Python bindings to Succinct Data Structure Library 2.0
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README.md
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README.md

Python bindings to Succinct Data Structure Library 2.0

The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operation performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical.

Most of examples from SDSL cheat sheet and SDSL tutorial are implemented.

Mutable bit-compressed vectors

Core classes (see pysdsl.int_vector for dict of all of them):

  • pysdsl.IntVector(size, default_value, bit_width=64) — dynamic bit width
  • pysdsl.BitVector(size, default_value) — static (fixed) bit width (1)
  • pysdsl.Int4Vector(size, default_value) — static bit width (4)
  • pysdsl.Int8Vector(size, default_value) — static bit width (8)
  • pysdsl.Int16Vector(size, default_value) — static bit width (16)
  • pysdsl.Int24Vector(size, default_value) — static bit width (24)
  • pysdsl.Int32Vector(size, default_value) — static bit width (32)
  • pysdsl.Int64Vector(size, default_value) — static bit width (64)

Construction from python sequences is also supported.

In [1]: import pysdsl

In [2]: %time v = pysdsl.IntVector(1024 * 1024 * 256)
CPU times: user 914 ms, sys: 509 ms, total: 1.42 s
Wall time: 1.42 s

In [3]: v.size_in_mega_bytes
Out[3]: 2048.000008583069

In [4]: %time v.set_to_id()  # like *v = range(len(v))
CPU times: user 8.19 s, sys: 1.3 ms, total: 8.19 s
Wall time: 8.19 s

In [5]: v.width
Out[5]: 64

In [6]: %time v.bit_compress()
CPU times: user 23.3 s, sys: 155 ms, total: 23.5 s
Wall time: 23.5 s

In [7]: v.width
Out[7]: 28

In [8]: v.size_in_mega_bytes
Out[8]: 896.0000085830688

Buffer interface:

In [9]: import array

In [10]: v = pysdsl.Int64Vector([1, 2, 3])

In [11]: array.array('Q', v)
Out[11]: array('Q', [1, 2, 3])

Immutable compressed integer vectors

(See pysdsl.enc_vector):

  • EncVectorEliasDelta(IntVector)
  • EncVectorEliasGamma(IntVector)
  • EncVectorFibonacci(IntVector)
  • EncVectorComma2(IntVector)
  • EncVectorComma4(IntVector)
In [9]: %time ev = pysdsl.EncVectorEliasDelta(v)
CPU times: user 26.5 s, sys: 31.8 ms, total: 26.5 s
Wall time: 26.5 s

In [10]: ev.size_in_mega_bytes
Out[10]: 45.75003242492676

Encoding values with variable length codes (see pysdsl.variable_length_codes_vector):

  • VariableLengthCodesVectorEliasDelta(IntVector)
  • VariableLengthCodesVectorEliasGamma(IntVector)
  • VariableLengthCodesVectorFibonacci(IntVector)
  • VariableLengthCodesVectorComma2(IntVector)
  • VariableLengthCodesVectorComma4(IntVector)

Encoding values with "escaping" technique (see pysdsl.direct_accessible_codes_vector):

  • DirectAccessibleCodesVector(IntVector)
  • DirectAccessibleCodesVector8(IntVector),
  • DirectAccessibleCodesVector16(IntVector),
  • DirectAccessibleCodesVector63(IntVector),
  • DirectAccessibleCodesVectorDP(IntVector) — number of layers is chosen with dynamic programming
  • DirectAccessibleCodesVectorDPRRR(IntVector) — same but built on top of RamanRamanRaoVector (see later)

Construction from python sequences is also supported.

Immutable compressed bit (boolean) vectors

(See pysdsl.all_immutable_bitvectors)

  • BitVectorInterLeaved64(BitVector)
  • BitVectorInterLeaved128(BitVector)
  • BitVectorInterLeaved256(BitVector)
  • BitVectorInterLeaved512(BitVector) — A bit vector which interleaves the original BitVector with rank information (see later)
  • SDVector(BitVector) — A bit vector which compresses very sparse populated bit vectors by representing the positions of 1 by the Elias-Fano representation for non-decreasing sequences
  • RamanRamanRaoVector15(BitVector)
  • RamanRamanRaoVector63(BitVector)
  • RamanRamanRaoVector256(BitVector) — An H₀-compressed bitvector representation.
  • HybVector8(BitVector)
  • HybVector16(BitVector) — A hybrid-encoded compressed bitvector representation

See also: pysdsl.raman_raman_rao_vectors, pysdsl.sparse_bit_vectors, pysdsl.hybrid_bit_vectors and pysdsl.bit_vector_interleaved.

Rank and select operations on bitvectors

For bitvector v rank(i) for pattern P (by default P is a bitstring of len 1: 1) is the number of patterns P in the prefix [0..i) in vector v.

For bitvector v select(i) for pattern P (by default P=1) is the position of the i-th occurrence of pattern P in vector v.

Create support instances for rank and/or select for different patterns via:

  • v.init_rank() or v.init_rank_1() for ranks of pattern 1 (e.g. the number of set bits in v)
  • v.init_rank_0() for ranks of pattern 0
  • v.init_rank_00() (if supported by vector class) for ranks of pattern 00
  • v.init_rank_01() (if supported by vector class) for ranks of pattern 01
  • v.init_rank_10() (if supported by vector class) for ranks of pattern 10
  • v.init_rank_11() (if supported by vector class) for ranks of pattern 11
  • v.init_support() or v.init_support_1() for support of pattern 1 (e.g. the positions of set bits)
  • v.init_support_0() for ranks of pattern 0
  • v.init_support_00() (if supported by vector class) for ranks of pattern 00
  • v.init_support_01() (if supported by vector class) for ranks of pattern 01
  • v.init_support_10() (if supported by vector class) for ranks of pattern 10
  • v.init_support_11() (if supported by vector class) for ranks of pattern 11

Once support instance s is created call it (s(idx) or s.__call__(idx)) or use corresponding methods s.rank(idx) or s.select(idx) to get the results.

s.rank(idx) and s.select(idx) are undefined if original bitvector is mutable and was modified.

Wavelet trees

The wavelet tree is a data structure that provides three efficient methods:

  • The []-operator: wt[i] returns the i-th symbol of vector for which the wavelet tree was build for.
  • The rank method: wt.rank(i, c) returns the number of occurrences of symbol c in the prefix [0..i-1] in the vector for which the wavelet tree was build for.
  • The select method: wt.select(j, c) returns the index i from [0..size()-1] of the j-th occurrence of symbol c.

Comressed suffix arrays

Suffix array is a sorted array of all suffixes of a string.

SDSL supports bitcompressed and compressed suffix arrays.

Byte representaion of original IntVector should have no zero symbols in order to construct SuffixArray.

Objects memory structure

Any object has a .structure property with technical information about an object. .structure_json also provided for web-view implementations. .write_structure_json() method puts that information into a file.

.size_in_bytes and .size_in_mega_bytes properties show how much memory the object is occupying.

Saving/Loading objects

All objects provide .store_to_checked_file() method allowing one to save object into a file.

All classes provide .load_from_checkded_file() static method allowing one to load object stored with .store_to_checked_file()

Building

Requirements: static libraries for sdsl and divsufsort.

Call pip with binaries disabled to fetch sources and build the package:

pip install --no-binaries :all: pysdsl