_bytes/crc32c/crc32c_codec.rs @@ -6,7 +6,7 @@ use crate::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, }; @@ -63,9 +63,9 @@ impl BytesToBytesCodecTraits for Crc32cCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let checksum = crc32c::crc32c(&decoded_value).to_le_bytes(); let mut encoded_value: Vec = Vec::with_capacity(decoded_value.len() + checksum.len()); encoded_value.extend_from_slice(&decoded_value); @@ -75,10 +75,10 @@ impl BytesToBytesCodecTraits for Crc32cCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { if encoded_value.len() >= CHECKSUM_SIZE { if options.validate_checksums() { let decoded_value = &encoded_value[..encoded_value.len() - CHECKSUM_SIZE]; diff --git a/src/array/codec/bytes_to_bytes/crc32c/crc32c_partial_decoder.rs b/src/array/codec/bytes_to_bytes/crc32c/crc32c_partial_decoder.rs index f8769c0b..4d034849 100644 --- a/src/array/codec/bytes_to_bytes/crc32c/crc32c_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/crc32c/crc32c_partial_decoder.rs @@ -1,7 +1,10 @@ use std::borrow::Cow; use crate::{ - array::codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + array::{ + codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + RawBytes, + }, byte_range::ByteRange, }; @@ -27,7 +30,7 @@ impl BytesPartialDecoderTraits for Crc32cPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let bytes = self.input_handle.partial_decode(decoded_regions, options)?; let Some(bytes) = bytes else { return Ok(None); @@ -80,7 +83,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncCrc32cPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let bytes = self .input_handle .partial_decode(decoded_regions, options) diff --git a/src/array/codec/bytes_to_bytes/gzip/gzip_codec.rs b/src/array/codec/bytes_to_bytes/gzip/gzip_codec.rs index a635315f..af024c25 100644 --- a/src/array/codec/bytes_to_bytes/gzip/gzip_codec.rs +++ b/src/array/codec/bytes_to_bytes/gzip/gzip_codec.rs @@ -11,7 +11,7 @@ use crate::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, }; @@ -78,9 +78,9 @@ impl BytesToBytesCodecTraits for GzipCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let mut encoder = GzEncoder::new( Cursor::new(decoded_value), flate2::Compression::new(self.compression_level.as_u32()), @@ -92,10 +92,10 @@ impl BytesToBytesCodecTraits for GzipCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let mut decoder = GzDecoder::new(Cursor::new(encoded_value)); let mut out: Vec = Vec::new(); decoder.read_to_end(&mut out)?; diff --git a/src/array/codec/bytes_to_bytes/gzip/gzip_partial_decoder.rs b/src/array/codec/bytes_to_bytes/gzip/gzip_partial_decoder.rs index dd86a86b..8ecff296 100644 --- a/src/array/codec/bytes_to_bytes/gzip/gzip_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/gzip/gzip_partial_decoder.rs @@ -6,7 +6,10 @@ use std::{ use flate2::bufread::GzDecoder; use crate::{ - array::codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + array::{ + codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + RawBytes, + }, byte_range::{extract_byte_ranges, ByteRange}, }; @@ -30,7 +33,7 @@ impl BytesPartialDecoderTraits for GzipPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options)?; let Some(encoded_value) = encoded_value else { return Ok(None); @@ -71,7 +74,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncGzipPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options).await?; let Some(encoded_value) = encoded_value else { return Ok(None); diff --git a/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_codec.rs b/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_codec.rs index c7723865..7730b8f6 100644 --- a/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_codec.rs +++ b/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_codec.rs @@ -1,12 +1,10 @@ -use std::borrow::Cow; - use crate::{ array::{ codec::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, }; @@ -56,18 +54,18 @@ impl BytesToBytesCodecTraits for TestUnboundedCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { Ok(decoded_value) } fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { Ok(encoded_value) } diff --git a/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_partial_decoder.rs b/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_partial_decoder.rs index e999809b..9838b28e 100644 --- a/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/test_unbounded/test_unbounded_partial_decoder.rs @@ -1,7 +1,10 @@ use std::borrow::Cow; use crate::{ - array::codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + array::{ + codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + RawBytes, + }, byte_range::{extract_byte_ranges, ByteRange}, }; @@ -25,7 +28,7 @@ impl BytesPartialDecoderTraits for TestUnboundedPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options)?; let Some(encoded_value) = encoded_value else { return Ok(None); @@ -62,7 +65,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncTestUnboundedPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options).await?; let Some(encoded_value) = encoded_value else { return Ok(None); diff --git a/src/array/codec/bytes_to_bytes/zstd/zstd_codec.rs b/src/array/codec/bytes_to_bytes/zstd/zstd_codec.rs index 29268056..187be17a 100644 --- a/src/array/codec/bytes_to_bytes/zstd/zstd_codec.rs +++ b/src/array/codec/bytes_to_bytes/zstd/zstd_codec.rs @@ -8,7 +8,7 @@ use crate::{ BytesPartialDecoderTraits, BytesToBytesCodecTraits, CodecError, CodecOptions, CodecTraits, RecommendedConcurrency, }, - ArrayMetadataOptions, BytesRepresentation, + ArrayMetadataOptions, BytesRepresentation, RawBytes, }, metadata::v3::MetadataV3, }; @@ -76,9 +76,9 @@ impl BytesToBytesCodecTraits for ZstdCodec { fn encode<'a>( &self, - decoded_value: Cow<'a, [u8]>, + decoded_value: RawBytes<'a>, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { let mut result = Vec::::new(); let mut encoder = zstd::Encoder::new(&mut result, self.compression)?; encoder.include_checksum(self.checksum)?; @@ -93,10 +93,10 @@ impl BytesToBytesCodecTraits for ZstdCodec { fn decode<'a>( &self, - encoded_value: Cow<'a, [u8]>, + encoded_value: RawBytes<'a>, _decoded_representation: &BytesRepresentation, _options: &CodecOptions, - ) -> Result, CodecError> { + ) -> Result, CodecError> { zstd::decode_all(std::io::Cursor::new(&encoded_value)) .map_err(CodecError::IOError) .map(Cow::Owned) diff --git a/src/array/codec/bytes_to_bytes/zstd/zstd_partial_decoder.rs b/src/array/codec/bytes_to_bytes/zstd/zstd_partial_decoder.rs index 432a6ab0..5a357b39 100644 --- a/src/array/codec/bytes_to_bytes/zstd/zstd_partial_decoder.rs +++ b/src/array/codec/bytes_to_bytes/zstd/zstd_partial_decoder.rs @@ -3,7 +3,10 @@ use std::borrow::Cow; use bytes::Buf; use crate::{ - array::codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + array::{ + codec::{BytesPartialDecoderTraits, CodecError, CodecOptions}, + RawBytes, + }, byte_range::{extract_byte_ranges, ByteRange}, }; @@ -27,7 +30,7 @@ impl BytesPartialDecoderTraits for ZstdPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options)?; let Some(encoded_value) = encoded_value else { return Ok(None); @@ -66,7 +69,7 @@ impl AsyncBytesPartialDecoderTraits for AsyncZstdPartialDecoder<'_> { &self, decoded_regions: &[ByteRange], options: &CodecOptions, - ) -> Result>>, CodecError> { + ) -> Result>>, CodecError> { let encoded_value = self.input_handle.decode(options).await?; let Some(encoded_value) = encoded_value else { return Ok(None); diff --git a/src/array/data_type.rs b/src/array/data_type.rs index 5b622f7f..1f745d22 100644 --- a/src/array/data_type.rs +++ b/src/array/data_type.rs @@ -22,6 +22,7 @@ use super::FillValue; /// A data type. #[derive(Clone, Debug)] #[non_exhaustive] +#[rustfmt::skip] pub enum DataType { /// `bool` Boolean. Bool, @@ -55,9 +56,13 @@ pub enum DataType { Complex128, /// `r*` raw bits, variable size given by *, limited to be a multiple of 8. RawBits(usize), // the stored usize is the size in bytes + /// A UTF-8 encoded string. + String, + /// Variable-sized binary data. + Binary, - // /// An extension data type. - // Extension(Box), + // /// An extension data type. + // Extension(Box), } /// An unsupported data type error. @@ -102,6 +107,17 @@ impl IncompatibleFillValueError { } } +/// The size of a data type. +#[derive(Copy, Clone, Debug, Eq, PartialEq)] +pub enum DataTypeSize { + /// Fixed size (in bytes). + Fixed(usize), + /// Variable sized. + /// + /// + Variable, +} + /// Extension data type traits. pub trait DataTypeExtension: dyn_clone::DynClone + core::fmt::Debug + Send + Sync { /// Returns the identifier. @@ -110,8 +126,8 @@ pub trait DataTypeExtension: dyn_clone::DynClone + core::fmt::Debug + Send + Syn /// Returns the name. fn name(&self) -> String; - /// Returns the size in bytes. - fn size(&self) -> usize; + /// Returns the data type size in bytes. + fn size(&self) -> DataTypeSize; /// Returns the data type metadata. fn metadata(&self) -> MetadataV3; @@ -154,6 +170,8 @@ impl DataType { Self::Complex64 => "complex64", Self::Complex128 => "complex128", Self::RawBits(_usize) => "r*", + Self::String => "string", + Self::Binary => "binary", // Self::Extension(extension) => extension.identifier(), } } @@ -178,20 +196,30 @@ impl DataType { // } } - /// Returns the size in bytes. + /// Returns the [`DataTypeSize`]. #[must_use] - pub const fn size(&self) -> usize { + pub const fn size(&self) -> DataTypeSize { match self { - Self::Bool | Self::Int8 | Self::UInt8 => 1, - Self::Int16 | Self::UInt16 | Self::Float16 | Self::BFloat16 => 2, - Self::Int32 | Self::UInt32 | Self::Float32 => 4, - Self::Int64 | Self::UInt64 | Self::Float64 | Self::Complex64 => 8, - Self::Complex128 => 16, - Self::RawBits(size) => *size, + Self::Bool | Self::Int8 | Self::UInt8 => DataTypeSize::Fixed(1), + Self::Int16 | Self::UInt16 | Self::Float16 | Self::BFloat16 => DataTypeSize::Fixed(2), + Self::Int32 | Self::UInt32 | Self::Float32 => DataTypeSize::Fixed(4), + Self::Int64 | Self::UInt64 | Self::Float64 | Self::Complex64 => DataTypeSize::Fixed(8), + Self::Complex128 => DataTypeSize::Fixed(16), + Self::RawBits(size) => DataTypeSize::Fixed(*size), + Self::String | Self::Binary => DataTypeSize::Variable, // Self::Extension(extension) => extension.size(), } } + /// Returns the size in bytes of a fixed-size data type, otherwise returns [`None`]. + #[must_use] + pub const fn fixed_size(&self) -> Option { + match self.size() { + DataTypeSize::Fixed(size) => Some(size), + DataTypeSize::Variable => None, + } + } + /// Create a data type from metadata. /// /// # Errors @@ -216,6 +244,8 @@ impl DataType { "bfloat16" => return Ok(Self::BFloat16), "complex64" => return Ok(Self::Complex64), "complex128" => return Ok(Self::Complex128), + "string" => return Ok(Self::String), + "binary" => return Ok(Self::Binary), _ => {} }; @@ -280,11 +310,26 @@ impl DataType { return Ok(FillValue::new(bytes.clone())); } } - Err(IncompatibleFillValueMetadataError( - self.name(), - fill_value.clone(), - )) - } // Self::Extension(extension) => extension.fill_value_from_metadata(fill_value), + Err(err()) + } + Self::Binary => { + if let FillValueMetadata::ByteArray(bytes) = fill_value { + Ok(FillValue::new(bytes.clone())) + } else { + Err(err()) + } + } + // Self::Extension(extension) => extension.fill_value_from_metadata(fill_value), + Self::String => match fill_value { + FillValueMetadata::String(string) => Ok(FillValue::new(string.as_bytes().to_vec())), + FillValueMetadata::Float(float) => match float { + FillValueFloat::HexString(hex_string) => Ok(String::from(hex_string).into()), + FillValueFloat::NonFinite(non_finite) => Ok(String::from(non_finite).into()), + FillValueFloat::Float(_) => Err(err()), + }, + FillValueMetadata::ByteArray(bytes) => Ok(FillValue::new(bytes.clone())), + _ => Err(err()), + }, } } @@ -346,7 +391,12 @@ impl DataType { Self::RawBits(size) => { debug_assert_eq!(fill_value.as_ne_bytes().len(), *size); FillValueMetadata::ByteArray(fill_value.as_ne_bytes().to_vec()) - } // DataType::Extension(extension) => extension.metadata_fill_value(fill_value), + } + // DataType::Extension(extension) => extension.metadata_fill_value(fill_value), + Self::String => FillValueMetadata::String( + String::from_utf8(fill_value.as_ne_bytes().to_vec()).unwrap(), + ), + Self::Binary => FillValueMetadata::ByteArray(fill_value.as_ne_bytes().to_vec()), } } } @@ -869,7 +919,7 @@ mod tests { assert_eq!(json, serde_json::to_string(&data_type.metadata()).unwrap()); assert_eq!(data_type.identifier(), "r*"); assert_eq!(data_type.name().as_str(), "r8"); - assert_eq!(data_type.size(), 1); + assert_eq!(data_type.size(), DataTypeSize::Fixed(1)); let metadata = serde_json::from_str::("[7]").unwrap(); let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); @@ -885,7 +935,7 @@ mod tests { assert_eq!(json, serde_json::to_string(&data_type.metadata()).unwrap()); assert_eq!(data_type.identifier(), "r*"); assert_eq!(data_type.name().as_str(), "r16"); - assert_eq!(data_type.size(), 2); + assert_eq!(data_type.size(), DataTypeSize::Fixed(2)); let metadata = serde_json::from_str::("[0, 255]").unwrap(); let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); @@ -949,7 +999,7 @@ mod tests { let json = r#""r16""#; let metadata = serde_json::from_str::(json).unwrap(); let data_type: DataType = DataType::from_metadata(&metadata).unwrap(); - assert_eq!(data_type.size(), 2); + assert_eq!(data_type.size(), DataTypeSize::Fixed(2)); } #[test] @@ -960,7 +1010,7 @@ mod tests { }"#; let metadata = serde_json::from_str::(json).unwrap(); let data_type: DataType = DataType::from_metadata(&metadata).unwrap(); - assert_eq!(data_type.size(), 2); + assert_eq!(data_type.size(), DataTypeSize::Fixed(2)); } #[test] @@ -1140,4 +1190,38 @@ mod tests { .fill_value_from_metadata(&metadata) .is_err()); } + + #[test] + fn data_type_string() { + let json = r#""string""#; + let metadata: MetadataV3 = serde_json::from_str(json).unwrap(); + let data_type = DataType::from_metadata(&metadata).unwrap(); + assert_eq!(json, serde_json::to_string(&data_type.metadata()).unwrap()); + assert_eq!(data_type.identifier(), "string"); + assert_eq!(data_type.name().as_str(), "string"); + assert_eq!(data_type.size(), DataTypeSize::Variable); + + let metadata = serde_json::from_str::(r#""hello world""#).unwrap(); + let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); + assert_eq!(fill_value.as_ne_bytes(), "hello world".as_bytes(),); + assert_eq!(metadata, data_type.metadata_fill_value(&fill_value)); + + let metadata = serde_json::from_str::( + r#"[104, 101, 108, 108, 111, 32, 119, 111, 114, 108, 100]"#, + ) + .unwrap(); + let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); + assert_eq!(fill_value.as_ne_bytes(), "hello world".as_bytes(),); + assert_ne!(metadata, data_type.metadata_fill_value(&fill_value)); // metadata is byte array rep, that is okay + + let metadata = serde_json::from_str::(r#""Infinity""#).unwrap(); + let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); + assert_eq!(fill_value.as_ne_bytes(), "Infinity".as_bytes(),); + assert_ne!(metadata, data_type.metadata_fill_value(&fill_value)); // metadata is float rep, that is okay + + let metadata = serde_json::from_str::(r#""0x7fc00000""#).unwrap(); + let fill_value = data_type.fill_value_from_metadata(&metadata).unwrap(); + assert_eq!(fill_value.as_ne_bytes(), "0x7fc00000".as_bytes(),); + assert_ne!(metadata, data_type.metadata_fill_value(&fill_value)); // metadata is float rep, that is okay + } } diff --git a/src/array/element.rs b/src/array/element.rs new file mode 100644 index 00000000..b4bec745 --- /dev/null +++ b/src/array/element.rs @@ -0,0 +1,267 @@ +use std::mem::ManuallyDrop; + +use itertools::Itertools; +use ArrayError::IncompatibleElementType as IET; + +use super::{convert_from_bytes_slice, transmute_to_bytes, ArrayBytes, ArrayError, DataType}; + +/// A trait representing an array element type. +pub trait Element: Sized + Clone { + /// Validate the data type. + /// + /// # Errors + /// Returns an [`ArrayError`] if the data type is incompatible with [`Element`]. + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError>; + + /// Convert a slice of elements into [`ArrayBytes`]. + /// + /// # Errors + /// Returns an [`ArrayError`] if the data type is incompatible with [`Element`]. + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError>; +} + +/// A trait representing an owned array element type. +pub trait ElementOwned: Element { + /// Convert bytes into a [`Vec`]. + /// + /// # Errors + /// Returns an [`ArrayError`] if the data type is incompatible with [`Element`]. + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError>; +} + +/// A marker trait for a fixed length element. +pub trait ElementFixedLength {} + +impl ElementFixedLength for bool {} +impl ElementFixedLength for u8 {} +impl ElementFixedLength for u16 {} +impl ElementFixedLength for u32 {} +impl ElementFixedLength for u64 {} +impl ElementFixedLength for i8 {} +impl ElementFixedLength for i16 {} +impl ElementFixedLength for i32 {} +impl ElementFixedLength for i64 {} +impl ElementFixedLength for half::f16 {} +impl ElementFixedLength for half::bf16 {} +impl ElementFixedLength for f32 {} +impl ElementFixedLength for f64 {} +impl ElementFixedLength for num::complex::Complex32 {} +impl ElementFixedLength for num::complex::Complex64 {} +impl ElementFixedLength for [u8; N] {} + +impl Element for bool { + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError> { + (data_type == &DataType::Bool).then_some(()).ok_or(IET) + } + + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + Ok(transmute_to_bytes(elements).into()) + } +} + +impl ElementOwned for bool { + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + let bytes = bytes.into_fixed()?; + let elements_u8 = convert_from_bytes_slice::(&bytes); + if elements_u8.iter().all(|&u| u <= 1) { + let length: usize = elements_u8.len(); + let capacity: usize = elements_u8.capacity(); + let mut manual_drop_vec = ManuallyDrop::new(elements_u8); + let vec_ptr: *mut u8 = manual_drop_vec.as_mut_ptr(); + let ptr: *mut Self = vec_ptr.cast::(); + Ok(unsafe { Vec::from_raw_parts(ptr, length, capacity) }) + } else { + Err(ArrayError::InvalidElementValue) + } + } +} + +macro_rules! impl_element_pod { + ($raw_type:ty, $data_type:expr) => { + impl Element for $raw_type { + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError> { + (data_type == &$data_type).then_some(()).ok_or(IET) + } + + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + Ok(transmute_to_bytes(elements).into()) + } + } + + impl ElementOwned for $raw_type { + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + let bytes = bytes.into_fixed()?; + Ok(convert_from_bytes_slice::(&bytes)) + } + } + }; +} + +impl_element_pod!(i8, DataType::Int8); +impl_element_pod!(i16, DataType::Int16); +impl_element_pod!(i32, DataType::Int32); +impl_element_pod!(i64, DataType::Int64); +impl_element_pod!(u8, DataType::UInt8); +impl_element_pod!(u16, DataType::UInt16); +impl_element_pod!(u32, DataType::UInt32); +impl_element_pod!(u64, DataType::UInt64); +impl_element_pod!(half::f16, DataType::Float16); +impl_element_pod!(f32, DataType::Float32); +impl_element_pod!(f64, DataType::Float64); +impl_element_pod!(half::bf16, DataType::BFloat16); +impl_element_pod!(num::complex::Complex32, DataType::Complex64); +impl_element_pod!(num::complex::Complex64, DataType::Complex128); + +impl Element for [u8; N] { + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError> { + if let DataType::RawBits(n) = data_type { + (*n == N).then_some(()).ok_or(IET) + } else { + Err(IET) + } + } + + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + Ok(transmute_to_bytes(elements).into()) + } +} + +impl ElementOwned for [u8; N] { + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + let bytes = bytes.into_fixed()?; + Ok(convert_from_bytes_slice::(&bytes)) + } +} + +macro_rules! impl_element_string { + ($raw_type:ty) => { + impl Element for $raw_type { + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError> { + (data_type == &DataType::String).then_some(()).ok_or(IET) + } + + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + + // Calculate offsets + let mut len: usize = 0; + let mut offsets = Vec::with_capacity(elements.len()); + for element in elements { + offsets.push(len); + len = len.checked_add(element.len()).unwrap(); + } + offsets.push(len); + + // Concatenate bytes + let mut bytes = Vec::with_capacity(usize::try_from(len).unwrap()); + for element in elements { + bytes.extend_from_slice(element.as_bytes()); + } + Ok(ArrayBytes::new_vlen(bytes, offsets)) + } + } + }; +} + +impl_element_string!(&str); +impl_element_string!(String); + +impl ElementOwned for String { + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + let (bytes, offsets) = bytes.into_variable()?; + let mut elements = Vec::with_capacity(offsets.len()); + for (curr, next) in offsets.iter().tuple_windows() { + elements.push( + String::from_utf8(bytes[*curr..*next].to_vec()) + .map_err(|_| ArrayError::InvalidElementValue)?, + ); + } + Ok(elements) + } +} + +macro_rules! impl_element_binary { + ($raw_type:ty) => { + impl Element for $raw_type { + fn validate_data_type(data_type: &DataType) -> Result<(), ArrayError> { + (data_type == &DataType::Binary).then_some(()).ok_or(IET) + } + + fn into_array_bytes<'a>( + data_type: &DataType, + elements: &'a [Self], + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + + // Calculate offsets + let mut len: usize = 0; + let mut offsets = Vec::with_capacity(elements.len()); + for element in elements { + offsets.push(len); + len = len.checked_add(element.len()).unwrap(); + } + offsets.push(len); + + // Concatenate bytes + let bytes = elements.concat(); + + Ok(ArrayBytes::new_vlen(bytes, offsets)) + } + } + }; +} + +impl_element_binary!(&[u8]); +impl_element_binary!(Vec); + +impl ElementOwned for Vec { + fn from_array_bytes( + data_type: &DataType, + bytes: ArrayBytes<'_>, + ) -> Result, ArrayError> { + Self::validate_data_type(data_type)?; + let (bytes, offsets) = bytes.into_variable()?; + let mut elements = Vec::with_capacity(offsets.len()); + for (curr, next) in offsets.iter().tuple_windows() { + elements.push(bytes[*curr..*next].to_vec()); + } + Ok(elements) + } +} diff --git a/src/array/fill_value.rs b/src/array/fill_value.rs index 6d60ec3e..70211940 100644 --- a/src/array/fill_value.rs +++ b/src/array/fill_value.rs @@ -20,6 +20,18 @@ impl From<&[u8]> for FillValue { } } +impl From<[u8; N]> for FillValue { + fn from(value: [u8; N]) -> Self { + Self(value.to_vec()) + } +} + +impl From<&[u8; N]> for FillValue { + fn from(value: &[u8; N]) -> Self { + Self(value.to_vec()) + } +} + impl From> for FillValue { fn from(value: Vec) -> Self { Self(value) @@ -122,6 +134,18 @@ impl From for FillValue { } } +impl From for FillValue { + fn from(value: String) -> Self { + Self(value.into_bytes()) + } +} + +impl From<&str> for FillValue { + fn from(value: &str) -> Self { + Self(value.as_bytes().to_vec()) + } +} + impl FillValue { /// Create a new fill value composed of `bytes`. #[must_use] @@ -146,6 +170,7 @@ impl FillValue { #[must_use] pub fn equals_all(&self, bytes: &[u8]) -> bool { match self.0.len() { + 0 => bytes.is_empty(), 1 => { let fill_value = self.0[0]; let fill_value_128 = u128::from_ne_bytes([self.0[0]; 16]); diff --git a/src/array_subset.rs b/src/array_subset.rs index e743c13b..3abc3352 100644 --- a/src/array_subset.rs +++ b/src/array_subset.rs @@ -6,8 +6,7 @@ //! [`iterators`] includes various types of [`ArraySubset`] iterators. //! //! This module also provides convenience functions for: -//! - computing the byte ranges of array subsets within an array, and -//! - extracting the bytes within subsets of an array. +//! - computing the byte ranges of array subsets within an array with a fixed element size. pub mod iterators; @@ -24,7 +23,6 @@ use thiserror::Error; use crate::{ array::{ArrayIndices, ArrayShape}, byte_range::ByteRange, - vec_spare_capacity_to_mut_slice, }; /// An array subset. @@ -39,25 +37,6 @@ pub struct ArraySubset { shape: ArrayShape, } -/// An array extract bytes error. -#[derive(Debug, Error)] -#[error("array subset {_0} is incompatible with array of shape {_1:?} and element size {_2}")] -pub struct ArrayExtractBytesError(ArraySubset, ArrayShape, usize); - -/// An array store bytes error. -#[derive(Debug, Error)] -pub enum ArrayStoreBytesError { - /// Incompatible array subset and array shape. - #[error(transparent)] - InvalidArrayShape(#[from] IncompatibleArraySubsetAndShapeError), - /// Invalid subset bytes. - #[error("expected subset bytes to have length {_1}, got {_0}")] - InvalidSubsetBytes(usize, usize), - /// Invalid array bytes. - #[error("expected array bytes to have length {_1}, got {_0}")] - InvalidArrayBytes(usize, usize), -} - impl ArraySubset { /// Create a new empty array subset. #[must_use] @@ -287,6 +266,12 @@ impl ArraySubset { usize::try_from(self.num_elements()).unwrap() } + /// Returns [`true`] if the array subset contains `indices`. + #[must_use] + pub fn contains(&self, indices: &[u64]) -> bool { + izip!(indices, &self.start, &self.shape).all(|(&i, &o, &s)| i >= o && i < o + s) + } + /// Return the byte ranges of an array subset in an array with `array_shape` and `element_size`. /// /// # Errors @@ -327,81 +312,11 @@ impl ArraySubset { byte_ranges } - /// Return the bytes in this array subset from an array with shape `array_shape` and `element_size`. - /// - /// # Errors - /// - /// Returns [`ArrayExtractBytesError`] if the length of `array_shape` does not match the array subset dimensionality or the array subset is outside of the bounds of `array_shape`. - /// - /// # Panics - /// - /// Panics if attempting to access a byte index beyond [`usize::MAX`]. - pub fn extract_bytes( - &self, - bytes: &[u8], - array_shape: &[u64], - element_size: usize, - ) -> Result, ArrayExtractBytesError> { - let element_size_u64 = element_size as u64; - if bytes.len() as u64 == array_shape.iter().product::() * element_size_u64 - && array_shape.len() == self.dimensionality() - && self - .end_exc() - .iter() - .zip(array_shape) - .all(|(end, shape)| end <= shape) - { - Ok(unsafe { self.extract_bytes_unchecked(bytes, array_shape, element_size) }) - } else { - Err(ArrayExtractBytesError( - self.clone(), - array_shape.to_vec(), - element_size, - )) - } - } - - /// Return the bytes in this array subset from an array with shape `array_shape` and `element_size`. - /// - /// # Safety - /// The length of `array_shape` must match the array subset dimensionality and the array subset must be within the bounds of `array_shape`. - /// - /// # Panics - /// Panics if attempting to reference a byte beyond `usize::MAX`. - #[must_use] - pub unsafe fn extract_bytes_unchecked( - &self, - bytes: &[u8], - array_shape: &[u64], - element_size: usize, - ) -> Vec { - debug_assert_eq!( - bytes.len() as u64, - array_shape.iter().product::() * element_size as u64 - ); - let num_bytes = self.num_elements_usize() * element_size; - let mut bytes_subset: Vec = Vec::with_capacity(num_bytes); - let bytes_subset_slice = vec_spare_capacity_to_mut_slice(&mut bytes_subset); - let mut subset_offset = 0; - let contiguous_indices = self.contiguous_linearised_indices_unchecked(array_shape); - let byte_length = contiguous_indices.contiguous_elements_usize() * element_size; - for (array_index, _contiguous_elements) in &contiguous_indices { - let byte_offset = usize::try_from(array_index).unwrap() * element_size; - debug_assert!(byte_offset + byte_length <= bytes.len()); - debug_assert!(subset_offset + byte_length <= num_bytes); - bytes_subset_slice[subset_offset..subset_offset + byte_length] - .copy_from_slice(&bytes[byte_offset..byte_offset + byte_length]); - subset_offset += byte_length; - } - unsafe { bytes_subset.set_len(num_bytes) }; - bytes_subset - } - /// Return the elements in this array subset from an array with shape `array_shape`. /// /// # Errors /// - /// Returns [`ArrayExtractBytesError`] if the length of `array_shape` does not match the array subset dimensionality or the array subset is outside of the bounds of `array_shape`. + /// Returns [`IncompatibleArraySubsetAndShapeError`] if the length of `array_shape` does not match the array subset dimensionality or the array subset is outside of the bounds of `array_shape`. /// /// # Panics /// Panics if attempting to access a byte index beyond [`usize::MAX`]. @@ -460,90 +375,6 @@ impl ArraySubset { bytes_subset } - /// Store `bytes_subset` corresponding to the bytes of an array (`array_bytes`) with shape `array_shape` and `element_size`. - /// - /// # Errors - /// - /// Returns [`ArrayStoreBytesError`] if: - /// - the length of `array_shape` does not match the array subset dimensionality or the array subset is outside of the bounds of `array_shape`. - /// - the length of `bytes_array` is not compatible with the `array_shape` and `element size`, or - /// - the length of `bytes_subset` is not compatible with the shape of this subset and `element_size`. - /// - /// # Panics - /// - /// Panics if attempting to reference a byte beyond `usize::MAX`. - pub fn store_bytes( - &self, - bytes_subset: &[u8], - bytes_array: &mut [u8], - array_shape: &[u64], - element_size: usize, - ) -> Result<(), ArrayStoreBytesError> { - let element_size_u64 = element_size as u64; - let expected_subset_size = self.num_elements() * element_size_u64; - let expected_array_size = array_shape.iter().product::() * element_size_u64; - if bytes_subset.len() as u64 != expected_subset_size { - Err(ArrayStoreBytesError::InvalidSubsetBytes( - bytes_subset.len(), - usize::try_from(expected_subset_size).unwrap(), - )) - } else if bytes_array.len() as u64 != expected_array_size { - Err(ArrayStoreBytesError::InvalidSubsetBytes( - bytes_array.len(), - usize::try_from(expected_array_size).unwrap(), - )) - } else { - let mut offset = 0; - let contiguous_indices = self.contiguous_linearised_indices(array_shape)?; - let byte_length = contiguous_indices.contiguous_elements_usize() * element_size; - for (array_index, _contiguous_elements) in &contiguous_indices { - let byte_index = usize::try_from(array_index).unwrap() * element_size; - debug_assert!(byte_index + byte_length <= bytes_array.len()); - debug_assert!(offset + byte_length <= bytes_subset.len()); - bytes_array[byte_index..byte_index + byte_length] - .copy_from_slice(&bytes_subset[offset..offset + byte_length]); - offset += byte_length; - } - Ok(()) - } - } - - /// Store `bytes_subset` corresponding to the bytes of an array (`array_bytes`) with shape `array_shape` and `element_size`. - /// - /// # Safety - /// - /// The length of `array_shape` must match the array subset dimensionality and the array subset must be within the bounds of `array_shape`. - /// The length of `bytes_array` must match the product of the `array_shape` components and `element_size`. - /// The length of `bytes_subset` must match the product of the array subset shape components and `element_size`. - /// - /// # Panics - /// - /// Panics if attempting to reference a byte beyond `usize::MAX`. - pub unsafe fn store_bytes_unchecked( - &self, - bytes_subset: &[u8], - bytes_array: &mut [u8], - array_shape: &[u64], - element_size: usize, - ) { - debug_assert_eq!(bytes_subset.len(), self.num_elements_usize() * element_size); - debug_assert_eq!( - bytes_array.len() as u64, - array_shape.iter().product::() * element_size as u64 - ); - let mut offset = 0; - let contiguous_indices = self.contiguous_linearised_indices_unchecked(array_shape); - let byte_length = contiguous_indices.contiguous_elements_usize() * element_size; - for (array_index, _contiguous_elements) in &contiguous_indices { - let byte_index = usize::try_from(array_index).unwrap() * element_size; - debug_assert!(byte_index + byte_length <= bytes_array.len()); - debug_assert!(offset + byte_length <= bytes_subset.len()); - bytes_array[byte_index..byte_index + byte_length] - .copy_from_slice(&bytes_subset[offset..offset + byte_length]); - offset += byte_length; - } - } - /// Returns an iterator over the indices of elements within the subset. #[must_use] pub fn indices(&self) -> Indices { @@ -812,28 +643,6 @@ mod tests { #[test] fn array_subset_bytes() { let array_subset = ArraySubset::new_with_ranges(&[1..3, 1..3]); - let mut bytes_array = vec![0; 4 * 4]; - array_subset - .store_bytes(&[1, 2, 3, 4], &mut bytes_array, &[4, 4], 1) - .unwrap(); - - assert!(array_subset - .store_bytes(&[1, 2, 3], &mut bytes_array, &[4, 4], 1) - .is_err()); - - assert!(array_subset - .store_bytes(&[1, 2, 3, 4], &mut bytes_array, &[2, 2], 1) - .is_err()); - - assert_eq!( - bytes_array, - vec![0, 0, 0, 0, 0, 1, 2, 0, 0, 3, 4, 0, 0, 0, 0, 0] - ); - unsafe { array_subset.store_bytes_unchecked(&[5, 6, 7, 8], &mut bytes_array, &[4, 4], 1) }; - assert_eq!( - bytes_array, - vec![0, 0, 0, 0, 0, 5, 6, 0, 0, 7, 8, 0, 0, 0, 0, 0] - ); assert!(array_subset.byte_ranges(&[1, 1], 1).is_err()); @@ -852,36 +661,5 @@ mod tests { ByteRange::FromStart(9, Some(2)) ] ); - - assert!(array_subset - .extract_bytes(&bytes_array, &[1, 1], 1) - .is_err()); - - assert_eq!( - array_subset - .extract_bytes(&bytes_array, &[4, 4], 1) - .unwrap(), - vec![5, 6, 7, 8] - ); - - assert_eq!( - unsafe { array_subset.extract_bytes_unchecked(&bytes_array, &[4, 4], 1) }, - vec![5, 6, 7, 8] - ); - - assert!(array_subset - .extract_elements(&bytes_array, &[1, 1]) - .is_err()); - - assert_eq!( - array_subset - .extract_elements(&bytes_array, &[4, 4]) - .unwrap(), - vec![5, 6, 7, 8] - ); - assert_eq!( - unsafe { array_subset.extract_elements_unchecked(&bytes_array, &[4, 4]) }, - vec![5, 6, 7, 8] - ); } } diff --git a/src/metadata/array.rs b/src/metadata/array.rs index f968e785..1573bb61 100644 --- a/src/metadata/array.rs +++ b/src/metadata/array.rs @@ -2,15 +2,18 @@ //! //! See . -use super::v2::{ - array::{ - array_metadata_fill_value_v2_to_v3, data_type_metadata_v2_to_endianness, - data_type_metadata_v2_to_v3_data_type, ArrayMetadataV2, ArrayMetadataV2DataType, - ArrayMetadataV2Order, DataTypeMetadataV2InvalidEndiannessError, FillValueMetadataV2, +pub use super::v3::ArrayMetadataV3; +use super::{ + v2::{ + array::{ + array_metadata_fill_value_v2_to_v3, data_type_metadata_v2_to_endianness, + data_type_metadata_v2_to_v3_data_type, ArrayMetadataV2, ArrayMetadataV2DataType, + ArrayMetadataV2Order, DataTypeMetadataV2InvalidEndiannessError, FillValueMetadataV2, + }, + codec::blosc::{codec_blosc_v2_numcodecs_to_v3, BloscCodecConfigurationNumcodecs}, }, - codec::blosc::{codec_blosc_v2_numcodecs_to_v3, BloscCodecConfigurationNumcodecs}, + v3::codec::vlen_interleaved::VlenInterleavedCodecConfigurationV1, }; -pub use super::v3::ArrayMetadataV3; use thiserror::Error; use derive_more::{Display, From}; @@ -138,22 +141,37 @@ pub fn array_metadata_v2_to_v3( codecs.push(transpose_metadata); } - // Filters (array to array codecs) + // Filters (array to array or array to bytes codecs) + let mut is_vlen = false; if let Some(filters) = &array_metadata_v2.filters { for filter in filters { - codecs.push(MetadataV3::new_with_configuration( - filter.id(), - filter.configuration().clone(), - )); + match filter.id() { + "vlen-utf8" | "vlen-bytes" | "vlen-array" => { + is_vlen = true; + let vlen_interleaved_metadata = + MetadataV3::new_with_serializable_configuration( + super::v3::codec::vlen_interleaved::IDENTIFIER, + &VlenInterleavedCodecConfigurationV1 {}, + )?; + codecs.push(vlen_interleaved_metadata); + } + _ => { + codecs.push(MetadataV3::new_with_configuration( + filter.id(), + filter.configuration().clone(), + )); + } + } } } - // Array-to-bytes codec - let bytes_metadata = MetadataV3::new_with_serializable_configuration( - super::v3::codec::bytes::IDENTIFIER, - &BytesCodecConfigurationV1 { endian: endianness }, - )?; - codecs.push(bytes_metadata); + if !is_vlen { + let bytes_metadata = MetadataV3::new_with_serializable_configuration( + super::v3::codec::bytes::IDENTIFIER, + &BytesCodecConfigurationV1 { endian: endianness }, + )?; + codecs.push(bytes_metadata); + } // Compressor (bytes to bytes codec) if let Some(compressor) = &array_metadata_v2.compressor { diff --git a/src/metadata/v2/array.rs b/src/metadata/v2/array.rs index 1e6426d2..c1872b51 100644 --- a/src/metadata/v2/array.rs +++ b/src/metadata/v2/array.rs @@ -159,7 +159,12 @@ pub fn data_type_metadata_v2_to_v3_data_type( "f8" => Ok(DataType::Float64), "c8" => Ok(DataType::Complex64), "c16" => Ok(DataType::Complex128), - // TODO "|V" + "|O" => Ok(DataType::String), // LEGACY: This is not part of the spec. The dtype for a PyObject, which is what zarr-python 2 uses for string arrays. + // TODO "|mX" timedelta + // TODO "|MX" datetime + // TODO "|SX" string (fixed length sequence of char) + // TODO "|UX" string (fixed length sequence of Py_UNICODE) + // TODO "|VX" other (void * – each item is a fixed-size chunk of memory) _ => Err(DataTypeMetadataV2UnsupportedDataTypeError( data_type.clone(), )), diff --git a/src/metadata/v2/codec/blosc.rs b/src/metadata/v2/codec/blosc.rs index 2d9b6b85..4fd14f8c 100644 --- a/src/metadata/v2/codec/blosc.rs +++ b/src/metadata/v2/codec/blosc.rs @@ -46,22 +46,42 @@ pub fn codec_blosc_v2_numcodecs_to_v3( blosc: &BloscCodecConfigurationNumcodecs, data_type: &DataType, ) -> BloscCodecConfiguration { + let (shuffle, typesize) = match (&blosc.shuffle, data_type.fixed_size()) { + (BloscShuffleModeNumCodecs::NoShuffle, _) => (BloscShuffleMode::NoShuffle, None), + // Fixed + (BloscShuffleModeNumCodecs::Shuffle, Some(data_type_size)) => { + (BloscShuffleMode::Shuffle, Some(data_type_size)) + } + (BloscShuffleModeNumCodecs::BitShuffle, Some(data_type_size)) => { + (BloscShuffleMode::BitShuffle, Some(data_type_size)) + } + (BloscShuffleModeNumCodecs::AutoShuffle, Some(data_type_size)) => { + if data_type_size == 1 { + (BloscShuffleMode::BitShuffle, Some(data_type_size)) + } else { + (BloscShuffleMode::Shuffle, Some(data_type_size)) + } + } + // Variable + ( + BloscShuffleModeNumCodecs::Shuffle + | BloscShuffleModeNumCodecs::BitShuffle + | BloscShuffleModeNumCodecs::AutoShuffle, + None, + ) => { + // FIXME: Check blosc auto behaviour with variable sized data type + // Currently defaulting to "bitshuffle" + // What do other implementations do for a variable sized data type? + // May need to make this function fallible + (BloscShuffleMode::NoShuffle, None) + } + }; + BloscCodecConfiguration::V1(BloscCodecConfigurationV1 { cname: blosc.cname, clevel: blosc.clevel, - shuffle: match blosc.shuffle { - BloscShuffleModeNumCodecs::NoShuffle => BloscShuffleMode::NoShuffle, - BloscShuffleModeNumCodecs::Shuffle => BloscShuffleMode::Shuffle, - BloscShuffleModeNumCodecs::BitShuffle => BloscShuffleMode::BitShuffle, - BloscShuffleModeNumCodecs::AutoShuffle => { - if data_type.size() == 1 { - BloscShuffleMode::BitShuffle - } else { - BloscShuffleMode::Shuffle - } - } - }, - typesize: Some(data_type.size()), + shuffle, + typesize, blocksize: blosc.blocksize, }) } diff --git a/src/metadata/v3.rs b/src/metadata/v3.rs index 396957b7..27b908d5 100644 --- a/src/metadata/v3.rs +++ b/src/metadata/v3.rs @@ -27,6 +27,10 @@ pub mod codec { pub mod sharding; /// `transpose` codec metadata. pub mod transpose; + /// `vlen` codec metadata. + pub mod vlen; + /// `vlen_interleaved` codec metadata. + pub mod vlen_interleaved; #[cfg(feature = "zfp")] /// `zfp` codec metadata. pub mod zfp; diff --git a/src/metadata/v3/codec/vlen.rs b/src/metadata/v3/codec/vlen.rs new file mode 100644 index 00000000..4244f1db --- /dev/null +++ b/src/metadata/v3/codec/vlen.rs @@ -0,0 +1,84 @@ +use derive_more::{Display, From}; +use serde::{Deserialize, Serialize}; + +use crate::metadata::MetadataV3; + +/// The identifier for the `vlen` codec. +pub const IDENTIFIER: &str = "https://codec.zarrs.dev/array_to_bytes/vlen"; + +/// A wrapper to handle various versions of `vlen` codec configuration parameters. +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, From)] +#[serde(untagged)] +pub enum VlenCodecConfiguration { + /// Version 1.0. + V1(VlenCodecConfigurationV1), +} + +/// Configuration parameters for the `vlen` codec (version 1.0). +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display)] +#[serde(deny_unknown_fields)] +#[display(fmt = "{}", "serde_json::to_string(self).unwrap_or_default()")] +pub struct VlenCodecConfigurationV1 { + /// Encoding for the variable length data indices (offsets). + pub index_codecs: Vec, + /// Encoding for the variable length data. + pub data_codecs: Vec, + /// The indices data type. + pub index_data_type: VlenIndexDataType, +} + +/// Data types for variable length chunk data indices. +#[derive(Serialize, Deserialize, Clone, Copy, Eq, PartialEq, Debug, Display)] +#[serde(rename_all = "lowercase")] +pub enum VlenIndexDataType { + // /// `uint8` Integer in `[0, 2^8-1]`. + // UInt8, + // /// `uint16` Integer in `[0, 2^16-1]`. + // UInt16, + /// `uint32` Integer in `[0, 2^32-1]`. + UInt32, + /// `uint64` Integer in `[0, 2^64-1]`. + UInt64, +} + +impl VlenCodecConfigurationV1 { + /// Create a new `vlen` codec configuration. + #[must_use] + pub fn new( + index_codecs: Vec, + data_codecs: Vec, + index_data_type: VlenIndexDataType, + ) -> Self { + Self { + index_codecs, + data_codecs, + index_data_type, + } + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn codec_vlen_simple() { + serde_json::from_str::( + r#"{ + "data_codecs": [{"name": "bytes"}], + "index_codecs": [{"name": "bytes","configuration": { "endian": "little" }}], + "index_data_type": "uint32" + }"#, + ) + .unwrap(); + } + + #[test] + fn codec_vlen_compressed() { + serde_json::from_str::(r#"{ + "data_codecs": [{"name": "bytes"},{"name": "blosc","configuration": {"cname": "zstd", "clevel":5,"shuffle": "bitshuffle", "typesize":1,"blocksize":0}}], + "index_codecs": [{"name": "bytes","configuration": { "endian": "little" }},{"name": "blosc","configuration":{"cname": "zstd", "clevel":5,"shuffle": "shuffle", "typesize":4,"blocksize":0}}], + "index_data_type": "uint32" + }"#).unwrap(); + } +} diff --git a/src/metadata/v3/codec/vlen_interleaved.rs b/src/metadata/v3/codec/vlen_interleaved.rs new file mode 100644 index 00000000..fa19a401 --- /dev/null +++ b/src/metadata/v3/codec/vlen_interleaved.rs @@ -0,0 +1,37 @@ +use derive_more::{Display, From}; +use serde::{Deserialize, Serialize}; + +/// The identifier for the `vlen_interleaved` codec. +pub const IDENTIFIER: &str = "https://codec.zarrs.dev/array_to_bytes/vlen_interleaved"; + +/// A wrapper to handle various versions of `vlen_interleaved` codec configuration parameters. +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, From)] +#[serde(untagged)] +pub enum VlenInterleavedCodecConfiguration { + /// Version 1.0. + V1(VlenInterleavedCodecConfigurationV1), +} + +/// Configuration parameters for the `vlen_interleaved` codec (version 1.0). +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, Default)] +#[serde(deny_unknown_fields)] +#[display(fmt = "{}", "serde_json::to_string(self).unwrap_or_default()")] +pub struct VlenInterleavedCodecConfigurationV1 {} + +impl VlenInterleavedCodecConfigurationV1 { + /// Create a new `vlen_interleaved` codec configuration. + #[must_use] + pub const fn new() -> Self { + Self {} + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn codec_vlen_interleaved() { + serde_json::from_str::(r#"{}"#).unwrap(); + } +} diff --git a/src/metadata/v3/fill_value.rs b/src/metadata/v3/fill_value.rs index 44dee963..7d5b7957 100644 --- a/src/metadata/v3/fill_value.rs +++ b/src/metadata/v3/fill_value.rs @@ -26,12 +26,16 @@ pub enum FillValueMetadata { Int(i64), /// A float. Float(FillValueFloat), - /// A raw data type. + /// An array of integers. Suitable for raw (`r`) and `binary` data types. #[display(fmt = "{_0:?}")] ByteArray(Vec), /// A complex number. #[display(fmt = "{{re:{_0}, im:{_1}}}")] Complex(FillValueFloat, FillValueFloat), + /// A string. + String(String), + /// An unsupported fill value. + Unsupported(serde_json::Value), } impl TryFrom<&str> for FillValueMetadata { @@ -103,6 +107,12 @@ impl HexString { } } +impl From<&HexString> for String { + fn from(value: &HexString) -> Self { + bytes_to_hex_string(value.as_be_bytes()) + } +} + impl core::fmt::Display for HexString { fn fmt(&self, f: &mut core::fmt::Formatter<'_>) -> core::fmt::Result { write!(f, "{:?}", self.0) @@ -162,6 +172,17 @@ pub enum FillValueFloatStringNonFinite { NaN, } +impl From<&FillValueFloatStringNonFinite> for String { + fn from(value: &FillValueFloatStringNonFinite) -> Self { + match value { + FillValueFloatStringNonFinite::PosInfinity => "Infinity", + FillValueFloatStringNonFinite::NegInfinity => "-Infinity", + FillValueFloatStringNonFinite::NaN => "NaN", + } + .to_string() + } +} + impl FillValueMetadata { /// Convert the fill value to a [`bool`]. #[must_use] @@ -546,4 +567,58 @@ mod tests { _ => unreachable!(), } } + + // Null is not currently supported, so recognise it as unknown fill value metadata + #[test] + fn fill_value_metadata_null() { + let json = r#"null"#; + let metadata: FillValueMetadata = json.try_into().unwrap(); + assert_eq!(json, serde_json::to_string(&metadata).unwrap()); + match metadata { + FillValueMetadata::Unsupported(fill_value) => { + assert!(fill_value.is_null()) + } + _ => unreachable!(), + } + } + + // A negative single byte, so recognise it as unknown fill value metadata + #[test] + fn fill_value_metadata_neg_array1() { + let json = r#"[-5]"#; + let metadata: FillValueMetadata = json.try_into().unwrap(); + assert_eq!(json, serde_json::to_string(&metadata).unwrap()); + match metadata { + FillValueMetadata::Unsupported(fill_value) => { + assert!(fill_value.is_array()) + } + _ => unreachable!(), + } + } + + // Two negative -> complex + #[test] + fn fill_value_metadata_neg_array2() { + let json = r#"[-5, -5]"#; + let metadata: FillValueMetadata = json.try_into().unwrap(); + assert_ne!(json, serde_json::to_string(&metadata).unwrap()); // [-5.0, -5.0] + match metadata { + FillValueMetadata::Complex(_re, _im) => {} + _ => unreachable!(), + } + } + + // Single array element > u8::MAX is currently unknown + #[test] + fn fill_value_metadata_large_array() { + let json = r#"[256]"#; + let metadata: FillValueMetadata = json.try_into().unwrap(); + assert_eq!(json, serde_json::to_string(&metadata).unwrap()); + match metadata { + FillValueMetadata::Unsupported(fill_value) => { + assert!(fill_value.is_array()) + } + _ => unreachable!(), + } + } } diff --git a/src/storage/storage_async.rs b/src/storage/storage_async.rs index f014ca05..e4164261 100644 --- a/src/storage/storage_async.rs +++ b/src/storage/storage_async.rs @@ -313,7 +313,7 @@ where { let prefixes = async_discover_children(storage, path).await?; let mut nodes: Vec = Vec::new(); - // FIXME: Asynchronously get metadata of all prefixes + // TODO: Asynchronously get metadata of all prefixes for prefix in &prefixes { let key = meta_key(&prefix.try_into()?); let child_metadata = match storage.get(&key).await? { diff --git a/src/storage/store/store_async/opendal.rs b/src/storage/store/store_async/opendal.rs index b0d6a1b3..abb4e010 100644 --- a/src/storage/store/store_async/opendal.rs +++ b/src/storage/store/store_async/opendal.rs @@ -63,7 +63,7 @@ impl AsyncReadableStorageTraits for AsyncOpendalStore { key: &StoreKey, byte_ranges: &[ByteRange], ) -> Result>, StorageError> { - // FIXME: Get OpenDAL to return an error if byte range is OOB instead of panic, then don't need to query size + // TODO: Get OpenDAL to return an error if byte range is OOB instead of panic, then don't need to query size let (size, reader) = futures::join!(self.size_key(key), self.operator.reader(key.as_str())); if let (Some(size), Some(reader)) = (size?, handle_result(reader)?) { let mut byte_ranges_fetch = Vec::with_capacity(byte_ranges.len()); diff --git a/src/storage/store/store_sync/opendal.rs b/src/storage/store/store_sync/opendal.rs index 46392e5d..de2d66d0 100644 --- a/src/storage/store/store_sync/opendal.rs +++ b/src/storage/store/store_sync/opendal.rs @@ -58,7 +58,7 @@ impl ReadableStorageTraits for OpendalStore { key: &StoreKey, byte_ranges: &[ByteRange], ) -> Result>, StorageError> { - // FIXME: Get OpenDAL to return an error if byte range is OOB instead of panic + // TODO: Get OpenDAL to return an error if byte range is OOB instead of panic let size = self.size_key(key)?; if let Some(size) = size { let reader = self.operator.reader(key.as_str())?; diff --git a/tests/array_async.rs b/tests/array_async.rs index 777108f2..3129755d 100644 --- a/tests/array_async.rs +++ b/tests/array_async.rs @@ -1,10 +1,13 @@ #![cfg(all(feature = "async", feature = "ndarray", feature = "object_store"))] -use zarrs::array::{ArrayBuilder, DataType, FillValue}; +use zarrs::array::codec::array_to_bytes::vlen::VlenCodec; +use zarrs::array::codec::TransposeCodec; +use zarrs::array::{Array, ArrayBuilder, DataType, FillValue}; use zarrs::array_subset::ArraySubset; use object_store::memory::InMemory; +use zarrs::metadata::v3::codec::transpose::TransposeOrder; use zarrs::storage::store::AsyncObjectStore; #[rustfmt::skip] @@ -48,15 +51,15 @@ async fn array_async_read(shard: bool) -> Result<(), Box> array.async_store_array_subset(&ArraySubset::new_with_ranges(&[1..3, 0..2]), &[5, 6, 9, 10]).await?; assert!(array.async_retrieve_chunk(&[0, 0, 0]).await.is_err()); - assert_eq!(array.async_retrieve_chunk(&[0, 0]).await?, [1, 2, 5, 6]); - assert_eq!(array.async_retrieve_chunk(&[0, 1]).await?, [3, 4, 7, 8]); - assert_eq!(array.async_retrieve_chunk(&[1, 0]).await?, [9, 10, 0, 0]); - assert_eq!(array.async_retrieve_chunk(&[1, 1]).await?, [0, 0, 0, 0]); + assert_eq!(array.async_retrieve_chunk(&[0, 0]).await?, vec![1, 2, 5, 6].into()); + assert_eq!(array.async_retrieve_chunk(&[0, 1]).await?, vec![3, 4, 7, 8].into()); + assert_eq!(array.async_retrieve_chunk(&[1, 0]).await?, vec![9, 10, 0, 0].into()); + assert_eq!(array.async_retrieve_chunk(&[1, 1]).await?, vec![0, 0, 0, 0].into()); assert!(array.async_retrieve_chunk_if_exists(&[0, 0, 0]).await.is_err()); - assert_eq!(array.async_retrieve_chunk_if_exists(&[0, 0]).await?, Some(vec![1, 2, 5, 6])); - assert_eq!(array.async_retrieve_chunk_if_exists(&[0, 1]).await?, Some(vec![3, 4, 7, 8])); - assert_eq!(array.async_retrieve_chunk_if_exists(&[1, 0]).await?, Some(vec![9, 10, 0, 0])); + assert_eq!(array.async_retrieve_chunk_if_exists(&[0, 0]).await?, Some(vec![1, 2, 5, 6].into())); + assert_eq!(array.async_retrieve_chunk_if_exists(&[0, 1]).await?, Some(vec![3, 4, 7, 8].into())); + assert_eq!(array.async_retrieve_chunk_if_exists(&[1, 0]).await?, Some(vec![9, 10, 0, 0].into())); assert_eq!(array.async_retrieve_chunk_if_exists(&[1, 1]).await?, None); assert!(array.async_retrieve_chunk_ndarray::(&[0, 0]).await.is_err()); @@ -72,9 +75,9 @@ async fn array_async_read(shard: bool) -> Result<(), Box> assert!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..2])).await.is_err()); assert!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..3, 0..3])).await.is_err()); - assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, [1, 2, 5, 6]); - assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..1, 0..2])).await?, [1, 2]); - assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 1..2])).await?, [2, 6]); + assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, vec![1, 2, 5, 6].into()); + assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..1, 0..2])).await?, vec![1, 2].into()); + assert_eq!(array.async_retrieve_chunk_subset(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 1..2])).await?, vec![2, 6].into()); assert!(array.async_retrieve_chunk_subset_ndarray::(&[0, 0], &ArraySubset::new_with_ranges(&[0..3, 0..3])).await.is_err()); assert!(array.async_retrieve_chunk_subset_ndarray::(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 0..2])).await.is_err()); @@ -83,11 +86,11 @@ async fn array_async_read(shard: bool) -> Result<(), Box> assert_eq!(array.async_retrieve_chunk_subset_ndarray::(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 1..2])).await?, ndarray::array![[2], [6]].into_dyn()); assert!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2])).await.is_err()); - assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..0, 0..0])).await?, Vec::::new()); - assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 0..1])).await?, [1, 2, 5, 6]); - assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0]); - assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 1..2])).await?, [3, 4, 7, 8, 0, 0, 0, 0]); - assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 1..3])).await?, [3, 4, 0, 0, 7, 8, 0, 0]); + assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..0, 0..0])).await?, vec![].into()); + assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 0..1])).await?, vec![1, 2, 5, 6].into()); + assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, vec![1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0].into()); + assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 1..2])).await?, vec![3, 4, 7, 8, 0, 0, 0, 0].into()); + assert_eq!(array.async_retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 1..3])).await?, vec![3, 4, 0, 0, 7, 8, 0, 0].into()); assert!(array.async_retrieve_chunks_ndarray::(&ArraySubset::new_with_ranges(&[0..2])).await.is_err()); assert!(array.async_retrieve_chunks_ndarray::(&ArraySubset::new_with_ranges(&[0..2, 0..2])).await.is_err()); @@ -96,13 +99,12 @@ async fn array_async_read(shard: bool) -> Result<(), Box> assert_eq!(array.async_retrieve_chunks_ndarray::(&ArraySubset::new_with_ranges(&[0..1, 1..3])).await?, ndarray::array![[3, 4, 0, 0], [7, 8, 0, 0]].into_dyn()); assert!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4])).await.is_err()); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0])).await?, Vec::::new()); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0])).await?, [] as [u8; 0]); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, [1, 2, 5, 6]); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4, 0..4])).await?, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0]); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[1..3, 1..3])).await?, [6, 7, 10 ,0]); - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[5..7, 5..6])).await?, [0, 0]); // OOB -> fill value - assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..5, 0..5])).await?, [1, 2, 3, 4, 0, 5, 6, 7, 8, 0, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]); // OOB -> fill value + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0])).await?, vec![].into()); + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..2, 0..2])).await?, vec![1, 2, 5, 6].into()); + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4, 0..4])).await?, vec![1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0].into()); + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[1..3, 1..3])).await?, vec![6, 7, 10 ,0].into()); + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[5..7, 5..6])).await?, vec![0, 0].into()); // OOB -> fill value + assert_eq!(array.async_retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..5, 0..5])).await?, vec![1, 2, 3, 4, 0, 5, 6, 7, 8, 0, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0].into()); // OOB -> fill value assert!(array.async_retrieve_array_subset_ndarray::(&ArraySubset::new_with_ranges(&[0..4])).await.is_err()); assert!(array.async_retrieve_array_subset_ndarray::(&ArraySubset::new_with_ranges(&[0..4, 0..4])).await.is_err()); @@ -114,9 +116,9 @@ async fn array_async_read(shard: bool) -> Result<(), Box> assert!(array.async_partial_decoder(&[0]).await.is_err()); assert!(array.async_partial_decoder(&[0, 0]).await?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1])]).await.is_err()); - assert_eq!(array.async_partial_decoder(&[0, 0]).await?.partial_decode(&[]).await?, Vec::>::new()); - assert_eq!(array.async_partial_decoder(&[5, 0]).await?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2])]).await?, [vec![0, 0]]); // OOB -> fill value - assert_eq!(array.async_partial_decoder(&[0, 0]).await?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2]), ArraySubset::new_with_ranges(&[0..2, 1..2])]).await?, [vec![1, 2], vec![2, 6]]); + assert_eq!(array.async_partial_decoder(&[0, 0]).await?.partial_decode(&[]).await?, []); + assert_eq!(array.async_partial_decoder(&[5, 0]).await?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2])]).await?, [vec![0, 0].into()]); // OOB -> fill value + assert_eq!(array.async_partial_decoder(&[0, 0]).await?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2]), ArraySubset::new_with_ranges(&[0..2, 1..2])]).await?, [vec![1, 2].into(), vec![2, 6].into()]); Ok(()) } @@ -132,3 +134,183 @@ async fn array_async_read_uncompressed() -> Result<(), Box Result<(), Box> { array_async_read(true).await } + +async fn array_str_impl( + array: Array>, +) -> Result<(), Box> { + // Store a single chunk + array + .async_store_chunk_elements(&[0, 0], &["a", "bb", "ccc", "dddd"]) + .await?; + assert_eq!( + array + .async_retrieve_chunk_elements::(&[0, 0]) + .await?, + &["a", "bb", "ccc", "dddd"] + ); + + // Write array subset with full chunks + array + .async_store_array_subset_elements( + &ArraySubset::new_with_ranges(&[2..4, 0..4]), + &[ + "1", "22", "333", "4444", "55555", "666666", "7777777", "88888888", + ], + ) + .await?; + assert_eq!( + array + .async_retrieve_chunk_elements::(&[1, 0]) + .await?, + &["1", "22", "55555", "666666"] + ); + assert_eq!( + array + .async_retrieve_chunk_elements::(&[1, 1]) + .await?, + &["333", "4444", "7777777", "88888888"] + ); + + // Write array subset with partial chunks + array + .async_store_array_subset_elements( + &ArraySubset::new_with_ranges(&[1..3, 1..3]), + &["S1", "S22", "S333", "S4444"], + ) + .await?; + assert_eq!( + array + .async_retrieve_chunk_elements::(&[0, 0]) + .await?, + &["a", "bb", "ccc", "S1"] + ); + assert_eq!( + array + .async_retrieve_chunk_elements::(&[0, 1]) + .await?, + &["", "", "S22", ""] + ); + assert_eq!( + array + .async_retrieve_chunk_elements::(&[1, 0]) + .await?, + &["1", "S333", "55555", "666666"] + ); + assert_eq!( + array + .async_retrieve_chunk_elements::(&[1, 1]) + .await?, + &["S4444", "4444", "7777777", "88888888"] + ); + + // Write multiple chunks + array + .async_store_chunks_elements( + &ArraySubset::new_with_ranges(&[0..1, 0..2]), + &["a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333"], + ) + .await?; + assert_eq!( + array + .async_retrieve_chunk_elements::(&[0, 0]) + .await?, + &["a", "bb", "C0", "C11"] + ); + assert_eq!( + array + .async_retrieve_chunk_elements::(&[0, 1]) + .await?, + &["ccc", "dddd", "C222", "C3333"] + ); + assert_eq!( + array + .async_retrieve_chunks_elements::(&ArraySubset::new_with_ranges(&[0..1, 0..2])) + .await?, + &["a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333"] + ); + + // Full chunk requests + assert_eq!( + array + .async_retrieve_array_subset_elements::(&ArraySubset::new_with_ranges(&[ + 0..4, + 0..4 + ])) + .await?, + &[ + "a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333", // + "1", "S333", "S4444", "4444", "55555", "666666", "7777777", "88888888" // + ] + ); + + // Partial chunk requests + assert_eq!( + array + .async_retrieve_array_subset_elements::(&ArraySubset::new_with_ranges(&[ + 1..3, + 1..3 + ])) + .await?, + &["C11", "C222", "S333", "S4444"] + ); + + // Incompatible chunks / bytes + assert!(array + .async_store_chunks_elements(&ArraySubset::new_with_ranges(&[0..0, 0..2]), &["a", "bb"]) + .await + .is_err()); + assert!(array + .async_store_chunks_elements(&ArraySubset::new_with_ranges(&[0..1, 0..2]), &["a", "bb"]) + .await + .is_err()); + + Ok(()) +} + +#[tokio::test] +async fn array_str_async_simple() -> Result<(), Box> { + let store = std::sync::Arc::new(AsyncObjectStore::new(InMemory::new())); + let array_path = "/array"; + let mut builder = ArrayBuilder::new( + vec![4, 4], // array shape + DataType::String, + vec![2, 2].try_into().unwrap(), // regular chunk shape + FillValue::from(""), + ); + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "gzip")] + Box::new(zarrs::array::codec::GzipCodec::new(5)?), + ]); + + let array = builder.build(store, array_path).unwrap(); + array_str_impl(array).await +} + +#[tokio::test] +async fn array_str_async_sharded_transpose() -> Result<(), Box> { + let store = std::sync::Arc::new(AsyncObjectStore::new(InMemory::new())); + let array_path = "/array"; + let mut builder = ArrayBuilder::new( + vec![4, 4], // array shape + DataType::String, + vec![2, 2].try_into().unwrap(), // regular chunk shape + FillValue::from(""), + ); + builder.array_to_array_codecs(vec![Box::new(TransposeCodec::new( + TransposeOrder::new(&[1, 0]).unwrap(), + ))]); + builder.array_to_bytes_codec(Box::new( + zarrs::array::codec::array_to_bytes::sharding::ShardingCodecBuilder::new( + vec![2, 1].try_into().unwrap(), + ) + .array_to_bytes_codec(Box::::default()) + .build(), + )); + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "gzip")] + Box::new(zarrs::array::codec::GzipCodec::new(5)?), + ]); + + let array = builder.build(store, array_path).unwrap(); + array_str_impl(array).await +} diff --git a/tests/array_sync.rs b/tests/array_sync.rs index 5ddcd859..b1263afc 100644 --- a/tests/array_sync.rs +++ b/tests/array_sync.rs @@ -22,15 +22,15 @@ fn array_sync_read(array: Array) -> Result<(), Box(&[0, 0]).is_err()); @@ -46,9 +46,9 @@ fn array_sync_read(array: Array) -> Result<(), Box(&[0, 0], &ArraySubset::new_with_ranges(&[0..3, 0..3])).is_err()); assert!(array.retrieve_chunk_subset_ndarray::(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 0..2])).is_err()); @@ -57,11 +57,11 @@ fn array_sync_read(array: Array) -> Result<(), Box(&[0, 0], &ArraySubset::new_with_ranges(&[0..2, 1..2]))?, ndarray::array![[2], [6]].into_dyn()); assert!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2])).is_err()); - assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..0, 0..0]))?, Vec::::new()); - assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 0..1]))?, [1, 2, 5, 6]); - assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 0..2]))?, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0]); - assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 1..2]))?, [3, 4, 7, 8, 0, 0, 0, 0]); - assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 1..3]))?, [3, 4, 0, 0, 7, 8, 0, 0]); + assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..0, 0..0]))?, vec![].into()); + assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 0..1]))?, vec![1, 2, 5, 6].into()); + assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 0..2]))?, vec![1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0].into()); + assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..2, 1..2]))?, vec![3, 4, 7, 8, 0, 0, 0, 0].into()); + assert_eq!(array.retrieve_chunks(&ArraySubset::new_with_ranges(&[0..1, 1..3]))?, vec![3, 4, 0, 0, 7, 8, 0, 0].into()); assert!(array.retrieve_chunks_ndarray::(&ArraySubset::new_with_ranges(&[0..2])).is_err()); assert!(array.retrieve_chunks_ndarray::(&ArraySubset::new_with_ranges(&[0..2, 0..2])).is_err()); @@ -70,13 +70,12 @@ fn array_sync_read(array: Array) -> Result<(), Box(&ArraySubset::new_with_ranges(&[0..1, 1..3]))?, ndarray::array![[3, 4, 0, 0], [7, 8, 0, 0]].into_dyn()); assert!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4])).is_err()); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0]))?, Vec::::new()); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0]))?, [] as [u8; 0]); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..2, 0..2]))?, [1, 2, 5, 6]); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4, 0..4]))?, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0]); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[1..3, 1..3]))?, [6, 7, 10 ,0]); - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[5..7, 5..6]))?, [0, 0]); // OOB -> fill value - assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..5, 0..5]))?, [1, 2, 3, 4, 0, 5, 6, 7, 8, 0, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]); // OOB -> fill value + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..0, 0..0]))?, vec![].into()); + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..2, 0..2]))?, vec![1, 2, 5, 6].into()); + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..4, 0..4]))?, vec![1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0].into()); + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[1..3, 1..3]))?, vec![6, 7, 10 ,0].into()); + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[5..7, 5..6]))?, vec![0, 0].into()); // OOB -> fill value + assert_eq!(array.retrieve_array_subset(&ArraySubset::new_with_ranges(&[0..5, 0..5]))?, vec![1, 2, 3, 4, 0, 5, 6, 7, 8, 0, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0].into()); // OOB -> fill value assert!(array.retrieve_array_subset_ndarray::(&ArraySubset::new_with_ranges(&[0..4])).is_err()); assert!(array.retrieve_array_subset_ndarray::(&ArraySubset::new_with_ranges(&[0..4, 0..4])).is_err()); @@ -88,9 +87,9 @@ fn array_sync_read(array: Array) -> Result<(), Box>::new()); - assert_eq!(array.partial_decoder(&[5, 0])?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2])])?, [vec![0, 0]]); // OOB -> fill value - assert_eq!(array.partial_decoder(&[0, 0])?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2]), ArraySubset::new_with_ranges(&[0..2, 1..2])])?, [vec![1, 2], vec![2, 6]]); + assert_eq!(array.partial_decoder(&[0, 0])?.partial_decode(&[])?, []); + assert_eq!(array.partial_decoder(&[5, 0])?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2])])?, [vec![0, 0].into()]); // OOB -> fill value + assert_eq!(array.partial_decoder(&[0, 0])?.partial_decode(&[ArraySubset::new_with_ranges(&[0..1, 0..2]), ArraySubset::new_with_ranges(&[0..2, 1..2])])?, [vec![1, 2].into(), vec![2, 6].into()]); Ok(()) } @@ -122,6 +121,7 @@ fn array_sync_read_uncompressed() -> Result<(), Box> { array_sync_read(array) } +#[cfg(feature = "sharding")] #[test] #[cfg_attr(miri, ignore)] fn array_sync_read_shard_compress() -> Result<(), Box> { @@ -133,7 +133,6 @@ fn array_sync_read_shard_compress() -> Result<(), Box> { vec![2, 2].try_into().unwrap(), // regular chunk shape FillValue::from(0u8), ); - #[cfg(feature = "sharding")] builder.array_to_bytes_codec(Box::new( zarrs::array::codec::array_to_bytes::sharding::ShardingCodecBuilder::new( vec![1, 1].try_into().unwrap(), @@ -159,3 +158,216 @@ fn array_sync_read_shard_compress() -> Result<(), Box> { array_sync_read(array) } + +fn array_str_impl(array: Array) -> Result<(), Box> { + // Store a single chunk + array.store_chunk_elements(&[0, 0], &["a", "bb", "ccc", "dddd"])?; + assert_eq!( + array.retrieve_chunk_elements::(&[0, 0])?, + &["a", "bb", "ccc", "dddd"] + ); + + // Write array subset with full chunks + array.store_array_subset_elements( + &ArraySubset::new_with_ranges(&[2..4, 0..4]), + &[ + "1", "22", "333", "4444", "55555", "666666", "7777777", "88888888", + ], + )?; + assert_eq!( + array.retrieve_chunk_elements::(&[1, 0])?, + &["1", "22", "55555", "666666"] + ); + assert_eq!( + array.retrieve_chunk_elements::(&[1, 1])?, + &["333", "4444", "7777777", "88888888"] + ); + + // Write array subset with partial chunks + array.store_array_subset_elements( + &ArraySubset::new_with_ranges(&[1..3, 1..3]), + &["S1", "S22", "S333", "S4444"], + )?; + assert_eq!( + array.retrieve_chunk_elements::(&[0, 0])?, + &["a", "bb", "ccc", "S1"] + ); + assert_eq!( + array.retrieve_chunk_elements::(&[0, 1])?, + &["", "", "S22", ""] + ); + assert_eq!( + array.retrieve_chunk_elements::(&[1, 0])?, + &["1", "S333", "55555", "666666"] + ); + assert_eq!( + array.retrieve_chunk_elements::(&[1, 1])?, + &["S4444", "4444", "7777777", "88888888"] + ); + + // Write multiple chunks + array.store_chunks_elements( + &ArraySubset::new_with_ranges(&[0..1, 0..2]), + &["a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333"], + )?; + assert_eq!( + array.retrieve_chunk_elements::(&[0, 0])?, + &["a", "bb", "C0", "C11"] + ); + assert_eq!( + array.retrieve_chunk_elements::(&[0, 1])?, + &["ccc", "dddd", "C222", "C3333"] + ); + assert_eq!( + array.retrieve_chunks_elements::(&ArraySubset::new_with_ranges(&[0..1, 0..2]))?, + &["a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333"] + ); + + // Full chunk requests + assert_eq!( + array.retrieve_array_subset_elements::(&ArraySubset::new_with_ranges(&[ + 0..4, + 0..4 + ]))?, + &[ + "a", "bb", "ccc", "dddd", "C0", "C11", "C222", "C3333", // + "1", "S333", "S4444", "4444", "55555", "666666", "7777777", "88888888" // + ] + ); + + // Partial chunk requests + assert_eq!( + array.retrieve_array_subset_elements::(&ArraySubset::new_with_ranges(&[ + 1..3, + 1..3 + ]))?, + &["C11", "C222", "S333", "S4444"] + ); + + // Incompatible chunks / bytes + assert!(array + .store_chunks_elements(&ArraySubset::new_with_ranges(&[0..0, 0..2]), &["a", "bb"]) + .is_err()); + assert!(array + .store_chunks_elements(&ArraySubset::new_with_ranges(&[0..1, 0..2]), &["a", "bb"]) + .is_err()); + + Ok(()) +} + +#[test] +fn array_str_sync_simple() -> Result<(), Box> { + let store = std::sync::Arc::new(MemoryStore::default()); + let array_path = "/array"; + let mut builder = ArrayBuilder::new( + vec![4, 4], // array shape + DataType::String, + vec![2, 2].try_into().unwrap(), // regular chunk shape + FillValue::from(""), + ); + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "gzip")] + Box::new(zarrs::array::codec::GzipCodec::new(5)?), + ]); + + let array = builder.build(store, array_path).unwrap(); + + array_str_impl(array) +} + +#[cfg(feature = "sharding")] +#[test] +fn array_str_sync_sharded_transpose() -> Result<(), Box> { + use zarrs::{ + array::codec::{array_to_bytes::vlen::VlenCodec, TransposeCodec}, + metadata::v3::codec::transpose::TransposeOrder, + }; + + let store = std::sync::Arc::new(MemoryStore::default()); + let array_path = "/array"; + let mut builder = ArrayBuilder::new( + vec![4, 4], // array shape + DataType::String, + vec![2, 2].try_into().unwrap(), // regular chunk shape + FillValue::from(""), + ); + builder.array_to_array_codecs(vec![Box::new(TransposeCodec::new( + TransposeOrder::new(&[1, 0]).unwrap(), + ))]); + builder.array_to_bytes_codec(Box::new( + zarrs::array::codec::array_to_bytes::sharding::ShardingCodecBuilder::new( + vec![2, 1].try_into().unwrap(), + ) + .array_to_bytes_codec(Box::::default()) + .build(), + )); + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "gzip")] + Box::new(zarrs::array::codec::GzipCodec::new(5)?), + ]); + + let array = builder.build(store, array_path).unwrap(); + + array_str_impl(array) +} + +#[rustfmt::skip] +#[test] +fn array_binary() -> Result<(), Box> { + let store = std::sync::Arc::new(MemoryStore::default()); + let array_path = "/array"; + let mut builder = ArrayBuilder::new( + vec![4, 4], // array shape + DataType::Binary, + vec![2, 2].try_into().unwrap(), // regular chunk shape + FillValue::from([]), + ); + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "gzip")] + Box::new(zarrs::array::codec::GzipCodec::new(5)?), + ]); + + let array = builder.build(store, array_path).unwrap(); + + array.store_array_subset_elements::<&[u8]>( + &ArraySubset::new_with_ranges(&[1..3, 1..3]), + &[&[0], &[0, 1], &[0, 1, 2], &[0, 1, 2, 3]], + )?; + assert_eq!( + array.retrieve_chunk_elements::>(&[0, 0])?, + vec![ + vec![], vec![], + vec![], vec![0] + ], + ); + assert_eq!( + array.retrieve_chunk_elements::>(&[0, 1])?, + vec![ + vec![], vec![], + vec![0, 1], vec![] + ], + ); + assert_eq!( + array.retrieve_chunk_elements::>(&[1, 0])?, + vec![ + vec![], vec![0, 1, 2], + vec![], vec![] + ], + ); + assert_eq!( + array.retrieve_chunk_elements::>(&[1, 1])?, + vec![ + vec![0, 1, 2, 3], vec![], + vec![], vec![] + ], + ); + assert_eq!( + array.retrieve_array_subset_elements::>(&ArraySubset::new_with_ranges(&[1..3, 0..4]))?, + vec![ + vec![], vec![0], vec![0, 1], vec![], + vec![], vec![0, 1, 2], vec![0, 1, 2, 3], vec![], + ], + ); + + Ok(()) +} diff --git a/tests/cities.rs b/tests/cities.rs new file mode 100644 index 00000000..0af6afc5 --- /dev/null +++ b/tests/cities.rs @@ -0,0 +1,132 @@ +use std::{ + error::Error, + fs::File, + io::{BufRead, BufReader}, +}; + +use zarrs::{ + array::{ + codec::{ + array_to_bytes::{ + sharding::ShardingCodecBuilder, vlen::VlenCodec, + vlen_interleaved::VlenInterleavedCodec, + }, + ArrayToBytesCodecTraits, ZstdCodec, + }, + ArrayBuilder, ArrayMetadataOptions, DataType, FillValue, + }, + array_subset::ArraySubset, + metadata::v3::codec::vlen::VlenCodecConfiguration, + storage::{ + store::{FilesystemStore, MemoryStore}, + ReadableWritableListableStorage, + }, +}; + +fn read_cities() -> std::io::Result> { + let reader = BufReader::new(File::open("tests/data/cities.csv")?); + let mut cities = Vec::with_capacity(47868); + for line in reader.lines() { + cities.push(line?); + } + Ok(cities) +} + +fn cities_impl( + cities: &[String], + compression_level: Option, + chunk_size: u64, + shard_size: Option, + vlen_codec: Box, + write_to_file: bool, +) -> Result> { + let store: ReadableWritableListableStorage = if write_to_file { + std::sync::Arc::new(FilesystemStore::new("tests/data/v3/cities.zarr")?) + } else { + std::sync::Arc::new(MemoryStore::default()) + }; + store.erase_prefix(&"".try_into().unwrap())?; + + let mut builder = ArrayBuilder::new( + vec![cities.len() as u64], // array shape + DataType::String, + vec![chunk_size].try_into()?, // regular chunk shape + FillValue::from(""), + ); + if let Some(shard_size) = shard_size { + builder.array_to_bytes_codec(Box::new( + ShardingCodecBuilder::new( + vec![shard_size].try_into()?, // inner chunk chape + ) + .array_to_bytes_codec(vlen_codec) + .build(), + )); + } else { + builder.array_to_bytes_codec(vlen_codec); + } + if let Some(compression_level) = compression_level { + builder.bytes_to_bytes_codecs(vec![ + #[cfg(feature = "zstd")] + Box::new(ZstdCodec::new(compression_level, false)), + ]); + } + + let array = builder.build(store.clone(), "/")?; + array.store_metadata_opt(&ArrayMetadataOptions::default().set_include_zarrs_metadata(false))?; + + let subset_all = ArraySubset::new_with_shape(array.shape().to_vec()); + array.store_array_subset_elements(&subset_all, &cities)?; + let cities_out = array.retrieve_array_subset_elements::(&subset_all)?; + assert_eq!(cities, cities_out); + + let last_block = array.retrieve_chunk(&[(cities.len() as u64).div_ceil(chunk_size)])?; + let (_bytes, offsets) = last_block.into_variable()?; + assert_eq!(offsets.len() as u64, chunk_size + 1); + + Ok(store.size_prefix(&"c/".try_into().unwrap())?) // only chunks +} + +#[rustfmt::skip] +#[test] +fn cities() -> Result<(), Box> { + let cities = read_cities()?; + assert_eq!(cities.len(), 47868); + assert_eq!(cities[0], "Tokyo"); + assert_eq!(cities[47862], "Sariwŏn-si"); + assert_eq!(cities[47867], "Charlotte Amalie"); + + let vlen_interleaved = Box::new(VlenInterleavedCodec::default()); + + // let vlen = Box::new(VlenCodec::default()); + let vlen_configuration: VlenCodecConfiguration = serde_json::from_str(r#"{ + "data_codecs": [{"name": "bytes"}], + "index_codecs": [{"name": "bytes","configuration": { "endian": "little" }}], + "index_data_type": "uint32" + }"#)?; + let vlen = Box::new(VlenCodec::new_with_configuration(&vlen_configuration)?); + + let vlen_compressed_configuration: VlenCodecConfiguration = serde_json::from_str(r#"{ + "data_codecs": [{"name": "bytes"},{"name": "blosc","configuration": {"cname": "zstd", "clevel":5,"shuffle": "bitshuffle", "typesize":1,"blocksize":0}}], + "index_codecs": [{"name": "bytes","configuration": { "endian": "little" }},{"name": "blosc","configuration":{"cname": "zstd", "clevel":5,"shuffle": "shuffle", "typesize":4,"blocksize":0}}], + "index_data_type": "uint32" + }"#)?; + let vlen_compressed = Box::new(VlenCodec::new_with_configuration(&vlen_compressed_configuration)?); + + print!("| encoding | compression | size |\n"); + print!("| ---------------- | ----------- | ------ |\n"); + print!("| vlen_interleaved | | {} |\n", cities_impl(&cities, None, 1000, None, vlen_interleaved.clone(), true)?); + print!("| vlen_interleaved | zstd 5 | {} |\n", cities_impl(&cities, Some(5), 1000, None, vlen_interleaved.clone(), false)?); + print!("| vlen | | {} |\n", cities_impl(&cities, None, 1000, None, vlen.clone(), false)?); + print!("| vlen | zstd 5 | {} |\n", cities_impl(&cities, None, 1000, None, vlen_compressed.clone(), false)?); + println!(); + // panic!(); + + // | encoding | compression | size | + // | ---------------- | ----------- | ------ | + // | vlen_interleaved | | 642196 | + // | vlen_interleaved | zstd 5 | 362626 | + // | vlen | | 642580 | + // | vlen | zstd 5 | 346950 | + + Ok(()) +} diff --git a/tests/data/cities.csv b/tests/data/cities.csv new file mode 100644 index 00000000..cfc78d01 --- /dev/null +++ b/tests/data/cities.csv @@ -0,0 +1,47868 @@ +Tokyo +Jakarta +Delhi +Guangzhou +Mumbai +Manila +Shanghai +São Paulo +Seoul +Mexico City +Cairo +New York +Dhaka +Beijing +Kolkāta +Bangkok +Shenzhen +Moscow +Buenos Aires +Lagos +Istanbul +Karachi +Bangalore +Ho Chi Minh City +Ōsaka +Chengdu +Tehran +Kinshasa +Rio de Janeiro +Chennai +Xi’an +Lahore +Chongqing +Los Angeles +Baoding +London +Paris +Linyi +Dongguan +Hyderābād +Tianjin +Lima +Wuhan +Nanyang +Hangzhou +Foshan +Nagoya +Tongshan +Luanda +Zhoukou +Ganzhou +Kuala Lumpur +Heze +Quanzhou +Johannesburg +Chicago +Nanjing +Jining +Hanoi +Pune +Fuyang +Ahmedabad +Bogotá +Shenyang +Dar es Salaam +Khartoum +Shangqiu +Hong Kong +Cangzhou +Riyadh +Santiago +Xingtai +Zhumadian +Chattogram +Surabaya +Zhanjiang +Bijie +Yancheng +Hengyang +Zunyi +Shaoyang +Sūrat +Shangrao +Xinyang +Madrid +Baghdad +Maoming +Jieyang +Miami +Singapore +Houston +Liaocheng +Huanggang +Dalian +Dallas +Qingdao +Yulin +Douala +Qujing +Nangandao +Philadelphia +Pudong +Toronto +Zhengzhou +Dezhou +Nanchong +Jinan +Giza +Nairobi +Guadalajara +Ankara +Tai’an +Langfang +Dazhou +Saint Petersburg +Monterrey +Belo Horizonte +Suzhou +Yongzhou +Changde +Xiangyang +Rangoon +Atlanta +Washington +Zhaotong +Zhangzhou +Melbourne +Yichun +Bozhou +Suqian +Abidjan +Ji’an +Guilin +Pingdingshan +Berlin +Alexandria +Mianyang +Sydney +Huanglongsi +Barcelona +Yuncheng +Cape Town +Changsha +Jeddah +Weinan +Chenzhou +Jiangmen +Jiujiang +Xinpu +Yibin +Huaihua +Yangzhou +Taizhou +Kunming +Yiyang +Changchun +Lu’an +Jiangguanchi +Meizhou +Ürümqi +Suzhou +Boston +İzmir +Guigang +Shantou +Kabul +Xiaoganzhan +Bamako +Luzhou +Hefei +Hengshui +Fortaleza +Anqing +Liuzhou +Zhangjiakou +Zhaoqing +Shijiazhuang +Ningbo +Qiqihar +Phoenix +Fuzhou +Chifeng +Xiaoxita +Amman +Chuzhou +Linfen +Qingyuan +Xianyang +Loudi +Binzhou +Zhuzhou +Taiyuan +Nanning +Harbin +Abuja +Yokohama +Suihua +Zaozhuang +Detroit +Xiamen +Neijiang +Montréal +Fuzhou +Baicheng +Wuhu +Yulinshi +Medan +Wenzhou +Changzhou +Puyang +Jiaozuo +Nanchang +Seattle +Ibadan +Casablanca +Kumasi +Deyang +Busan +Hohhot +Hechi +Algiers +Tangshan +Shiyan +Lucknow +Mashhad +San Francisco +Boankra +Dubai +Anshan +Baojishi +Qinzhou +Guiyang +Bengbu +Bazhou +Suining +Wuxi +Kotla Qasim Khan +Hanzhong +Putian +Zhenjiang +Guang’an +Faisalabad +Changzhi +Tongren +Leshan +Santa Cruz de la Sierra +Qinhuangdao +Jaipur +Xinzhou +Lanzhou +Wuzhou +Athens +San Diego +Addis Ababa +Taichung +Huainan +Guatemala City +Kuwait City +Budapest +Qincheng +Rizhao +Quezon City +Sanaa +Tashkent +Kyiv +Meishan +Incheon +Birmingham +Ningde +Zhongshan +Weihai +Bursa +Minneapolis +Mbuji-Mayi +Haikou +Tongliao +Chaoyang +La Paz +Pyongyang +Tampa +Shaoguan +Heyuan +Brasília +Omdurman +Malang +Stuttgart +Daqing +Rome +Brooklyn +Kaohsiung +Xiangtan +Longyan +Baotou +Handan +Jinzhou +Kanpur +Denver +Nanping +Gāzipura +Shanwei +Chaozhou +Guayaquil +Weifang +Huai’an +Zibo +Ankang +Mogadishu +Munich +Gulou +Taipei +Bekasi +Damascus +Sanming +Yangjiang +Jiamusi +Luohe +Medellín +Dingxi +Shaoxing +Yantai +Huizhou +Lishui +Xuanzhou +Khowrhesht +Mirzāpur +Zigong +Hamburg +Guangyuan +Cali +Huangshi +Xining +Lusaka +Ouagadougou +Yaoundé +Zhuhai +Huludao +Baoshan +Mecca +Vancouver +Lianshan +Beirut +Salvador +Bucharest +Longba +Nāgpur +Queens +Jilin +Tieling +Accra +Yunfu +Bekasi Kota +Daegu +Ghāziābād +Luoyang +Brisbane +Anshun +Riverside +Yingkou +Colombo +Yanjiang +Baku +Antananarivo +Mudanjiang +Fukuoka +Yan’an +Jincheng +Nantong +Lincang +Yuxi +Las Vegas +Caracas +Tangerang +Laibin +Konya +Supaul +Vienna +Eşfahān +Baltimore +Shengli +Dandong +Qinbaling +Gaoping +Awka +Taizhou +Ma’anshan +Harare +Perth +St. Louis +Phnom Penh +Depok +Stockholm +Puning +Huaibei +Kowloon +Córdoba +Haiphong +Zamboanga City +Chongzuo +Rawalpindi +Portland +Kano +Yushan +Havana +Hezhou +Pingliang +Vadodara +Manaus +Qingyang +San Antonio +Rājkot +Shangzhou +Vishākhapatnam +Sanmenxia +Baicheng +Gujranwala +Aleppo +Tijuana +Bamenda +Minsk +Indore +Karaj +Kananga +Peshawar +Sapporo +Sacramento +Tilburg +Pingxiang +Ecatepec +Almaty +Austin +Yinchuan +Santos +Blantyre +Thāne +Orlando +Tainan +Xiping +Multan +Santa Cruz +Port Harcourt +Jixi +Fushun +Warsaw +Beihai +Fuxin +Wuwei +Siping +San Juan +Mersin +Bhopāl +Mosul +Lubumbashi +Davao +Curitiba +San Jose +Shuyangzha +Adana +Quito +Pittsburgh +Brazzaville +Hyderabad City +Diyarbakır +Indianapolis +Pimpri-Chinchwad +Masqaţ +Montevideo +Shuozhou +Manhattan +Cincinnati +Kansas City +Patna +Tegucigalpa +Kampala +Cleveland +Sanzhou +Changshu +Heihe +Conakry +Ximeicun +Caloocan City +Masvingo +Zhongli +Novosibirsk +Bilāspur +Semarang +Jingdezhen +Ludhiāna +Liaoyang +Chengtangcun +Rājshāhi +Balandougou +Jiangyin +Valencia +Āgra +León de los Aldama +Puebla +Columbus +Yopougon +Hebi +Shīrāz +Madurai +Huzhou +Tabrīz +Jamshedpur +Maracaibo +Sofia +San José +Prayagraj +Palembang +Kawasaki +Kōbe +Jiaxing +Kigali +Zhangjiajie +Baiyin +Guiping +Lianjiang +Jianguang +Yucheng +Xushan +Panama City +Nneyi-Umuleri +Leizhou +Gwangju +Katako-Kombe +Recife +Nāsik +Valencia +Onitsha +Abu Dhabi +Zapopan +Daejeon +Bronx +Yekaterinburg +Huazhou +Jinhua +Kyōto +Amsterdam +Pizhou +Kismaayo +Yangshe +Virginia Beach +Dakar +Goiânia +Charlotte +Rui’an +Muscat +Kharkiv +Wenling +Gaozhou +Farīdābād +Medina +Khulna +Ulaanbaatar +Fuqing +Kayseri +Tel Aviv-Yafo +Wuzhong +Pingdu +Sangereng +Yangquan +Samsun +Yutan +Copenhagen +Helsinki +Prague +Milan +Auckland +Santiago +Chizhou +Makassar +Liangshi +Porto Alegre +Huangshan +Barranquilla +Al Başrah +Benxi +Saitama +Guarulhos +Juárez +Mandalay +Xintai +Wusong +Calgary +Meerut +Yushu +Belém +Kuaidamao +Huazhou +Baishan +Adelaide +Haicheng +Milwaukee +Providence +Jacksonville +Yicheng +Cacuaco +Porto +Rosario +Canagatan +Soweto +Bagam +Jabalpur +Rucheng +Huaiyin +Dublin +Kazan +Dayan +Shaoyang +Balıkesir +Comayagüela +Laiwu +Sharjah +Jingling +Kalyān +Nizhniy Novgorod +Yongcheng +Sumedang +Cần Thơ +Brussels +Suwon +Yiwu +Beidao +Vasai-Virar +Xiangshui +Dadukou +Campinas +Lingcheng +Shuangyashan +Mombasa +Najafgarh +Xinyu +Qom +Hargeysa +Baidoa +Zhangye +Vārānasi +Hiroshima +Chiang Mai +Belgrade +Maiduguri +Chelyabinsk +Batam Centre +Rongcheng +Mbandaka +Doha +Ahvāz +Shymkent +Tripoli +Srīnagar +Nashville +Liaoyuan +Aurangābād +Cilacap +Salt Lake City +Omsk +Pikine +Samara +Guankou +Bandar Lampung +Raleigh +Lianyuan +Rongcheng +Dhanbād +Nay Pyi Taw +Aba +Kaiyuan +Zhuji +Yingtan +Edmonton +Leiyang +Ulsan +Yichun +Benin City +Bujumbura +Guyuan +Xiantao +Rostov +Maputo +Bukavu +Amritsar +Shagamu +Yingchuan +Alīgarh +Santo Domingo +Bogor +Bishkek +Tbilisi +Guwāhāti +Ufa +Fès +Mwanza +Biên Hòa +Mexicali +Sevilla +Ikare +Dongtai +Dingzhou +Xibeijie +Tamale +Yuyao +Hanchuan +Gongzhuling +N’Djamena +Ubungo +Cologne +Krasnoyarsk +Zhufeng +Ezhou +Astana +Nezahualcóyotl +Nouakchott +Hāora +Tongjin +Xiashi +Yerevan +Rānchi +Richmond +Ciudad Nezahualcóyotl +Gwalior +Ottawa +Zhongwei +Oslo +Goyang +Sendai +Mizhou +Xishan +Barquisimeto +Hegang +Chandīgarh +Voronezh +Managua +Haldwāni +Vijayavāda +Perm +Fangchenggang +Jiancheng +Cazenga +Kisangani +Shouguang +Memphis +São Luís +Jodhpur +Matola +Ogbomoso +Sanya +Rangapukur +Ashgabat +Wutong +Linhai +Denizli +Niamey +Shubrā al Khaymah +Wafangdian +Zhongxiang +Monrovia +San Cristóbal +Islamabad +Xinyi +Thủ Đức +Morelia +Odesa +Raipur +Changwon +Arequipa +Volgograd +Zaoyang +Xingyi +Shuizhai +Kota +Quetta +Quảng Hà +Domaa-Ahenkro +Bareilly +Oklahoma City +Bordeaux +Xingcheng +Taixing +Xinhualu +Lilongwe +Port-au-Prince +Yingcheng +Al Mijlad +Luocheng +Pekanbaru +Natal +Chiba +Kirkuk +Hartford +Huilong +Wuchuan +Dnipro +Nārāyanganj +Gqeberha +Málaga +Marrakech +Cebu City +Louisville +Asmara +Coimbatore +Maceió +Nada +Taishan +Teresina +Solāpur +Freetown +Santo Domingo Este +Krasnodar +Vientiane +Tangier +Anqiu +Kermānshāh +Feicheng +Kibanseke Première +Seberang Jaya +Buffalo +Hubli +El Alto +Çankaya +Hwasu-dong +Setagaya +Keçiören +Jerusalem +Khartoum North +Meishan +Mushin +Trujillo +Kitakyūshū +Aguascalientes +New Orleans +Fort Worth +Taihe +Riga +Xin’an +Taihecun +Kashgar +Sŏngnam +Trichinopoly +Cartagena +Qingzhou +Naples +Santiago del Estero +Naucalpan de Juárez +Daye +Hengzhou +Padang +Bridgeport +Owerri +Zhuanghe +Bobo-Dioulasso +Ad Dammām +Quzhou +Donetsk +Ashmūn +Bunia +Jiaozhou +Campo Grande +Wuchang +São Gonçalo +Bucaramanga +Mérida +Yangchun +Osmangazi +Esenyurt +Morādābād +Bangui +Abeokuta +Cancún +Antipolo +Dengtalu +Taguig City +Tabūk +Zhoushan +Tucson +As Sulaymānīyah +Chihuahua +Klang +Tiruppūr +Gurgaon +Ar Ramādī +Hai’an +Laiyang +Barinas +Jalandhar +Marseille +Kaifeng Chengguanzhen +Eskişehir +Gaomi +Lhasa +Ipoh +El Paso +Saltillo +Dushanbe +Ikeja +El Dorado +Cochabamba +Portsmouth +Tyumen +Southampton +Hermosillo +Wuxi +Leping +Cheongju +Shache +Sale +Hailun +Macheng +Akure +Ilorin +Erbil +Kathmandu +Saratov +Iguaçu +Zijinglu +Turin +Yuci +Dehui +Pietermaritzburg +Durban +Bhubaneshwar +Denpasar +Tongchuan +João Pessoa +Samarinda +Chengxiang +Rongjiawan +Weichanglu +Sakai +Renqiu +Omaha +Xindi +Wu’an +Qingping +Gaoyou +São Bernardo do Campo +Yiyang +Hejian +Puxi +Bhayandar +Androtsy +Culiacán +Cúcuta +Danyang +Dongyang +Kraków +Pasig City +Thessaloníki +Querétaro +Palermo +Xigazê +Qamdo +McAllen +Libreville +Seyhan +San Pedro Sula +Niigata +Hempstead +Leeds +Hamamatsu +Pointe-Noire +Xiangxiang +Birmingham +Chaohucun +Bucheon +Lubango +Homs +Bilbao +Zouping +Frankfurt +San Luis Potosí +Dali +Fuyang +Khŭjand +Korla +Albuquerque +Hamhŭng +Erzurum +Zagreb +Al ‘Ayn +Songzi +Patiāla +Laixi +Zhongba +Bahawalpur +Qingnian +Kaduna +Winnipeg +Trabzon +Guangshui +Baardheere +Shīshgarh +Nerima +Sizhan +Ciudad Guayana +Natal +Lichuan +Licheng +Santo André +Ōta-ku +Gaalkacyo +Thiruvananthapuram +Osasco +Nampula +Pretoria +Kyaukse +Chengguan +Nehe +Cabinda +Kumamoto +Kermān +Zunhua +Orūmīyeh +Wugang +Bağcılar +Quebec City +Shuangqiao +Umraniye +Yanggok +Tshikapa +Tulsa +Osogbo +Comodoro Rivadavia +Nottingham +Hamilton +Langzhong +Cagayan de Oro +Qian’an +Fresno +An Najaf +Cencheng +Sorocaba +Guli +Sagamihara +Pīshbar +Okayama +Anlu +Concepción +Mississauga +Changsha +Songyang +Lviv +Shihezi +Vilnius +Marka +Enugu +Valenzuela +Yatou +Uberlândia +Xichang +Zaporizhzhia +Bhiwandi +George Town +Bristol +Charleston 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[ + 47868 + ], + "data_type": "string", + "chunk_grid": { + "name": "regular", + "configuration": { + "chunk_shape": [ + 1000 + ] + } + }, + "chunk_key_encoding": { + "name": "default", + "configuration": { + "separator": "/" + } + }, + "fill_value": "", + "codecs": [ + { + "name": "https://codec.zarrs.dev/array_to_bytes/vlen_interleaved" + } + ] +} \ No newline at end of file From 495473f939f964f1dce53306716fabf5c635ba18 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Thu, 25 Jul 2024 13:41:10 +1000 Subject: [PATCH 2/6] Fix store value truncation --- CHANGELOG.md | 1 + src/storage/storage_async.rs | 4 +++- src/storage/storage_sync.rs | 4 +++- src/storage/store/store_sync/memory_store.rs | 2 ++ 4 files changed, 9 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2086bd88..03a5a2ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -52,6 +52,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix an unnecessary copy in `async_store_set_partial_values` - Fix error when `bytes` metadata is encoded without a configuration, even if empty - Fix an error in `ChunkGrid` docs + - Fixed `[async_]store_set_partial_values` and `MemoryStore::set` to correctly truncate the bytes of store value if they shrink ## [0.15.1] - 2024-07-11 diff --git a/src/storage/storage_async.rs b/src/storage/storage_async.rs index e4164261..66ff26a2 100644 --- a/src/storage/storage_async.rs +++ b/src/storage/storage_async.rs @@ -204,7 +204,9 @@ pub async fn async_store_set_partial_values( vec.resize_with(end_max, Default::default); vec } else { - bytes.to_vec() + let mut bytes = bytes.to_vec(); + bytes.truncate(end_max); + bytes }; // Update the store key diff --git a/src/storage/store/store_sync/memory_store.rs b/src/storage/store/store_sync/memory_store.rs index ec3061d6..e0833e39 100644 --- a/src/storage/store/store_sync/memory_store.rs +++ b/src/storage/store/store_sync/memory_store.rs @@ -66,6 +66,8 @@ impl MemoryStore { let length = usize::try_from(offset + value.len() as u64).unwrap(); if data.len() < length { data.resize(length, 0); + } else { + data.truncate(length); } let offset = usize::try_from(offset).unwrap(); data[offset..offset + value.len()].copy_from_slice(value); From 222d149ef0df7e4c7fffb200e51094c4bc566ec5 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Thu, 25 Jul 2024 14:05:24 +1000 Subject: [PATCH 3/6] Add `ArraySize::new`, fix `ArrayBytes::new_fill_value`, fix `FillValue::equals_all` with vlen data --- CHANGELOG.md | 1 + src/array/array_async_readable.rs | 20 +++++----- src/array/array_bytes.rs | 39 ++++++++++++------- src/array/array_representation.rs | 14 +++++++ src/array/array_sync_readable.rs | 20 +++++----- src/array/array_sync_sharded_readable_ext.rs | 9 ++--- src/array/chunk_shape.rs | 18 ++++++--- .../array_to_bytes/sharding/sharding_codec.rs | 13 ++++--- .../sharding/sharding_partial_decoder.rs | 20 ++++++++-- .../codec/array_to_bytes/vlen/vlen_codec.rs | 4 ++ .../vlen/vlen_partial_decoder.rs | 10 ++--- .../vlen_interleaved_partial_decoder.rs | 11 +++--- src/array/fill_value.rs | 7 ++++ 13 files changed, 121 insertions(+), 65 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03a5a2ea..86788c58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add `DataType::fixed_size()` that returns `Option`. Returns `None` for variable length data types. - Add `ArrayError::IncompatibleElementType` (replaces `ArrayError::IncompatibleElementSize`) - Add `ArrayError::InvalidElementValue` + - Add `ChunkShape::num_elements_u64` ### Changed - Use `[async_]retrieve_array_subset_opt` internally in `Array::[async_]retrieve_chunks_opt` diff --git a/src/array/array_async_readable.rs b/src/array/array_async_readable.rs index e540e59e..e037d6c3 100644 --- a/src/array/array_async_readable.rs +++ b/src/array/array_async_readable.rs @@ -22,7 +22,7 @@ use super::{ element::ElementOwned, unsafe_cell_slice::UnsafeCellSlice, Array, ArrayBytes, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV2, - ArrayMetadataV3, DataTypeSize, + ArrayMetadataV3, ArraySize, DataTypeSize, }; #[cfg(feature = "ndarray")] @@ -349,11 +349,10 @@ impl Array { if let Some(chunk) = chunk { Ok(chunk) } else { - let chunk_representation = self.chunk_array_representation(chunk_indices)?; - Ok(ArrayBytes::new_fill_value( - chunk_representation.num_elements_usize(), - self.fill_value(), - )) + let chunk_shape = self.chunk_shape(chunk_indices)?; + let array_size = + ArraySize::new(self.data_type().size(), chunk_shape.num_elements_u64()); + Ok(ArrayBytes::new_fill_value(array_size, self.fill_value())) } } @@ -542,10 +541,11 @@ impl Array { // Retrieve chunk bytes let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => Ok(ArrayBytes::new_fill_value( - array_subset.num_elements_usize(), - self.fill_value(), - )), + 0 => { + let array_size = + ArraySize::new(self.data_type().size(), array_subset.num_elements()); + Ok(ArrayBytes::new_fill_value(array_size, self.fill_value())) + } 1 => { let chunk_indices = chunks.start(); let chunk_subset = self.chunk_subset(chunk_indices)?; diff --git a/src/array/array_bytes.rs b/src/array/array_bytes.rs index 5bed39d7..0cd34ea8 100644 --- a/src/array/array_bytes.rs +++ b/src/array/array_bytes.rs @@ -8,7 +8,9 @@ use crate::{ byte_range::extract_byte_ranges_concat_unchecked, }; -use super::{codec::CodecError, ravel_indices, ArrayShape, DataType, DataTypeSize, FillValue}; +use super::{ + codec::CodecError, ravel_indices, ArrayShape, ArraySize, DataType, DataTypeSize, FillValue, +}; /// Array element bytes. pub type RawBytes<'a> = Cow<'a, [u8]>; @@ -50,17 +52,28 @@ impl<'a> ArrayBytes<'a> { } /// Create a new [`ArrayBytes`] with `num_elements` composed entirely of the `fill_value`. + /// + /// # Panics + /// Panics if the number of elements in `array_size` exceeds [`usize::MAX`]. #[must_use] - pub fn new_fill_value(num_elements: usize, fill_value: &FillValue) -> Self { - if fill_value.size() == 0 { - Self::new_vlen( - fill_value.as_ne_bytes().repeat(num_elements), - (0..=num_elements) - .map(|i| i * fill_value.size()) - .collect::>(), - ) - } else { - Self::new_flen(fill_value.as_ne_bytes().repeat(num_elements)) + pub fn new_fill_value(array_size: ArraySize, fill_value: &FillValue) -> Self { + match array_size { + ArraySize::Fixed { + num_elements, + data_type_size: _, + } => { + let num_elements = usize::try_from(num_elements).unwrap(); + Self::new_flen(fill_value.as_ne_bytes().repeat(num_elements)) + } + ArraySize::Variable { num_elements } => { + let num_elements = usize::try_from(num_elements).unwrap(); + Self::new_vlen( + fill_value.as_ne_bytes().repeat(num_elements), + (0..=num_elements) + .map(|i| i * fill_value.size()) + .collect::>(), + ) + } } } @@ -290,9 +303,7 @@ pub(crate) fn update_bytes_vlen<'a>( ) -> ArrayBytes<'a> { // Get the current and new length of the bytes in the chunk subset let size_subset_new = { - let chunk_subset_indices = subset - .relative_to(subset.start()) - .unwrap() + let chunk_subset_indices = ArraySubset::new_with_shape(subset.shape().to_vec()) .linearised_indices(subset.shape()) .unwrap(); chunk_subset_indices diff --git a/src/array/array_representation.rs b/src/array/array_representation.rs index d74a81ab..175c126a 100644 --- a/src/array/array_representation.rs +++ b/src/array/array_representation.rs @@ -44,6 +44,20 @@ pub enum ArraySize { }, } +impl ArraySize { + /// Create a new [`ArraySize`] from a data type size and number of elements. + #[must_use] + pub fn new(data_type_size: DataTypeSize, num_elements: u64) -> Self { + match data_type_size { + DataTypeSize::Fixed(data_type_size) => Self::Fixed { + num_elements, + data_type_size, + }, + DataTypeSize::Variable => Self::Variable { num_elements }, + } + } +} + impl ArrayRepresentationBase where TDim: Into + core::fmt::Debug + Copy, diff --git a/src/array/array_sync_readable.rs b/src/array/array_sync_readable.rs index ecb17187..4b41d968 100644 --- a/src/array/array_sync_readable.rs +++ b/src/array/array_sync_readable.rs @@ -23,7 +23,7 @@ use super::{ concurrency::concurrency_chunks_and_codec, element::ElementOwned, unsafe_cell_slice::UnsafeCellSlice, - Array, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV3, DataTypeSize, + Array, ArrayCreateError, ArrayError, ArrayMetadata, ArrayMetadataV3, ArraySize, DataTypeSize, }; #[cfg(feature = "ndarray")] @@ -484,11 +484,10 @@ impl Array { if let Some(chunk) = chunk { Ok(chunk) } else { - let chunk_representation = self.chunk_array_representation(chunk_indices)?; - Ok(ArrayBytes::new_fill_value( - chunk_representation.num_elements_usize(), - self.fill_value(), - )) + let chunk_shape = self.chunk_shape(chunk_indices)?; + let array_size = + ArraySize::new(self.data_type().size(), chunk_shape.num_elements_u64()); + Ok(ArrayBytes::new_fill_value(array_size, self.fill_value())) } } @@ -625,10 +624,11 @@ impl Array { // Retrieve chunk bytes let num_chunks = chunks.num_elements_usize(); match num_chunks { - 0 => Ok(ArrayBytes::new_fill_value( - array_subset.num_elements_usize(), - self.fill_value(), - )), + 0 => { + let array_size = + ArraySize::new(self.data_type().size(), array_subset.num_elements()); + Ok(ArrayBytes::new_fill_value(array_size, self.fill_value())) + } 1 => { let chunk_indices = chunks.start(); let chunk_subset = self.chunk_subset(chunk_indices)?; diff --git a/src/array/array_sync_sharded_readable_ext.rs b/src/array/array_sync_sharded_readable_ext.rs index 048733db..7c6ac1b2 100644 --- a/src/array/array_sync_sharded_readable_ext.rs +++ b/src/array/array_sync_sharded_readable_ext.rs @@ -9,7 +9,7 @@ use super::{ codec::CodecOptions, concurrency::concurrency_chunks_and_codec, Array, ArrayError, ArrayShardedExt, ChunkGrid, UnsafeCellSlice, }; -use super::{ArrayBytes, DataTypeSize}; +use super::{ArrayBytes, ArraySize, DataTypeSize}; use crate::storage::ReadableStorageTraits; use crate::{array::codec::ArrayPartialDecoderTraits, array_subset::ArraySubset}; @@ -340,10 +340,9 @@ impl ArrayShardedReadableExt // Retrieve chunk bytes let num_shards = shards.num_elements_usize(); if num_shards == 0 { - Ok(ArrayBytes::new_fill_value( - array_subset.num_elements_usize(), - self.fill_value(), - )) + let array_size = + ArraySize::new(self.data_type().size(), array_subset.num_elements()); + Ok(ArrayBytes::new_fill_value(array_size, self.fill_value())) } else { // Calculate chunk/codec concurrency let chunk_representation = diff --git a/src/array/chunk_shape.rs b/src/array/chunk_shape.rs index 1ee384c0..a2edfd0f 100644 --- a/src/array/chunk_shape.rs +++ b/src/array/chunk_shape.rs @@ -17,7 +17,7 @@ impl ChunkShape { pub fn num_elements(&self) -> NonZeroU64 { unsafe { // Multiplying NonZeroU64 must result in NonZeroU64 - NonZeroU64::new_unchecked(self.0.iter().copied().map(NonZeroU64::get).product::()) + NonZeroU64::new_unchecked(self.num_elements_u64()) } } @@ -30,13 +30,19 @@ impl ChunkShape { #[must_use] pub fn num_elements_nonzero_usize(&self) -> NonZeroUsize { unsafe { - NonZeroUsize::new_unchecked( - usize::try_from(self.0.iter().copied().map(NonZeroU64::get).product::()) - .unwrap(), - ) + // Multiplying NonZeroU64 must result in NonZeroUsize + NonZeroUsize::new_unchecked(usize::try_from(self.num_elements_u64()).unwrap()) } } + /// Return the number of elements as a u64. + /// + /// Equal to the product of the components of its shape. + #[must_use] + pub fn num_elements_u64(&self) -> u64 { + self.0.iter().copied().map(NonZeroU64::get).product::() + } + /// Return the number of elements as a usize. /// /// Equal to the product of the components of its shape. @@ -45,7 +51,7 @@ impl ChunkShape { /// Panics if the number of elements exceeds [`usize::MAX`]. #[must_use] pub fn num_elements_usize(&self) -> usize { - usize::try_from(self.0.iter().copied().map(NonZeroU64::get).product::()).unwrap() + usize::try_from(self.num_elements_u64()).unwrap() } } diff --git a/src/array/codec/array_to_bytes/sharding/sharding_codec.rs b/src/array/codec/array_to_bytes/sharding/sharding_codec.rs index 757894bf..134b6709 100644 --- a/src/array/codec/array_to_bytes/sharding/sharding_codec.rs +++ b/src/array/codec/array_to_bytes/sharding/sharding_codec.rs @@ -12,8 +12,8 @@ use crate::{ concurrency::calc_concurrency_outer_inner, transmute_to_bytes_vec, unravel_index, unsafe_cell_slice::UnsafeCellSlice, - ArrayBytes, ArrayMetadataOptions, BytesRepresentation, ChunkRepresentation, ChunkShape, - DataTypeSize, FillValue, RawBytes, + ArrayBytes, ArrayMetadataOptions, ArraySize, BytesRepresentation, ChunkRepresentation, + ChunkShape, DataTypeSize, FillValue, RawBytes, }, array_subset::ArraySubset, metadata::v3::MetadataV3, @@ -221,10 +221,11 @@ impl ArrayToBytesCodecTraits for ShardingCodec { let offset = shard_index[chunk_index * 2]; let size = shard_index[chunk_index * 2 + 1]; let chunk_bytes = if offset == u64::MAX && size == u64::MAX { - ArrayBytes::new_fill_value( - chunk_representation.num_elements_usize(), - chunk_representation.fill_value(), - ) + let array_size = ArraySize::new( + chunk_representation.data_type().size(), + chunk_representation.num_elements(), + ); + ArrayBytes::new_fill_value(array_size, chunk_representation.fill_value()) } else if usize::try_from(offset + size).unwrap() > encoded_shard.len() { return Err(CodecError::Other( "The shard index references out-of-bounds bytes. The chunk may be corrupted." diff --git a/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs b/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs index 17ce5bd2..0b84c263 100644 --- a/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/sharding/sharding_partial_decoder.rs @@ -15,7 +15,7 @@ use crate::{ concurrency::{calc_concurrency_outer_inner, RecommendedConcurrency}, ravel_indices, unsafe_cell_slice::UnsafeCellSlice, - ArrayBytes, ChunkRepresentation, ChunkShape, DataType, DataTypeSize, + ArrayBytes, ArraySize, ChunkRepresentation, ChunkShape, DataType, DataTypeSize, }, byte_range::ByteRange, }; @@ -205,8 +205,12 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { unsafe { array_subset.overlap_unchecked(&chunk_subset) }; let chunk_subset_bytes = if offset == u64::MAX && size == u64::MAX { + let array_size = ArraySize::new( + chunk_representation.data_type().size(), + chunk_subset_overlap.num_elements(), + ); ArrayBytes::new_fill_value( - chunk_subset_overlap.num_elements_usize(), + array_size, chunk_representation.fill_value(), ) } else { @@ -282,8 +286,12 @@ impl ArrayPartialDecoderTraits for ShardingPartialDecoder<'_> { unsafe { array_subset.overlap_unchecked(&chunk_subset) }; let decoded_bytes = if offset == u64::MAX && size == u64::MAX { + let array_size = ArraySize::new( + chunk_representation.data_type().size(), + chunk_subset_overlap.num_elements(), + ); ArrayBytes::new_fill_value( - chunk_subset_overlap.num_elements_usize(), + array_size, chunk_representation.fill_value(), ) } else { @@ -509,8 +517,12 @@ impl AsyncArrayPartialDecoderTraits for AsyncShardingPartialDecoder<'_> { unsafe { array_subset.overlap_unchecked(&chunk_subset) }; let chunk_subset_bytes = if offset == u64::MAX && size == u64::MAX { + let array_size = ArraySize::new( + self.data_type().size(), + chunk_subset_overlap.num_elements(), + ); ArrayBytes::new_fill_value( - chunk_subset_overlap.num_elements_usize(), + array_size, chunk_representation.fill_value(), ) } else { diff --git a/src/array/codec/array_to_bytes/vlen/vlen_codec.rs b/src/array/codec/array_to_bytes/vlen/vlen_codec.rs index fc2e6004..9284715d 100644 --- a/src/array/codec/array_to_bytes/vlen/vlen_codec.rs +++ b/src/array/codec/array_to_bytes/vlen/vlen_codec.rs @@ -120,6 +120,10 @@ impl ArrayToBytesCodecTraits for VlenCodec { decoded_representation.data_type().size(), )?; let (data, offsets) = bytes.into_variable()?; + assert_eq!( + offsets.len(), + decoded_representation.num_elements_usize() + 1 + ); // Encode offsets let num_offsets = diff --git a/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs b/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs index d142a8df..f004a208 100644 --- a/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/vlen/vlen_partial_decoder.rs @@ -9,7 +9,7 @@ use crate::{ ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, CodecOptions, }, - ArrayBytes, ChunkRepresentation, CodecChain, DataType, FillValue, RawBytes, + ArrayBytes, ArraySize, ChunkRepresentation, CodecChain, DataType, FillValue, RawBytes, }, metadata::v3::codec::vlen::VlenIndexDataType, }; @@ -86,10 +86,10 @@ fn decode_vlen_bytes<'a>( // Chunk is empty, all decoded regions are empty let mut output = Vec::with_capacity(decoded_regions.len()); for decoded_region in decoded_regions { - output.push(ArrayBytes::new_fill_value( - decoded_region.num_elements_usize(), - fill_value, - )); + let array_size = ArraySize::Variable { + num_elements: decoded_region.num_elements(), + }; + output.push(ArrayBytes::new_fill_value(array_size, fill_value)); } Ok(output) } diff --git a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs index bb707fb8..04bac67f 100644 --- a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs @@ -5,7 +5,7 @@ use crate::array::{ codec::{ ArrayPartialDecoderTraits, ArraySubset, BytesPartialDecoderTraits, CodecError, CodecOptions, }, - ArrayBytes, ChunkRepresentation, DataType, FillValue, RawBytes, + ArrayBytes, ArraySize, ChunkRepresentation, DataType, DataTypeSize, FillValue, RawBytes, }; #[cfg(feature = "async")] @@ -33,6 +33,7 @@ impl<'a> VlenInterleavedPartialDecoder<'a> { fn decode_vlen_bytes<'a>( bytes: Option, decoded_regions: &[ArraySubset], + data_type_size: DataTypeSize, fill_value: &FillValue, shape: &[u64], ) -> Result>, CodecError> { @@ -44,10 +45,8 @@ fn decode_vlen_bytes<'a>( // Chunk is empty, all decoded regions are empty let mut output = Vec::with_capacity(decoded_regions.len()); for decoded_region in decoded_regions { - output.push(ArrayBytes::new_fill_value( - decoded_region.num_elements_usize(), - fill_value, - )); + let array_size = ArraySize::new(data_type_size, decoded_region.num_elements()); + output.push(ArrayBytes::new_fill_value(array_size, fill_value)); } Ok(output) } @@ -68,6 +67,7 @@ impl ArrayPartialDecoderTraits for VlenInterleavedPartialDecoder<'_> { decode_vlen_bytes( bytes, decoded_regions, + self.decoded_representation.data_type().size(), self.decoded_representation.fill_value(), &self.decoded_representation.shape_u64(), ) @@ -112,6 +112,7 @@ impl AsyncArrayPartialDecoderTraits for AsyncVlenInterleavedPartialDecoder<'_> { decode_vlen_bytes( bytes, decoded_regions, + self.decoded_representation.data_type().size(), self.decoded_representation.fill_value(), &self.decoded_representation.shape_u64(), ) diff --git a/src/array/fill_value.rs b/src/array/fill_value.rs index 70211940..4de19490 100644 --- a/src/array/fill_value.rs +++ b/src/array/fill_value.rs @@ -2,6 +2,8 @@ //! //! See . +use num::Integer; + /// The fill value of the Zarr array. /// /// Provides an element value to use for uninitialised portions of the Zarr array. @@ -169,6 +171,11 @@ impl FillValue { #[allow(clippy::missing_panics_doc)] #[must_use] pub fn equals_all(&self, bytes: &[u8]) -> bool { + // Special cases for variable length data + if !bytes.len().is_multiple_of(&self.0.len()) || bytes.len() < self.0.len() { + return false; + } + match self.0.len() { 0 => bytes.is_empty(), 1 => { From 71b9d784e4e4e839715e15ad65a60bc7914a59b9 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Thu, 25 Jul 2024 14:14:36 +1000 Subject: [PATCH 4/6] Add `array_write_read_string` example --- Cargo.toml | 5 ++ examples/array_write_read_string.rs | 119 ++++++++++++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 examples/array_write_read_string.rs diff --git a/Cargo.toml b/Cargo.toml index c2bbe2cc..348470b5 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -97,6 +97,11 @@ name = "array_write_read_ndarray" required-features = ["ndarray"] doc-scrape-examples = true +[[example]] +name = "array_write_read_string" +required-features = ["ndarray"] +doc-scrape-examples = true + [[example]] name = "async_array_write_read" required-features = ["ndarray", "async", "object_store"] diff --git a/examples/array_write_read_string.rs b/examples/array_write_read_string.rs new file mode 100644 index 00000000..97f1444a --- /dev/null +++ b/examples/array_write_read_string.rs @@ -0,0 +1,119 @@ +use itertools::Itertools; +use ndarray::{array, Array2, ArrayD}; +use zarrs::storage::{ + storage_transformer::{StorageTransformerExtension, UsageLogStorageTransformer}, + ReadableWritableListableStorage, +}; + +fn array_write_read() -> Result<(), Box> { + use std::sync::Arc; + use zarrs::{ + array::{DataType, FillValue}, + array_subset::ArraySubset, + storage::store, + }; + + // Create a store + // let path = tempfile::TempDir::new()?; + // let mut store: ReadableWritableListableStorage = Arc::new(store::FilesystemStore::new(path.path())?); + // let mut store: ReadableWritableListableStorage = Arc::new(store::FilesystemStore::new( + // "tests/data/array_write_read.zarr", + // )?); + let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new()); + if let Some(arg1) = std::env::args().collect::>().get(1) { + if arg1 == "--usage-log" { + let log_writer = Arc::new(std::sync::Mutex::new( + // std::io::BufWriter::new( + std::io::stdout(), + // ) + )); + let usage_log = Arc::new(UsageLogStorageTransformer::new(log_writer, || { + chrono::Utc::now().format("[%T%.3f] ").to_string() + })); + store = usage_log + .clone() + .create_readable_writable_listable_transformer(store); + } + } + + // Create a group + let group_path = "/group"; + let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?; + + // Update group metadata + group + .attributes_mut() + .insert("foo".into(), serde_json::Value::String("bar".into())); + + // Write group metadata to store + group.store_metadata()?; + + println!( + "The group metadata is:\n{}\n", + serde_json::to_string_pretty(&group.metadata()).unwrap() + ); + + // Create an array + let array_path = "/group/array"; + let array = zarrs::array::ArrayBuilder::new( + vec![4, 4], // array shape + DataType::String, + vec![2, 2].try_into()?, // regular chunk shape + FillValue::from("_"), + ) + // .bytes_to_bytes_codecs(vec![]) // uncompressed + .dimension_names(["y", "x"].into()) + // .storage_transformers(vec![].into()) + .build(store.clone(), array_path)?; + + // Write array metadata to store + array.store_metadata()?; + + println!( + "The array metadata is:\n{}\n", + serde_json::to_string_pretty(&array.metadata()).unwrap() + ); + + // Write some chunks + array.store_chunk_ndarray( + &[0, 0], + ArrayD::<&str>::from_shape_vec(vec![2, 2], vec!["a", "bb", "ccc", "dddd"]).unwrap(), + )?; + array.store_chunk_ndarray( + &[0, 1], + ArrayD::<&str>::from_shape_vec(vec![2, 2], vec!["4444", "333", "22", "1"]).unwrap(), + )?; + let subset_all = ArraySubset::new_with_shape(array.shape().to_vec()); + let data_all = array.retrieve_array_subset_ndarray::(&subset_all)?; + println!("store_chunk [0, 0] and [0, 1]:\n{data_all}\n"); + + // Write a subset spanning multiple chunks, including updating chunks already written + let ndarray_subset: Array2<&str> = array![["!", "@@"], ["###", "$$$$"]]; + array.store_array_subset_ndarray( + ArraySubset::new_with_ranges(&[1..3, 1..3]).start(), + ndarray_subset, + )?; + let data_all = array.retrieve_array_subset_ndarray::(&subset_all)?; + println!("store_array_subset [1..3, 1..3]:\nndarray::ArrayD\n{data_all}"); + + // Retrieve bytes directly, convert into a single string allocation, create a &str ndarray + // TODO: Add a convenience function for this? + let data_all = array.retrieve_array_subset(&subset_all)?; + let (bytes, offsets) = data_all.into_variable()?; + let string = String::from_utf8(bytes.into_owned())?; + let elements = offsets + .iter() + .tuple_windows() + .map(|(&curr, &next)| &string[curr..next]) + .collect::>(); + let ndarray = ArrayD::<&str>::from_shape_vec(subset_all.shape_usize(), elements)?; + println!("ndarray::ArrayD<&str>:\n{ndarray}"); + + Ok(()) +} + +fn main() { + if let Err(err) = array_write_read() { + println!("{:?}", err); + } +} From 36c6e8051bfb196afe2d4ea49268714fc35cd2f7 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Thu, 25 Jul 2024 14:22:07 +1000 Subject: [PATCH 5/6] Rename `vlen_interleaved` to `vlen_v2` --- CHANGELOG.md | 4 +- doc/status/codecs.md | 34 ++++++++--------- src/array/array_builder.rs | 2 +- src/array/codec/array_to_bytes.rs | 2 +- .../{vlen_interleaved.rs => vlen_v2.rs} | 26 ++++++------- .../vlen_v2_codec.rs} | 24 ++++++------ .../vlen_v2_partial_decoder.rs} | 12 +++--- src/metadata/array.rs | 10 ++--- src/metadata/v3.rs | 4 +- src/metadata/v3/codec/vlen_interleaved.rs | 37 ------------------- src/metadata/v3/codec/vlen_v2.rs | 37 +++++++++++++++++++ tests/cities.rs | 12 +++--- tests/data/v3/cities.zarr/zarr.json | 2 +- 13 files changed, 103 insertions(+), 103 deletions(-) rename src/array/codec/array_to_bytes/{vlen_interleaved.rs => vlen_v2.rs} (73%) rename src/array/codec/array_to_bytes/{vlen_interleaved/vlen_interleaved_codec.rs => vlen_v2/vlen_v2_codec.rs} (85%) rename src/array/codec/array_to_bytes/{vlen_interleaved/vlen_interleaved_partial_decoder.rs => vlen_v2/vlen_v2_partial_decoder.rs} (91%) delete mode 100644 src/metadata/v3/codec/vlen_interleaved.rs create mode 100644 src/metadata/v3/codec/vlen_v2.rs diff --git a/CHANGELOG.md b/CHANGELOG.md index 86788c58..2ea5d24d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,8 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add `array::Element[Owned]` traits representing array elements - Supports conversion to and from `ArrayBytes` - Add `array::ElementFixedLength` marker trait - - Add experimental `vlen` and `vlen_interleaved` codec for variable length data types - - `vlen_interleaved` is for legacy support of Zarr V2 `vlen-utf8`/`vlen-bytes`/`vlen-array` codecs + - Add experimental `vlen` and `vlen_v2` codec for variable length data types + - `vlen_v2` is for legacy support of Zarr V2 `vlen-utf8`/`vlen-bytes`/`vlen-array` codecs - Add `DataType::{String,Binary}` data types - These are likely to become standardised in the future and are not feature gated - Add `ArraySubset::contains()` diff --git a/doc/status/codecs.md b/doc/status/codecs.md index 205aa0f3..f7a3dd93 100644 --- a/doc/status/codecs.md +++ b/doc/status/codecs.md @@ -1,18 +1,18 @@ -| Codec Type | Codec† | ZEP | V3 | V2 | Feature Flag* | -| -------------- | -------------------------------------- | ----------------- | ------- | ------- | ------------- | -| Array to Array | [transpose] | [ZEP0001] | ✓ | | **transpose** | -| | [bitround] (experimental) | | ✓ | | bitround | -| Array to Bytes | [bytes] | [ZEP0001] | ✓ | | | -| | [sharding_indexed] | [ZEP0002] | ✓ | | **sharding** | -| | [zfp] (experimental) | | ✓ | | zfp | -| | [pcodec] (experimental) | | ✓ | | pcodec | -| | [vlen] (experimental) | | ✓ | | | -| | V3 [vlen_interleaved] (experimental)
V2 vlen-utf8/vlen-bytes/vlen-array | | ✓ | ✓ | | -| Bytes to Bytes | [blosc] | [ZEP0001] | ✓ | ✓ | **blosc** | -| | [gzip] | [ZEP0001] | ✓ | ✓ | **gzip** | -| | [crc32c] | [ZEP0002] | ✓ | | **crc32c** | -| | [zstd] | [zarr-specs #256] | ✓ | | zstd | -| | [bz2] (experimental) | | ✓ | ✓ | bz2 | +| Codec Type | Codec† | ZEP | V3 | V2 | Feature Flag* | +| -------------- | ------------------------------------------------- | ----------------- | ------- | ------- | ------------- | +| Array to Array | [transpose] | [ZEP0001] | ✓ | | **transpose** | +| | [bitround] (experimental) | | ✓ | | bitround | +| Array to Bytes | [bytes] | [ZEP0001] | ✓ | | | +| | [sharding_indexed] | [ZEP0002] | ✓ | | **sharding** | +| | [zfp] (experimental) | | ✓ | | zfp | +| | [pcodec] (experimental) | | ✓ | | pcodec | +| | [vlen] (experimental) | | ✓ | | | +| | [vlen_v2] (experimental)
`vlen-*` in Zarr V2 | | ✓ | ✓ | | +| Bytes to Bytes | [blosc] | [ZEP0001] | ✓ | ✓ | **blosc** | +| | [gzip] | [ZEP0001] | ✓ | ✓ | **gzip** | +| | [crc32c] | [ZEP0002] | ✓ | | **crc32c** | +| | [zstd] | [zarr-specs #256] | ✓ | | zstd | +| | [bz2] (experimental) | | ✓ | ✓ | bz2 | \* Bolded feature flags are part of the default set of features.
@@ -34,7 +34,7 @@ [zstd]: crate::array::codec::bytes_to_bytes::zstd [bz2]: crate::array::codec::bytes_to_bytes::bz2 [vlen]: crate::array::codec::array_to_bytes::vlen -[vlen_interleaved]: crate::array::codec::array_to_bytes::vlen_interleaved +[vlen_v2]: crate::array::codec::array_to_bytes::vlen_v2 The `"name"` of of experimental codecs in array metadata links the codec documentation in this crate. @@ -45,4 +45,4 @@ The `"name"` of of experimental codecs in array metadata links the codec documen | `pcodec` | | | `bz2` | | | `vlen` | | -| `vlen_interleaved` | | +| `vlen_v2` | | diff --git a/src/array/array_builder.rs b/src/array/array_builder.rs index 269d7906..255b8def 100644 --- a/src/array/array_builder.rs +++ b/src/array/array_builder.rs @@ -106,7 +106,7 @@ impl ArrayBuilder { Box::::default() } else { Box::::default() - // Box::::default() + // Box::::default() }, bytes_to_bytes_codecs: Vec::default(), attributes: serde_json::Map::default(), diff --git a/src/array/codec/array_to_bytes.rs b/src/array/codec/array_to_bytes.rs index 765b7544..1d1b75f3 100644 --- a/src/array/codec/array_to_bytes.rs +++ b/src/array/codec/array_to_bytes.rs @@ -3,7 +3,7 @@ pub mod bytes; pub mod codec_chain; pub mod vlen; -pub mod vlen_interleaved; +pub mod vlen_v2; #[cfg(feature = "pcodec")] pub mod pcodec; diff --git a/src/array/codec/array_to_bytes/vlen_interleaved.rs b/src/array/codec/array_to_bytes/vlen_v2.rs similarity index 73% rename from src/array/codec/array_to_bytes/vlen_interleaved.rs rename to src/array/codec/array_to_bytes/vlen_v2.rs index 06d1164d..6c8c9778 100644 --- a/src/array/codec/array_to_bytes/vlen_interleaved.rs +++ b/src/array/codec/array_to_bytes/vlen_v2.rs @@ -1,21 +1,21 @@ -//! The `vlen_interleaved` array to bytes codec. +//! The `vlen_v2` array to bytes codec. -mod vlen_interleaved_codec; -mod vlen_interleaved_partial_decoder; +mod vlen_v2_codec; +mod vlen_v2_partial_decoder; use std::mem::size_of; -pub use vlen_interleaved::IDENTIFIER; +pub use vlen_v2::IDENTIFIER; -pub use crate::metadata::v3::codec::vlen_interleaved::{ - VlenInterleavedCodecConfiguration, VlenInterleavedCodecConfigurationV1, +pub use crate::metadata::v3::codec::vlen_v2::{ + VlenV2CodecConfiguration, VlenV2CodecConfigurationV1, }; use crate::{ array::{codec::CodecError, RawBytes}, - metadata::v3::codec::vlen_interleaved, + metadata::v3::codec::vlen_v2, }; -pub use vlen_interleaved_codec::VlenInterleavedCodec; +pub use vlen_v2_codec::VlenV2Codec; use crate::{ array::codec::{Codec, CodecPlugin}, @@ -25,20 +25,20 @@ use crate::{ // Register the codec. inventory::submit! { - CodecPlugin::new(IDENTIFIER, is_name_vlen_interleaved, create_codec_vlen_interleaved) + CodecPlugin::new(IDENTIFIER, is_name_vlen_v2, create_codec_vlen_v2) } -fn is_name_vlen_interleaved(name: &str) -> bool { +fn is_name_vlen_v2(name: &str) -> bool { name.eq(IDENTIFIER) } -pub(crate) fn create_codec_vlen_interleaved( +pub(crate) fn create_codec_vlen_v2( metadata: &MetadataV3, ) -> Result { - let configuration: VlenInterleavedCodecConfiguration = metadata + let configuration: VlenV2CodecConfiguration = metadata .to_configuration() .map_err(|_| PluginMetadataInvalidError::new(IDENTIFIER, "codec", metadata.clone()))?; - let codec = Box::new(VlenInterleavedCodec::new_with_configuration(&configuration)); + let codec = Box::new(VlenV2Codec::new_with_configuration(&configuration)); Ok(Codec::ArrayToBytes(codec)) } diff --git a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs b/src/array/codec/array_to_bytes/vlen_v2/vlen_v2_codec.rs similarity index 85% rename from src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs rename to src/array/codec/array_to_bytes/vlen_v2/vlen_v2_codec.rs index db610d77..76dba610 100644 --- a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_codec.rs +++ b/src/array/codec/array_to_bytes/vlen_v2/vlen_v2_codec.rs @@ -18,13 +18,13 @@ use crate::{ #[cfg(feature = "async")] use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; -use super::{VlenInterleavedCodecConfiguration, VlenInterleavedCodecConfigurationV1}; +use super::{VlenV2CodecConfiguration, VlenV2CodecConfigurationV1}; -/// The `vlen_interleaved` codec implementation. +/// The `vlen_v2` codec implementation. #[derive(Debug, Clone, Default)] -pub struct VlenInterleavedCodec {} +pub struct VlenV2Codec {} -impl VlenInterleavedCodec { +impl VlenV2Codec { /// Create a new `vlen` codec. #[must_use] pub fn new() -> Self { @@ -33,15 +33,15 @@ impl VlenInterleavedCodec { /// Create a new `vlen` codec from configuration. #[must_use] - pub fn new_with_configuration(_configuration: &VlenInterleavedCodecConfiguration) -> Self { - // let VlenInterleavedCodecConfiguration::V1(configuration) = configuration; + pub fn new_with_configuration(_configuration: &VlenV2CodecConfiguration) -> Self { + // let VlenV2CodecConfiguration::V1(configuration) = configuration; Self {} } } -impl CodecTraits for VlenInterleavedCodec { +impl CodecTraits for VlenV2Codec { fn create_metadata_opt(&self, _options: &ArrayMetadataOptions) -> Option { - let configuration = VlenInterleavedCodecConfigurationV1 {}; + let configuration = VlenV2CodecConfigurationV1 {}; Some( MetadataV3::new_with_serializable_configuration(super::IDENTIFIER, &configuration) .unwrap(), @@ -57,7 +57,7 @@ impl CodecTraits for VlenInterleavedCodec { } } -impl ArrayCodecTraits for VlenInterleavedCodec { +impl ArrayCodecTraits for VlenV2Codec { fn recommended_concurrency( &self, _decoded_representation: &ChunkRepresentation, @@ -67,7 +67,7 @@ impl ArrayCodecTraits for VlenInterleavedCodec { } #[cfg_attr(feature = "async", async_trait::async_trait)] -impl ArrayToBytesCodecTraits for VlenInterleavedCodec { +impl ArrayToBytesCodecTraits for VlenV2Codec { fn encode<'a>( &self, bytes: ArrayBytes<'a>, @@ -118,7 +118,7 @@ impl ArrayToBytesCodecTraits for VlenInterleavedCodec { _options: &CodecOptions, ) -> Result, CodecError> { Ok(Box::new( - super::vlen_interleaved_partial_decoder::VlenInterleavedPartialDecoder::new( + super::vlen_v2_partial_decoder::VlenV2PartialDecoder::new( input_handle, decoded_representation.clone(), ), @@ -133,7 +133,7 @@ impl ArrayToBytesCodecTraits for VlenInterleavedCodec { _options: &CodecOptions, ) -> Result, CodecError> { Ok(Box::new( - super::vlen_interleaved_partial_decoder::AsyncVlenInterleavedPartialDecoder::new( + super::vlen_v2_partial_decoder::AsyncVlenV2PartialDecoder::new( input_handle, decoded_representation.clone(), ), diff --git a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs b/src/array/codec/array_to_bytes/vlen_v2/vlen_v2_partial_decoder.rs similarity index 91% rename from src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs rename to src/array/codec/array_to_bytes/vlen_v2/vlen_v2_partial_decoder.rs index 04bac67f..00b27bca 100644 --- a/src/array/codec/array_to_bytes/vlen_interleaved/vlen_interleaved_partial_decoder.rs +++ b/src/array/codec/array_to_bytes/vlen_v2/vlen_v2_partial_decoder.rs @@ -12,12 +12,12 @@ use crate::array::{ use crate::array::codec::{AsyncArrayPartialDecoderTraits, AsyncBytesPartialDecoderTraits}; /// Partial decoder for the `bytes` codec. -pub struct VlenInterleavedPartialDecoder<'a> { +pub struct VlenV2PartialDecoder<'a> { input_handle: Box, decoded_representation: ChunkRepresentation, } -impl<'a> VlenInterleavedPartialDecoder<'a> { +impl<'a> VlenV2PartialDecoder<'a> { /// Create a new partial decoder for the `bytes` codec. pub fn new( input_handle: Box, @@ -52,7 +52,7 @@ fn decode_vlen_bytes<'a>( } } -impl ArrayPartialDecoderTraits for VlenInterleavedPartialDecoder<'_> { +impl ArrayPartialDecoderTraits for VlenV2PartialDecoder<'_> { fn data_type(&self) -> &DataType { self.decoded_representation.data_type() } @@ -76,13 +76,13 @@ impl ArrayPartialDecoderTraits for VlenInterleavedPartialDecoder<'_> { #[cfg(feature = "async")] /// Asynchronous partial decoder for the `bytes` codec. -pub struct AsyncVlenInterleavedPartialDecoder<'a> { +pub struct AsyncVlenV2PartialDecoder<'a> { input_handle: Box, decoded_representation: ChunkRepresentation, } #[cfg(feature = "async")] -impl<'a> AsyncVlenInterleavedPartialDecoder<'a> { +impl<'a> AsyncVlenV2PartialDecoder<'a> { /// Create a new partial decoder for the `bytes` codec. pub fn new( input_handle: Box, @@ -97,7 +97,7 @@ impl<'a> AsyncVlenInterleavedPartialDecoder<'a> { #[cfg(feature = "async")] #[async_trait::async_trait] -impl AsyncArrayPartialDecoderTraits for AsyncVlenInterleavedPartialDecoder<'_> { +impl AsyncArrayPartialDecoderTraits for AsyncVlenV2PartialDecoder<'_> { fn data_type(&self) -> &DataType { self.decoded_representation.data_type() } diff --git a/src/metadata/array.rs b/src/metadata/array.rs index 1573bb61..09f9ca8c 100644 --- a/src/metadata/array.rs +++ b/src/metadata/array.rs @@ -12,7 +12,7 @@ use super::{ }, codec::blosc::{codec_blosc_v2_numcodecs_to_v3, BloscCodecConfigurationNumcodecs}, }, - v3::codec::vlen_interleaved::VlenInterleavedCodecConfigurationV1, + v3::codec::vlen_v2::VlenV2CodecConfigurationV1, }; use thiserror::Error; @@ -148,12 +148,12 @@ pub fn array_metadata_v2_to_v3( match filter.id() { "vlen-utf8" | "vlen-bytes" | "vlen-array" => { is_vlen = true; - let vlen_interleaved_metadata = + let vlen_v2_metadata = MetadataV3::new_with_serializable_configuration( - super::v3::codec::vlen_interleaved::IDENTIFIER, - &VlenInterleavedCodecConfigurationV1 {}, + super::v3::codec::vlen_v2::IDENTIFIER, + &VlenV2CodecConfigurationV1 {}, )?; - codecs.push(vlen_interleaved_metadata); + codecs.push(vlen_v2_metadata); } _ => { codecs.push(MetadataV3::new_with_configuration( diff --git a/src/metadata/v3.rs b/src/metadata/v3.rs index 27b908d5..4924a09b 100644 --- a/src/metadata/v3.rs +++ b/src/metadata/v3.rs @@ -29,8 +29,8 @@ pub mod codec { pub mod transpose; /// `vlen` codec metadata. pub mod vlen; - /// `vlen_interleaved` codec metadata. - pub mod vlen_interleaved; + /// `vlen_v2` codec metadata. + pub mod vlen_v2; #[cfg(feature = "zfp")] /// `zfp` codec metadata. pub mod zfp; diff --git a/src/metadata/v3/codec/vlen_interleaved.rs b/src/metadata/v3/codec/vlen_interleaved.rs deleted file mode 100644 index fa19a401..00000000 --- a/src/metadata/v3/codec/vlen_interleaved.rs +++ /dev/null @@ -1,37 +0,0 @@ -use derive_more::{Display, From}; -use serde::{Deserialize, Serialize}; - -/// The identifier for the `vlen_interleaved` codec. -pub const IDENTIFIER: &str = "https://codec.zarrs.dev/array_to_bytes/vlen_interleaved"; - -/// A wrapper to handle various versions of `vlen_interleaved` codec configuration parameters. -#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, From)] -#[serde(untagged)] -pub enum VlenInterleavedCodecConfiguration { - /// Version 1.0. - V1(VlenInterleavedCodecConfigurationV1), -} - -/// Configuration parameters for the `vlen_interleaved` codec (version 1.0). -#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, Default)] -#[serde(deny_unknown_fields)] -#[display(fmt = "{}", "serde_json::to_string(self).unwrap_or_default()")] -pub struct VlenInterleavedCodecConfigurationV1 {} - -impl VlenInterleavedCodecConfigurationV1 { - /// Create a new `vlen_interleaved` codec configuration. - #[must_use] - pub const fn new() -> Self { - Self {} - } -} - -#[cfg(test)] -mod tests { - use super::*; - - #[test] - fn codec_vlen_interleaved() { - serde_json::from_str::(r#"{}"#).unwrap(); - } -} diff --git a/src/metadata/v3/codec/vlen_v2.rs b/src/metadata/v3/codec/vlen_v2.rs new file mode 100644 index 00000000..373a6cf8 --- /dev/null +++ b/src/metadata/v3/codec/vlen_v2.rs @@ -0,0 +1,37 @@ +use derive_more::{Display, From}; +use serde::{Deserialize, Serialize}; + +/// The identifier for the `vlen_v2` codec. +pub const IDENTIFIER: &str = "https://codec.zarrs.dev/array_to_bytes/vlen_v2"; + +/// A wrapper to handle various versions of `vlen_v2` codec configuration parameters. +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, From)] +#[serde(untagged)] +pub enum VlenV2CodecConfiguration { + /// Version 1.0. + V1(VlenV2CodecConfigurationV1), +} + +/// Configuration parameters for the `vlen_v2` codec (version 1.0). +#[derive(Serialize, Deserialize, Clone, Eq, PartialEq, Debug, Display, Default)] +#[serde(deny_unknown_fields)] +#[display(fmt = "{}", "serde_json::to_string(self).unwrap_or_default()")] +pub struct VlenV2CodecConfigurationV1 {} + +impl VlenV2CodecConfigurationV1 { + /// Create a new `vlen_v2` codec configuration. + #[must_use] + pub const fn new() -> Self { + Self {} + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn codec_vlen_v2() { + serde_json::from_str::(r#"{}"#).unwrap(); + } +} diff --git a/tests/cities.rs b/tests/cities.rs index 0af6afc5..d12e0244 100644 --- a/tests/cities.rs +++ b/tests/cities.rs @@ -9,7 +9,7 @@ use zarrs::{ codec::{ array_to_bytes::{ sharding::ShardingCodecBuilder, vlen::VlenCodec, - vlen_interleaved::VlenInterleavedCodec, + vlen_v2::VlenV2Codec, }, ArrayToBytesCodecTraits, ZstdCodec, }, @@ -95,7 +95,7 @@ fn cities() -> Result<(), Box> { assert_eq!(cities[47862], "Sariwŏn-si"); assert_eq!(cities[47867], "Charlotte Amalie"); - let vlen_interleaved = Box::new(VlenInterleavedCodec::default()); + let vlen_v2 = Box::new(VlenV2Codec::default()); // let vlen = Box::new(VlenCodec::default()); let vlen_configuration: VlenCodecConfiguration = serde_json::from_str(r#"{ @@ -114,8 +114,8 @@ fn cities() -> Result<(), Box> { print!("| encoding | compression | size |\n"); print!("| ---------------- | ----------- | ------ |\n"); - print!("| vlen_interleaved | | {} |\n", cities_impl(&cities, None, 1000, None, vlen_interleaved.clone(), true)?); - print!("| vlen_interleaved | zstd 5 | {} |\n", cities_impl(&cities, Some(5), 1000, None, vlen_interleaved.clone(), false)?); + print!("| vlen_v2 | | {} |\n", cities_impl(&cities, None, 1000, None, vlen_v2.clone(), true)?); + print!("| vlen_v2 | zstd 5 | {} |\n", cities_impl(&cities, Some(5), 1000, None, vlen_v2.clone(), false)?); print!("| vlen | | {} |\n", cities_impl(&cities, None, 1000, None, vlen.clone(), false)?); print!("| vlen | zstd 5 | {} |\n", cities_impl(&cities, None, 1000, None, vlen_compressed.clone(), false)?); println!(); @@ -123,8 +123,8 @@ fn cities() -> Result<(), Box> { // | encoding | compression | size | // | ---------------- | ----------- | ------ | - // | vlen_interleaved | | 642196 | - // | vlen_interleaved | zstd 5 | 362626 | + // | vlen_v2 | | 642196 | + // | vlen_v2 | zstd 5 | 362626 | // | vlen | | 642580 | // | vlen | zstd 5 | 346950 | diff --git a/tests/data/v3/cities.zarr/zarr.json b/tests/data/v3/cities.zarr/zarr.json index 90ba194e..f4e5a16e 100644 --- a/tests/data/v3/cities.zarr/zarr.json +++ b/tests/data/v3/cities.zarr/zarr.json @@ -22,7 +22,7 @@ "fill_value": "", "codecs": [ { - "name": "https://codec.zarrs.dev/array_to_bytes/vlen_interleaved" + "name": "https://codec.zarrs.dev/array_to_bytes/vlen_v2" } ] } \ No newline at end of file From 16b6c2f2e66578dc897170c8c80648ce130697d0 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Thu, 25 Jul 2024 14:23:12 +1000 Subject: [PATCH 6/6] Fmt pass --- src/array/codec/array_to_bytes/vlen_v2.rs | 4 +--- src/metadata/array.rs | 9 ++++----- tests/cities.rs | 3 +-- 3 files changed, 6 insertions(+), 10 deletions(-) diff --git a/src/array/codec/array_to_bytes/vlen_v2.rs b/src/array/codec/array_to_bytes/vlen_v2.rs index 6c8c9778..d4d2a2c5 100644 --- a/src/array/codec/array_to_bytes/vlen_v2.rs +++ b/src/array/codec/array_to_bytes/vlen_v2.rs @@ -32,9 +32,7 @@ fn is_name_vlen_v2(name: &str) -> bool { name.eq(IDENTIFIER) } -pub(crate) fn create_codec_vlen_v2( - metadata: &MetadataV3, -) -> Result { +pub(crate) fn create_codec_vlen_v2(metadata: &MetadataV3) -> Result { let configuration: VlenV2CodecConfiguration = metadata .to_configuration() .map_err(|_| PluginMetadataInvalidError::new(IDENTIFIER, "codec", metadata.clone()))?; diff --git a/src/metadata/array.rs b/src/metadata/array.rs index 09f9ca8c..57d29652 100644 --- a/src/metadata/array.rs +++ b/src/metadata/array.rs @@ -148,11 +148,10 @@ pub fn array_metadata_v2_to_v3( match filter.id() { "vlen-utf8" | "vlen-bytes" | "vlen-array" => { is_vlen = true; - let vlen_v2_metadata = - MetadataV3::new_with_serializable_configuration( - super::v3::codec::vlen_v2::IDENTIFIER, - &VlenV2CodecConfigurationV1 {}, - )?; + let vlen_v2_metadata = MetadataV3::new_with_serializable_configuration( + super::v3::codec::vlen_v2::IDENTIFIER, + &VlenV2CodecConfigurationV1 {}, + )?; codecs.push(vlen_v2_metadata); } _ => { diff --git a/tests/cities.rs b/tests/cities.rs index d12e0244..08a544e0 100644 --- a/tests/cities.rs +++ b/tests/cities.rs @@ -8,8 +8,7 @@ use zarrs::{ array::{ codec::{ array_to_bytes::{ - sharding::ShardingCodecBuilder, vlen::VlenCodec, - vlen_v2::VlenV2Codec, + sharding::ShardingCodecBuilder, vlen::VlenCodec, vlen_v2::VlenV2Codec, }, ArrayToBytesCodecTraits, ZstdCodec, },