compressed_intvec/

lib.rs

//! # Compressed Integer Vector Library
//!
//! [![crates.io](https://img.shields.io/crates/v/compressed-intvec.svg)](https://crates.io/crates/compressed-intvec)
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//! [![docs](https://docs.rs/compressed-intvec/badge.svg)](https://docs.rs/compressed-intvec)
//! [![downloads](https://img.shields.io/crates/d/compressed-intvec)](https://crates.io/crates/compressed-intvec)
//! ![license](https://img.shields.io/crates/l/compressed-intvec)
//!
//! A Rust library for compressing vectors of `u64` integers using instantaneous codes the from [dsi-bitstream](https://docs.rs/dsi-bitstream) library. Offers fast random access via sampling to balance speed and memory. Choose between big-endian (`BEIntVec`) or little-endian (`LEIntVec`) encoding.
//!
//! ## Features
//!
//! - **Efficient Compression**: Leverage various codecs like Gamma, Delta, and Rice coding.
//! - **Fast Random Access**: Achieve $O(1)$ access with configurable sampling.
//! - **Memory Analysis**: Integrate with [`mem-dbg`](https://crates.io/crates/mem-dbg) for memory profiling.
//! - **Flexible Codecs**: Select codecs based on data distribution for optimal compression.
//!
//! The sampling parameter determines how often full positions are stored to speed up access. Higher values reduce memory overhead but may increase access time. For example, `sampling_param = 32` is usually a good trade-off for large datasets.
//!
//! ### A Quick Example
//!
//! Let's consider the _universal_ code **Gamma** introduced by Elias in the 1960s. This code represents an integer as a unary prefix followed by the binary representation of the integer (thus the name universal, as for every integer `x` the length of the code is always $O(\log x)$ long, so just a constant factor longer than its binary form). So for example `9` will be encoded as `0001001`.
//!
//! ```rust
//! use compressed_intvec::intvec::BEIntVec;
//! use compressed_intvec::codecs::GammaCodec;
//!
//! let vec = vec![1, 3, 6, 8, 13, 3];
//!
//! // The compressed-intvec needs a sampling parameter
//! let sampling_param = 2; // small since the vector is small
//! let compressed_be = BEIntVec::<GammaCodec>::from(&vec, sampling_param).unwrap();
//!
//! assert_eq!(compressed_be.get(3), 8);
//!
//! for (i, val) in compressed_be.iter().enumerate() {
//!   assert_eq!(val, vec[i]);
//! }
//!
//! ```
//!
//! Or alternatively, you can use the `LEIntVec` for little-endian representation:
//!
//! ```rust
//! use compressed_intvec::intvec::LEIntVec;
//! use compressed_intvec::codecs::GammaCodec;
//!
//! let vec = vec![1, 3, 6, 8, 13, 3];
//! let compressed_le = LEIntVec::<GammaCodec>::from(&vec, 2).unwrap();
//!
//! for (i, val) in compressed_le.iter().enumerate() {
//!     assert_eq!(val, vec[i]);
//! }
//! ```
//!
//! ## Available Codecs
//!
//! | Codec Name           | Description                                                                                                                                                                                                |
//! | -------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
//! | `GammaCodec`         | Uses gamma coding without requiring extra runtime parameters.                                                                                                                                              |
//! | `DeltaCodec`         | Uses delta coding, likewise without extra parameters.                                                                                                                                                      |
//! | `ExpGolombCodec`     | Requires an extra parameter (e.g., a parameter `k`) for encoding/decoding.                                                                                                                                 |
//! | `ZetaCodec`          | Uses additional runtime parameters ζ.                                                                                                                                                                      |
//! | `RiceCodec`          | Uses a Rice parameter for encoding/decoding. Ideal for skewed distributions. In this case you may want to set this paramater as the floor of the log_2 of the mean of your values                          |
//! | `MinimalBinaryCodec` | A minimal binary code with upper bound `u > 0` ([truncated binary encoding](https://en.wikipedia.org/wiki/Truncated_binary_encoding)). This is optimal for uniformly distributed data in the range [0, u). |
//! | `ParamZetaCodec`     | Parameterized variant of Zeta codec using compile-time flags.                                                                                                                                              |
//! | `ParamDeltaCodec`    | Parameterized variant of Delta codec using compile-time flags.                                                                                                                                             |
//! | `ParamGammaCodec`    | Parameterized variant of Gamma codec using compile-time flags.                                                                                                                                             |
//!
//! For codecs that require extra parameters, we can create a compressed int-vec with the method `from_with_param`:
//!
//! ```rust
//! use compressed_intvec::intvec::BEIntVec;
//! use compressed_intvec::codecs::RiceCodec;
//!
//! let vec = vec![1, 3, 6, 8, 13, 3];
//! let rice_param = 3; // for example
//! let sampling_param = 2;
//! let compressed = BEIntVec::<RiceCodec>::from_with_param(&vec, sampling_param, rice_param).unwrap();
//! ```
//!
//! Choosing the right codec is crucial for achieving optimal compression. The efficiency of a codec is highly dependent on the underlying data distribution. For example, Rice coding is usually effective for skewed distributions, while Minimal Binary coding is optimal for uniformly distributed data.
//!
//! ## Endianness
//!
//! Choose `BEIntVec` or `LEIntVec` based on data interoperability needs. Performance is equivalent; endianness affects byte order in compressed storage.
//!
//! ## Memory Analysis (and why choosing the right codec is important)
//!
//! Both the little-endian and big-endian version of the compressed int-vec include support for the [MemDbg/MemSize](https://docs.rs/mem-dbg/) traits from the [mem_dbg](https://crates.io/crates/mem-dbg) crate. For example, this is the output of `mem_dbg(DbgFlags::empty()` for a very large `BEIntVec` instance:
//!
//! ```bash
//! 11536 B ⏺
//! 10864 B ├╴data
//!   656 B ├╴samples
//!     0 B ├╴codec
//!     8 B ├╴k
//!     8 B ├╴len
//!     0 B ├╴codec_param
//!     0 B ╰╴endian
//! ```
//!
//! Consider now a vector of `u64` values uniformly distributed in the range `[0, u64::MAX)` and see it's memory usage
//!
//! ```rust
//! use rand::distr::{Distribution, Uniform};
//! use rand::SeedableRng;
//! use mem_dbg::{MemDbg, DbgFlags};
//!
//! fn generate_uniform_vec(size: usize, max: u64) -> Vec<u64> {
//!     let mut rng = rand::rngs::StdRng::seed_from_u64(42);
//!     let uniform = Uniform::new(0, max).unwrap();
//!     (0..size).map(|_| uniform.sample(&mut rng)).collect()
//! }
//!
//! let input_vec = generate_uniform_vec(1000, u64::MAX);
//!
//! println!("Size of the standard Vec<u64>");
//! input_vec.mem_dbg(DbgFlags::empty());
//! ```
//!
//! This outputs:
//!
//! ```bash
//! Size of the standard Vec<u64>
//! 8024 B ⏺
//! ```
//!
//! Next, we compress the vector using both `MinimalBinaryCodec` and `DeltaCodec` using for both a sampling parameter of `32`:
//!
//! ```rust
//! use compressed_intvec::intvec::BEIntVec;
//! use compressed_intvec::codecs::{MinimalBinaryCodec, DeltaCodec};
//! use mem_dbg::{MemDbg, DbgFlags};
//! use rand::distr::{Distribution, Uniform};
//! use rand::SeedableRng;
//!
//! fn generate_uniform_vec(size: usize, max: u64) -> Vec<u64> {
//!     let mut rng = rand::rngs::StdRng::seed_from_u64(42);
//!     let uniform = Uniform::new(0, max).unwrap();
//!     (0..size).map(|_| uniform.sample(&mut rng)).collect()
//! }
//!
//! let input_vec = generate_uniform_vec(1000, u64::MAX);
//! println!("Size of the standard Vec<u64>");
//! input_vec.mem_dbg(DbgFlags::empty());
//!
//! let minimal_intvec = BEIntVec::<MinimalBinaryCodec>::from_with_param(&input_vec, 32, 10).unwrap();
//! let delta_intvec = BEIntVec::<DeltaCodec>::from(&input_vec, 32).unwrap();
//!
//! println!("Size of the compressed IntVec with MinimalBinaryCodec");
//! minimal_intvec.mem_dbg(DbgFlags::empty());
//!
//! println!("\nSize of the compressed IntVec with DeltaCodec");
//! delta_intvec.mem_dbg(DbgFlags::empty());
//! ```
//!
//! The compression results are:
//!
//! ```bash
//! Size of the standard Vec<u64>
//! 8024 B ⏺
//!
//! Size of the compressed IntVec with MinimalBinaryCodec
//! 832 B ⏺
//! 528 B ├╴data
//! 280 B ├╴samples
//!   0 B ├╴codec
//!   8 B ├╴k
//!   8 B ├╴len
//!   8 B ├╴codec_param
//!   0 B ╰╴endian
//!
//! Size of the compressed IntVec with DeltaCodec
//! 9584 B ⏺
//! 9288 B ├╴data
//! 280 B ├╴samples
//!   0 B ├╴codec
//!   8 B ├╴k
//!   8 B ├╴len
//!   0 B ├╴codec_param
//!   0 B ╰╴endian
//! ```
//!
//! As shown, `MinimalBinaryCodec` is the most efficient for uniformly distributed data, reducing the size to 832 bytes, an order of magnitude smaller than the original vector. In contrast, `DeltaCodec` actually increases the size to 9584 bytes, as it is poorly suited for uniform distributions.
//!
//! ## Benchmarks
//!
//! Benchmarks are provided to evaluate both the random access speed and space occupancy of compressed vectors.
//!
//! - **Random Access Benchmarks:** These benchmarks measure the time required to access individual elements.
//! - **Space Occupancy Benchmarks:** These benchmarks report the memory footprint of various codec configurations and compressed representations.
//!
//! To run the benchmarks, execute:
//!
//! ```bash
//! cargo bench
//! ```
pub mod codecs;
pub mod intvec;