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//! Zarr arrays.
//!
//! An array is a node in a Zarr hierarchy used to hold multidimensional array data and associated metadata.
//! See <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#array>.
//!
//! Use [`ArrayBuilder`] to setup a new array, or use [`Array::new`] for an existing array.
//! The documentation for [`Array`] details how to interact with arrays.
mod array_builder;
mod array_errors;
mod array_metadata;
mod array_metadata_options;
mod array_representation;
mod array_view;
mod bytes_representation;
pub mod chunk_grid;
pub mod chunk_key_encoding;
mod chunk_shape;
pub mod codec;
pub mod concurrency;
pub mod data_type;
mod dimension_name;
mod fill_value;
mod fill_value_metadata;
mod nan_representations;
mod unsafe_cell_slice;
#[cfg(feature = "sharding")]
mod array_sharded_ext;
#[cfg(feature = "sharding")]
mod array_sync_sharded_readable_ext;
use std::sync::Arc;
pub use self::{
array_builder::ArrayBuilder,
array_errors::{ArrayCreateError, ArrayError},
array_metadata::{ArrayMetadata, ArrayMetadataV3},
array_metadata_options::ArrayMetadataOptions,
array_representation::{ArrayRepresentation, ChunkRepresentation},
array_view::{ArrayView, ArrayViewCreateError},
bytes_representation::BytesRepresentation,
chunk_grid::ChunkGrid,
chunk_key_encoding::ChunkKeyEncoding,
chunk_shape::{chunk_shape_to_array_shape, ChunkShape},
codec::ArrayCodecTraits,
codec::CodecChain,
concurrency::RecommendedConcurrency,
data_type::DataType,
dimension_name::DimensionName,
fill_value::FillValue,
fill_value_metadata::FillValueMetadata,
nan_representations::{ZARR_NAN_BF16, ZARR_NAN_F16, ZARR_NAN_F32, ZARR_NAN_F64},
unsafe_cell_slice::UnsafeCellSlice,
};
#[cfg(feature = "sharding")]
pub use array_sharded_ext::ArrayShardedExt;
#[cfg(feature = "sharding")]
pub use array_sync_sharded_readable_ext::{ArrayShardedReadableExt, ArrayShardedReadableExtCache};
// TODO: Add AsyncArrayShardedReadableExt and AsyncArrayShardedReadableExtCache
use serde::Serialize;
use thiserror::Error;
use crate::{
array_subset::{ArraySubset, IncompatibleDimensionalityError},
metadata::AdditionalFields,
node::NodePath,
storage::storage_transformer::StorageTransformerChain,
};
/// An ND index to an element in an array.
pub type ArrayIndices = Vec<u64>;
/// The shape of an array.
pub type ArrayShape = Vec<u64>;
/// A non zero error.
///
/// This is used in cases where a non-zero type cannot be converted to its equivalent integer type (e.g. [`NonZeroU64`](std::num::NonZeroU64) to [`u64`]).
/// It is used in the [`ChunkShape`] `try_from` methods.
#[derive(Debug, Error)]
#[error("value must be non-zero")]
pub struct NonZeroError;
/// An alias for bytes which may or may not be available.
///
/// When a value is read from a store, it returns `MaybeBytes` which is [`None`] if the key is not available.
/// A bytes to bytes codec only decodes `MaybeBytes` holding actual bytes, otherwise the bytes are propagated to the next decoder.
/// An array to bytes partial decoder must take care of converting missing chunks to the fill value.
pub type MaybeBytes = Option<Vec<u8>>;
/// A Zarr array.
///
/// See <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#array-metadata>.
///
/// ### Metadata
///
/// An array is defined by the following parameters (which are encoded in its JSON metadata):
/// - **shape**: defines the length of the array dimensions,
/// - **data type**: defines the numerical representation array elements,
/// - **chunk grid**: defines how the array is subdivided into chunks,
/// - **chunk key encoding**: defines how chunk grid cell coordinates are mapped to keys in a store,
/// - **fill value**: an element value to use for uninitialised portions of the array.
/// - **codecs**: used to encode and decode chunks,
///
/// and optional parameters:
/// - **attributes**: user-defined attributes,
/// - **storage transformers**: used to intercept and alter the storage keys and bytes of an array before they reach the underlying physical storage, and
/// - **dimension names**: defines the names of the array dimensions.
///
/// See <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html#array-metadata> for more information on array metadata.
///
/// ### Initilisation
///
/// A *new* array can be initialised with an [`ArrayBuilder`] or [`Array::new_with_metadata`].
///
/// An *existing* array can be initialised with [`Array::new`], its metadata is read from the store.
///
/// The `shape` and `attributes` of an array are mutable and can be updated after construction.
/// However, array metadata must be written explicitly to the store with [`store_metadata`](Array<WritableStorageTraits>::store_metadata) if an array is newly created or its metadata has been mutated.
///
/// ### Methods
///
/// #### Sync API
/// Array operations are divided into several categories based on the traits implemented for the backing [storage](crate::storage).
/// The core array methods are:
/// - [`ReadableStorageTraits`](crate::storage::ReadableStorageTraits): read array data and metadata
/// - [`new`](Array::new)
/// - [`retrieve_chunk_if_exists`](Array::retrieve_chunk_if_exists)
/// - [`retrieve_chunk`](Array::retrieve_chunk)
/// - [`retrieve_chunk_into_array_view`](Array::retrieve_chunk_into_array_view)
/// - [`retrieve_chunks`](Array::retrieve_chunks)
/// - [`retrieve_chunks_into_array_view`](Array::retrieve_chunks_into_array_view)
/// - [`retrieve_chunk_subset`](Array::retrieve_chunk_subset)
/// - [`retrieve_chunk_subset_into_array_view`](Array::retrieve_chunk_subset_into_array_view)
/// - [`retrieve_array_subset`](Array::retrieve_array_subset)
/// - [`retrieve_array_subset_into_array_view`](Array::retrieve_array_subset_into_array_view)
/// - [`partial_decoder`](Array::partial_decoder)
/// - [`WritableStorageTraits`](crate::storage::WritableStorageTraits): store/erase array data and store metadata
/// - [`store_metadata`](Array::store_metadata)
/// - [`store_chunk`](Array::store_chunk)
/// - [`store_chunks`](Array::store_chunks)
/// - [`erase_chunk`](Array::erase_chunk)
/// - [`erase_chunks`](Array::erase_chunks)
/// - [`ReadableWritableStorageTraits`](crate::storage::ReadableWritableStorageTraits): store operations requiring reading
/// - [`store_chunk_subset`](Array::store_chunk_subset)
/// - [`store_array_subset`](Array::store_array_subset)
///
/// All `retrieve` and `store` methods have multiple variants:
/// - Standard variants store or retrieve data represented as bytes.
/// - `_elements` suffix variants can store or retrieve chunks with a known type.
/// - `_ndarray` suffix variants can store or retrieve [`ndarray::Array`]s (requires `ndarray` feature).
/// - Retrieve and store methods have an `_opt` variant with an additional [`CodecOptions`](crate::array::codec::CodecOptions) argument for fine-grained concurrency control.
/// - Variants without the `_opt` suffix use default [`CodecOptions`](crate::array::codec::CodecOptions) which just maximises concurrent operations. This is preferred unless using external parallelisation.
///
/// #### Async API
/// With the `async` feature and an async store, there are equivalent methods to the sync API with an `async_` prefix.
///
/// <div class="warning">
/// The async API is not as performant as the sync API.
/// </div>
///
/// This crate is async runtime-agnostic and does not spawn tasks internally.
/// The implication is that methods like [`async_retrieve_array_subset`](Array::async_retrieve_array_subset) or [`async_retrieve_chunks`](Array::async_retrieve_chunks) do not parallelise over chunks and can be slow compared to the sync API (especially when they involve a large number of chunks).
///
/// This limitation can be circumvented by spawning tasks outside of zarrs.
/// For example, instead of using [`async_retrieve_chunks`](Array::async_retrieve_chunks), multiple tasks executing [`async_retrieve_chunk_into_array_view`](Array::async_retrieve_chunk_into_array_view) could be spawned that output to a preallocated buffer.
/// An example of such an approach can be found in the [`zarrs_benchmark_read_async`](https://github.com/LDeakin/zarrs_tools/blob/v0.3.0/src/bin/zarrs_benchmark_read_async.rs) application in the [zarrs_tools](https://github.com/LDeakin/zarrs_tools) crate.
///
/// ### Parallel Writing
/// If a chunk is written more than once, its element values depend on whichever operation wrote to the chunk last.
/// The [`ReadableWritableStorageTraits`](crate::storage::ReadableWritableStorageTraits) [`store_chunk_subset`](Array::store_chunk_subset) and [`store_array_subset`](Array::store_array_subset) methods and their variants internally retrieve a chunk, update it, then store it.
/// It is the responsibility of zarrs consumers to ensure that:
/// - [`Array::store_chunk_subset`] is not called concurrently on the same chunk, and
/// - [`Array::store_array_subset`] is not called concurrently on regions sharing chunks.
///
/// Partial writes to a chunk may be lost if these rules are not respected.
///
/// zarrs does not currently offer an API for locking chunks or regions.
///
/// ### Best Practices
///
/// #### Writing
/// For optimum write performance, an array should be written using [`store_chunk`](Array::store_chunk) or [`store_chunks`](Array::store_chunks) where possible.
/// The [`store_chunk_subset`](Array::store_chunk_subset) and [`store_array_subset`](Array::store_array_subset) are less preferred because they may incur decoding overhead and require careful usage if executed concurrently (see previous section).
///
/// #### Reading
/// It is fastest to load arrays using [`retrieve_chunk`](Array::retrieve_chunk) or [`retrieve_chunks`](Array::retrieve_chunks) where possible.
/// In contrast, the [`retrieve_chunk_subset`](Array::retrieve_chunk_subset) and [`retrieve_array_subset`](Array::retrieve_array_subset) may use partial decoders which can be less efficient with some codecs/stores.
///
/// ### `zarrs` Metadata
/// By default, the `zarrs` version and a link to its source code is written to the `_zarrs` attribute in array metadata.
/// This can be disabled with [`set_include_zarrs_metadata(false)`](Array::set_include_zarrs_metadata).
#[derive(Debug)]
pub struct Array<TStorage: ?Sized> {
/// The storage (including storage transformers).
storage: Arc<TStorage>,
/// The path of the array in a store.
path: NodePath,
/// An array of integers providing the length of each dimension of the Zarr array.
shape: ArrayShape,
/// The data type of the Zarr array.
data_type: DataType,
/// The chunk grid of the Zarr array.
chunk_grid: ChunkGrid,
/// The mapping from chunk grid cell coordinates to keys in the underlying store.
chunk_key_encoding: ChunkKeyEncoding,
/// Provides an element value to use for uninitialised portions of the Zarr array. It encodes the underlying data type.
fill_value: FillValue,
/// Specifies a list of codecs to be used for encoding and decoding chunks.
codecs: CodecChain,
/// Optional user defined attributes.
attributes: serde_json::Map<String, serde_json::Value>,
/// An optional list of storage transformers.
storage_transformers: StorageTransformerChain,
/// An optional list of dimension names.
dimension_names: Option<Vec<DimensionName>>,
/// Additional fields annotated with `"must_understand": false`.
additional_fields: AdditionalFields,
/// Zarrs metadata.
include_zarrs_metadata: bool,
}
impl<TStorage: ?Sized> Array<TStorage> {
/// Create an array in `storage` at `path` with `metadata`.
/// This does **not** write to the store, use [`store_metadata`](Array<WritableStorageTraits>::store_metadata) to write `metadata` to `storage`.
///
/// # Errors
/// Returns [`ArrayCreateError`] if:
/// - any metadata is invalid or,
/// - a plugin (e.g. data type/chunk grid/chunk key encoding/codec/storage transformer) is invalid.
pub fn new_with_metadata(
storage: Arc<TStorage>,
path: &str,
metadata: ArrayMetadata,
) -> Result<Self, ArrayCreateError> {
let path = NodePath::new(path)?;
let ArrayMetadata::V3(metadata) = metadata;
if !metadata.validate_format() {
return Err(ArrayCreateError::InvalidZarrFormat(metadata.zarr_format));
}
if !metadata.validate_node_type() {
return Err(ArrayCreateError::InvalidNodeType(metadata.node_type));
}
metadata
.additional_fields
.validate()
.map_err(ArrayCreateError::UnsupportedAdditionalFieldError)?;
let data_type = DataType::from_metadata(&metadata.data_type)
.map_err(ArrayCreateError::DataTypeCreateError)?;
let chunk_grid = ChunkGrid::from_metadata(&metadata.chunk_grid)
.map_err(ArrayCreateError::ChunkGridCreateError)?;
if chunk_grid.dimensionality() != metadata.shape.len() {
return Err(ArrayCreateError::InvalidChunkGridDimensionality(
chunk_grid.dimensionality(),
metadata.shape.len(),
));
}
let fill_value = data_type
.fill_value_from_metadata(&metadata.fill_value)
.map_err(ArrayCreateError::InvalidFillValueMetadata)?;
let codecs = CodecChain::from_metadata(&metadata.codecs)
.map_err(ArrayCreateError::CodecsCreateError)?;
let storage_transformers =
StorageTransformerChain::from_metadata(&metadata.storage_transformers)
.map_err(ArrayCreateError::StorageTransformersCreateError)?;
let chunk_key_encoding = ChunkKeyEncoding::from_metadata(&metadata.chunk_key_encoding)
.map_err(ArrayCreateError::ChunkKeyEncodingCreateError)?;
if let Some(dimension_names) = &metadata.dimension_names {
if dimension_names.len() != metadata.shape.len() {
return Err(ArrayCreateError::InvalidDimensionNames(
dimension_names.len(),
metadata.shape.len(),
));
}
}
Ok(Self {
storage,
path,
shape: metadata.shape,
data_type,
chunk_grid,
chunk_key_encoding,
fill_value,
codecs,
attributes: metadata.attributes,
additional_fields: metadata.additional_fields,
storage_transformers,
dimension_names: metadata.dimension_names,
include_zarrs_metadata: true,
})
}
/// Set the shape of the array.
pub fn set_shape(&mut self, shape: ArrayShape) {
self.shape = shape;
}
/// Mutably borrow the array attributes.
#[must_use]
pub fn attributes_mut(&mut self) -> &mut serde_json::Map<String, serde_json::Value> {
&mut self.attributes
}
/// Get the node path.
#[must_use]
pub const fn path(&self) -> &NodePath {
&self.path
}
/// Get the data type.
#[must_use]
pub const fn data_type(&self) -> &DataType {
&self.data_type
}
/// Get the fill value.
#[must_use]
pub const fn fill_value(&self) -> &FillValue {
&self.fill_value
}
/// Get the array shape.
#[must_use]
pub fn shape(&self) -> &[u64] {
&self.shape
}
/// Get the array dimensionality.
#[must_use]
pub fn dimensionality(&self) -> usize {
self.shape.len()
}
/// Get the codecs.
#[must_use]
pub const fn codecs(&self) -> &CodecChain {
&self.codecs
}
/// Get the chunk grid.
#[must_use]
pub const fn chunk_grid(&self) -> &ChunkGrid {
&self.chunk_grid
}
/// Get the chunk key encoding.
#[must_use]
pub const fn chunk_key_encoding(&self) -> &ChunkKeyEncoding {
&self.chunk_key_encoding
}
/// Get the storage transformers.
#[must_use]
pub const fn storage_transformers(&self) -> &StorageTransformerChain {
&self.storage_transformers
}
/// Get the dimension names.
#[must_use]
pub const fn dimension_names(&self) -> &Option<Vec<DimensionName>> {
&self.dimension_names
}
/// Get the attributes.
#[must_use]
pub const fn attributes(&self) -> &serde_json::Map<String, serde_json::Value> {
&self.attributes
}
/// Get the additional fields.
#[must_use]
pub const fn additional_fields(&self) -> &AdditionalFields {
&self.additional_fields
}
/// Enable or disable the inclusion of zarrs metadata in the array attributes. Enabled by default.
///
/// Zarrs metadata includes the zarrs version and some parameters.
pub fn set_include_zarrs_metadata(&mut self, include_zarrs_metadata: bool) {
self.include_zarrs_metadata = include_zarrs_metadata;
}
/// Create [`ArrayMetadata`].
#[must_use]
pub fn metadata_opt(&self, options: &ArrayMetadataOptions) -> ArrayMetadata {
let attributes = if self.include_zarrs_metadata {
#[derive(Serialize)]
struct ZarrsMetadata {
description: String,
repository: String,
version: String,
}
let zarrs_metadata = ZarrsMetadata {
description: "This array was created with zarrs".to_string(),
repository: env!("CARGO_PKG_REPOSITORY").to_string(),
version: env!("CARGO_PKG_VERSION").to_string(),
};
let mut attributes = self.attributes().clone();
attributes.insert("_zarrs".to_string(), unsafe {
serde_json::to_value(zarrs_metadata).unwrap_unchecked()
});
attributes
} else {
self.attributes().clone()
};
ArrayMetadataV3::new(
self.shape().to_vec(),
self.data_type().metadata(),
self.chunk_grid().create_metadata(),
self.chunk_key_encoding().create_metadata(),
self.data_type().metadata_fill_value(self.fill_value()),
self.codecs().create_metadatas_opt(options),
attributes,
self.storage_transformers().create_metadatas(),
self.dimension_names().clone(),
self.additional_fields().clone(),
)
.into()
}
/// Create [`ArrayMetadata`] with default options.
#[must_use]
pub fn metadata(&self) -> ArrayMetadata {
self.metadata_opt(&ArrayMetadataOptions::default())
}
/// Create an array builder matching the parameters of this array.
#[must_use]
pub fn builder(&self) -> ArrayBuilder {
ArrayBuilder::from_array(self)
}
/// Return the shape of the chunk grid (i.e., the number of chunks).
#[must_use]
pub fn chunk_grid_shape(&self) -> Option<ArrayShape> {
unsafe { self.chunk_grid().grid_shape_unchecked(self.shape()) }
}
/// Return the origin of the chunk at `chunk_indices`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunk_origin(&self, chunk_indices: &[u64]) -> Result<ArrayIndices, ArrayError> {
self.chunk_grid()
.chunk_origin(chunk_indices, self.shape())
.map_err(|_| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))?
.ok_or_else(|| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))
}
/// Return the shape of the chunk at `chunk_indices`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunk_shape(&self, chunk_indices: &[u64]) -> Result<ChunkShape, ArrayError> {
self.chunk_grid()
.chunk_shape(chunk_indices, self.shape())
.map_err(|_| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))?
.ok_or_else(|| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))
}
/// Return the shape of the chunk at `chunk_indices`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
///
/// # Panics
/// Panics if any component of the chunk shape exceeds [`usize::MAX`].
pub fn chunk_shape_usize(&self, chunk_indices: &[u64]) -> Result<Vec<usize>, ArrayError> {
Ok(self
.chunk_shape(chunk_indices)?
.iter()
.map(|d| usize::try_from(d.get()).unwrap())
.collect())
}
/// Return the array subset of the chunk at `chunk_indices`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunk_subset(&self, chunk_indices: &[u64]) -> Result<ArraySubset, ArrayError> {
self.chunk_grid()
.subset(chunk_indices, self.shape())
.map_err(|_| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))?
.ok_or_else(|| ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec()))
}
/// Return the array subset of the chunk at `chunk_indices` bounded by the array shape.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunk_subset_bounded(&self, chunk_indices: &[u64]) -> Result<ArraySubset, ArrayError> {
let chunk_subset = self.chunk_subset(chunk_indices)?;
Ok(unsafe { chunk_subset.bound_unchecked(self.shape()) })
}
/// Return the array subset of `chunks`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if a chunk in `chunks` is incompatible with the chunk grid.
#[allow(clippy::similar_names)]
pub fn chunks_subset(&self, chunks: &ArraySubset) -> Result<ArraySubset, ArrayError> {
match chunks.end_inc() {
Some(end) => {
let chunk0 = self.chunk_subset(chunks.start())?;
let chunk1 = self.chunk_subset(&end)?;
let start = chunk0.start();
let end = chunk1.end_exc();
Ok(unsafe { ArraySubset::new_with_start_end_exc_unchecked(start.to_vec(), end) })
}
None => Ok(ArraySubset::new_empty(chunks.dimensionality())),
}
}
/// Return the array subset of `chunks` bounded by the array shape.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunks_subset_bounded(&self, chunks: &ArraySubset) -> Result<ArraySubset, ArrayError> {
let chunks_subset = self.chunks_subset(chunks)?;
Ok(unsafe { chunks_subset.bound_unchecked(self.shape()) })
}
/// Get the chunk array representation at `chunk_index`.
///
/// # Errors
/// Returns [`ArrayError::InvalidChunkGridIndicesError`] if the `chunk_indices` are incompatible with the chunk grid.
pub fn chunk_array_representation(
&self,
chunk_indices: &[u64],
) -> Result<ChunkRepresentation, ArrayError> {
(self.chunk_grid().chunk_shape(chunk_indices, self.shape())?).map_or_else(
|| {
Err(ArrayError::InvalidChunkGridIndicesError(
chunk_indices.to_vec(),
))
},
|chunk_shape| {
Ok(unsafe {
ChunkRepresentation::new_unchecked(
chunk_shape.to_vec(),
self.data_type().clone(),
self.fill_value().clone(),
)
})
},
)
}
/// Return an array subset indicating the chunks intersecting `array_subset`.
///
/// Returns [`None`] if the intersecting chunks cannot be determined.
///
/// # Errors
/// Returns [`IncompatibleDimensionalityError`] if the array subset has an incorrect dimensionality.
pub fn chunks_in_array_subset(
&self,
array_subset: &ArraySubset,
) -> Result<Option<ArraySubset>, IncompatibleDimensionalityError> {
match array_subset.end_inc() {
Some(end) => {
let chunks_start = self
.chunk_grid()
.chunk_indices(array_subset.start(), self.shape())?;
let chunks_end = self
.chunk_grid()
.chunk_indices(&end, self.shape())?
.map_or_else(|| self.chunk_grid_shape(), Some);
Ok(
if let (Some(chunks_start), Some(chunks_end)) = (chunks_start, chunks_end) {
Some(unsafe {
ArraySubset::new_with_start_end_inc_unchecked(chunks_start, chunks_end)
})
} else {
None
},
)
}
None => Ok(Some(ArraySubset::new_empty(self.dimensionality()))),
}
}
/// Calculate the recommended codec concurrency.
fn recommended_codec_concurrency(
&self,
chunk_representation: &ChunkRepresentation,
) -> Result<RecommendedConcurrency, ArrayError> {
Ok(self
.codecs()
.recommended_concurrency(chunk_representation)?)
}
}
macro_rules! array_store_elements {
( $self:expr, $elements:ident, $func:ident($($arg:tt)*) ) => {
if $self.data_type.size() != std::mem::size_of::<T>() {
Err(ArrayError::IncompatibleElementSize(
$self.data_type.size(),
std::mem::size_of::<T>(),
))
} else {
let $elements = crate::array::transmute_to_bytes_vec($elements);
$self.$func($($arg)*)
}
};
}
#[cfg(feature = "ndarray")]
macro_rules! array_store_ndarray {
( $self:expr, $array:ident, $func:ident($($arg:tt)*) ) => {
if $self.data_type.size() != std::mem::size_of::<T>() {
Err(ArrayError::IncompatibleElementSize(
$self.data_type.size(),
std::mem::size_of::<T>(),
))
} else {
if $array.is_standard_layout() {
let $array = $array.into_raw_vec();
$self.$func($($arg)*)
} else {
let $array = $array.as_standard_layout().into_owned().into_raw_vec();
$self.$func($($arg)*)
}
}
};
}
#[cfg(feature = "async")]
macro_rules! array_async_store_elements {
( $self:expr, $elements:ident, $func:ident($($arg:tt)*) ) => {
if $self.data_type.size() != std::mem::size_of::<T>() {
Err(ArrayError::IncompatibleElementSize(
$self.data_type.size(),
std::mem::size_of::<T>(),
))
} else {
let $elements = crate::array::transmute_to_bytes_vec($elements);
$self.$func($($arg)*).await
}
};
}
#[cfg(feature = "async")]
#[cfg(feature = "ndarray")]
macro_rules! array_async_store_ndarray {
( $self:expr, $array:ident, $func:ident($($arg:tt)*) ) => {
if $self.data_type.size() != std::mem::size_of::<T>() {
Err(ArrayError::IncompatibleElementSize(
$self.data_type.size(),
std::mem::size_of::<T>(),
))
} else {
if $array.is_standard_layout() {
let $array = $array.into_raw_vec();
$self.$func($($arg)*).await
} else {
let $array = $array.as_standard_layout().into_owned().into_raw_vec();
$self.$func($($arg)*).await
}
}
};
}
mod array_sync_readable;
mod array_sync_writable;
mod array_sync_readable_writable;
#[cfg(feature = "async")]
mod array_async_readable;
#[cfg(feature = "async")]
mod array_async_writable;
#[cfg(feature = "async")]
mod array_async_readable_writable;
/// Transmute from `Vec<u8>` to `Vec<T>`.
#[must_use]
pub fn transmute_from_bytes_vec<T: bytemuck::Pod>(from: Vec<u8>) -> Vec<T> {
bytemuck::allocation::try_cast_vec(from)
.unwrap_or_else(|(_err, from)| bytemuck::allocation::pod_collect_to_vec(&from))
}
/// Transmute from `Vec<T>` to `Vec<u8>`.
#[must_use]
pub fn transmute_to_bytes_vec<T: bytemuck::NoUninit>(from: Vec<T>) -> Vec<u8> {
bytemuck::allocation::try_cast_vec(from)
.unwrap_or_else(|(_err, from)| bytemuck::allocation::pod_collect_to_vec(&from))
}
/// Unravel a linearised index to ND indices.
#[must_use]
pub fn unravel_index(mut index: u64, shape: &[u64]) -> ArrayIndices {
let len = shape.len();
let mut indices: ArrayIndices = Vec::with_capacity(len);
for (indices_i, &dim) in std::iter::zip(
indices.spare_capacity_mut().iter_mut().rev(),
shape.iter().rev(),
) {
indices_i.write(index % dim);
index /= dim;
}
unsafe { indices.set_len(len) };
indices
}
/// Ravel ND indices to a linearised index.
#[must_use]
pub fn ravel_indices(indices: &[u64], shape: &[u64]) -> u64 {
let mut index: u64 = 0;
let mut count = 1;
for (i, s) in std::iter::zip(indices, shape).rev() {
index += i * count;
count *= s;
}
index
}
#[cfg(feature = "ndarray")]
fn iter_u64_to_usize<'a, I: Iterator<Item = &'a u64>>(iter: I) -> Vec<usize> {
iter.map(|v| usize::try_from(*v).unwrap())
.collect::<Vec<_>>()
}
fn validate_element_size<T>(data_type: &DataType) -> Result<(), ArrayError> {
if data_type.size() == std::mem::size_of::<T>() {
Ok(())
} else {
Err(ArrayError::IncompatibleElementSize(
data_type.size(),
std::mem::size_of::<T>(),
))
}
}
#[cfg(feature = "ndarray")]
/// Convert a vector of elements to an [`ndarray::ArrayD`].
///
/// # Errors
/// Returns an error if the length of `elements` is not equal to the product of the components in `shape`.
pub fn elements_to_ndarray<T>(
shape: &[u64],
elements: Vec<T>,
) -> Result<ndarray::ArrayD<T>, ArrayError> {
let length = elements.len();
ndarray::ArrayD::<T>::from_shape_vec(iter_u64_to_usize(shape.iter()), elements).map_err(|_| {
ArrayError::CodecError(codec::CodecError::UnexpectedChunkDecodedSize(
length * std::mem::size_of::<T>(),
shape.iter().product::<u64>() * std::mem::size_of::<T>() as u64,
))
})
}
#[cfg(feature = "ndarray")]
/// Convert a vector of bytes to an [`ndarray::ArrayD`].
///
/// # Errors
/// Returns an error if the length of `bytes` is not equal to the product of the components in `shape` and the size of `T`.
pub fn bytes_to_ndarray<T: bytemuck::Pod>(
shape: &[u64],
bytes: Vec<u8>,
) -> Result<ndarray::ArrayD<T>, ArrayError> {
let expected_len = shape.iter().product::<u64>() * core::mem::size_of::<T>() as u64;
if bytes.len() as u64 != expected_len {
return Err(ArrayError::InvalidBytesInputSize(bytes.len(), expected_len));
}
let elements = transmute_from_bytes_vec::<T>(bytes);
elements_to_ndarray(shape, elements)
}
#[cfg(test)]
mod tests {
use crate::storage::store::MemoryStore;
use super::*;
#[test]
fn test_array_metadata_write_read() {
let store = Arc::new(MemoryStore::new());
let array_path = "/array";
let array = ArrayBuilder::new(
vec![8, 8],
DataType::UInt8,
vec![4, 4].try_into().unwrap(),
FillValue::from(0u8),
)
.build(store.clone(), array_path)
.unwrap();
array.store_metadata().unwrap();
// let metadata: ArrayMetadata =
// serde_json::from_slice(&store.get(&meta_key(&array_path))?)?;
// println!("{:?}", metadata);
let metadata = Array::new(store, array_path).unwrap().metadata();
assert_eq!(metadata, array.metadata());
}
#[test]
fn array_set_shape_and_attributes() {
let store = MemoryStore::new();
let array_path = "/group/array";
let mut array = ArrayBuilder::new(
vec![8, 8], // array shape
DataType::Float32,
vec![4, 4].try_into().unwrap(),
FillValue::from(ZARR_NAN_F32),
)
.bytes_to_bytes_codecs(vec![
#[cfg(feature = "gzip")]
Box::new(codec::GzipCodec::new(5).unwrap()),
])
.build(store.into(), array_path)
.unwrap();
array.set_shape(vec![16, 16]);
array
.attributes_mut()
.insert("test".to_string(), "apple".into());
assert_eq!(array.shape(), &[16, 16]);
assert_eq!(
array.attributes().get_key_value("test"),
Some((
&"test".to_string(),
&serde_json::Value::String("apple".to_string())
))
);
}
#[test]
fn array_subset_round_trip() {
let store = Arc::new(MemoryStore::default());
let array_path = "/array";
let array = ArrayBuilder::new(
vec![8, 8], // array shape
DataType::Float32,
vec![4, 4].try_into().unwrap(), // regular chunk shape
FillValue::from(1f32),
)
.bytes_to_bytes_codecs(vec![
#[cfg(feature = "gzip")]
Box::new(codec::GzipCodec::new(5).unwrap()),
])
// .storage_transformers(vec![].into())
.build(store, array_path)
.unwrap();
array
.store_array_subset_elements::<f32>(
&ArraySubset::new_with_ranges(&[3..6, 3..6]),
vec![1.0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
)
.unwrap();
let subset_all = ArraySubset::new_with_shape(array.shape().to_vec());
let data_all = array
.retrieve_array_subset_elements::<f32>(&subset_all)
.unwrap();
assert_eq!(
data_all,
vec![
// (0,0) | (0, 1)
//0 1 2 3 |4 5 6 7
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, // 0
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, // 1
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, // 2
1.0, 1.0, 1.0, 1.0, 0.2, 0.3, 1.0, 1.0, //_3____________
1.0, 1.0, 1.0, 0.4, 0.5, 0.6, 1.0, 1.0, // 4
1.0, 1.0, 1.0, 0.7, 0.8, 0.9, 1.0, 1.0, // 5 (1, 1)
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, // 6
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, // 7
]
);
assert!(array
.retrieve_chunk_elements_if_exists::<f32>(&[0; 2])
.unwrap()
.is_none());
#[cfg(feature = "ndarray")]
assert!(array
.retrieve_chunk_ndarray_if_exists::<f32>(&[0; 2])
.unwrap()
.is_none());
}
// fn array_subset_locking(locks: StoreLocks, expect_equal: bool) {
// let store = Arc::new(MemoryStore::new_with_locks(locks));
// let array_path = "/array";
// let array = ArrayBuilder::new(
// vec![100, 4],
// DataType::UInt8,
// vec![10, 2].try_into().unwrap(),
// FillValue::from(0u8),
// )
// .build(store, array_path)
// .unwrap();
// let mut any_not_equal = false;
// for j in 1..10 {
// (0..100).into_par_iter().for_each(|i| {
// let subset = ArraySubset::new_with_ranges(&[i..i + 1, 0..4]);
// array.store_array_subset(&subset, vec![j; 4]).unwrap();
// });
// let subset_all = ArraySubset::new_with_shape(array.shape().to_vec());
// let data_all = array.retrieve_array_subset(&subset_all).unwrap();
// let all_equal = data_all.iter().all_equal_value() == Ok(&j);
// if expect_equal {
// assert!(all_equal);
// } else {
// any_not_equal |= !all_equal;
// }
// }
// if !expect_equal {
// assert!(any_not_equal);
// }
// }
// #[test]
// #[cfg_attr(miri, ignore)]
// fn array_subset_locking_default() {
// array_subset_locking(Arc::new(DefaultStoreLocks::default()), true);
// }
// // Due to the nature of this test, it can fail sometimes. It was used for development but is now disabled.
// #[test]
// fn array_subset_locking_disabled() {
// array_subset_locking(
// Arc::new(crate::storage::store_lock::DisabledStoreLocks::default()),
// false,
// );
// }
}