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# cython: infer_types=True
# cython: cdivision=True
#
from libc.string cimport memcpy
from libcpp.algorithm cimport copy as cpp_copy
from murmurhash.mrmr cimport hash128_x86
import math
import struct
try:
import copy_reg
except ImportError:
import copyreg as copy_reg
cdef struct BloomStruct:
vector[key_t] bitfield
key_t hcount # hash count, number of hash functions
key_t length
uint32_t seed
cdef str FORMAT = "<QQQQL"
# this can't be in the enum because it depends on a string
cdef uint32_t STRUCT_SIZE = struct.calcsize(FORMAT)
cdef enum:
KEY_BITS = 8 * sizeof(key_t)
VERSION = 1
LEGACY_UNIT_SIZE = 8
LEGACY_OFFSET = 24 # 8 * 3
LEGACY_WINDOWS_UNIT_SIZE = 4
LEGACY_WINDOWS_OFFSET = 12 # 4 * 3
def calculate_size_and_hash_count(members, error_rate):
"""Calculate the optimal size in bits and number of hash functions for a
given number of members and error rate.
"""
base = math.log(1 / (2 ** math.log(2)))
bit_count = math.ceil((members * math.log(error_rate)) / base)
hash_count = math.floor((bit_count / members) * math.log(2))
return (bit_count, hash_count)
cdef class BloomFilter:
"""Bloom filter that allows for basic membership tests.
Only integers are supported as keys.
"""
def __init__(self, key_t size=(2 ** 10), key_t hash_funcs=23, uint32_t seed=0):
assert size > 0, "Size must be greater than zero"
assert hash_funcs > 0, "Hash function count must be greater than zero"
self.c_bloom = make_unique[BloomStruct]()
bloom_init(self.c_bloom.get(), hash_funcs, size, seed)
@classmethod
def from_error_rate(cls, members, error_rate=1E-4):
params = calculate_size_and_hash_count(members, error_rate)
return cls(*params)
def add(self, key_t item):
bloom_add(self.c_bloom.get(), item)
def __contains__(self, item):
return bloom_contains(self.c_bloom.get(), item)
cdef inline bint contains(self, key_t item) nogil:
return bloom_contains(self.c_bloom.get(), item)
def to_bytes(self):
return bloom_to_bytes(self.c_bloom.get())
def from_bytes(self, bytes byte_string):
bloom_from_bytes(self.c_bloom.get(), byte_string)
return self
cdef bytes bloom_to_bytes(const BloomStruct* bloom):
cdef key_t pad = 0 # to differentiate new from old data format
cdef key_t buflen
prefix = struct.pack(FORMAT, pad, VERSION, bloom.hcount, bloom.length, bloom.seed)
# note that the modulus check is only required for data that has come from
# legacy deserialization - otherwise length is always a multiple of
# KEY_BITS.
buflen = bloom.length // KEY_BITS
if bloom.length % KEY_BITS > 0:
buflen += 1
buffer = (<const char*>bloom.bitfield.data())[0:buflen * sizeof(key_t)]
return prefix + buffer
cdef void bloom_from_bytes(BloomStruct* bloom, bytes data):
# new-style memory structure (each unit is a key_t/64 bits):
# - pad1: 0 (not valid in old data)
# - VERSION: 1 (can be raised later if necessary
# (following values are same as old-style, except length semantics changed)
# - hcount: number of hashes
# - length: bitfield length in bits
# - seed: seed value for hashes
if len(data) < STRUCT_SIZE:
# unlikely but possible with old data
bloom_from_bytes_legacy(bloom, data)
return
pad, ver, hcount, length, seed = struct.unpack(FORMAT, data[0:STRUCT_SIZE])
if pad != 0:
bloom_from_bytes_legacy(bloom, data)
return
if ver != VERSION:
raise ValueError("Unknown serialization version")
bloom.hcount = hcount
bloom.length = length
# Technically overflow is possible here, but in valid data nothing will be
# lost.
bloom.seed = <uint32_t>seed
cdef key_t buflen = length // KEY_BITS
if length % KEY_BITS > 0:
buflen += 1
assert buflen > 0, "Tried to allocate an empty buffer"
contents = data[STRUCT_SIZE:]
cdef key_t* contents_c = <key_t*><char*>contents
bloom.bitfield = vector[key_t](buflen)
bloom.bitfield.assign(contents_c, contents_c + buflen)
cdef void bloom_from_bytes_legacy(BloomStruct* bloom, bytes data):
# Older versions of this library used the array module with type L for
# serialization. Types in array guarantee a minimum size, not an actual
# size, and it turns out L is 8 bytes on Linux and most platforms, but 4 on
# Windows.
# As a separate issue, due to bits/bytes confusion, each container in the
# serialized data has only one byte actually used.
# The code in this function reads in data in the old format and converts it
# to the current format losslessly. It also packs the actually used bytes into
# contiguous memory.
# on non-Windows platforms
unit = "Q"
unit_size = LEGACY_UNIT_SIZE # size of container in bytes
cdef uint32_t offset = LEGACY_OFFSET
hcount, length, seed = struct.unpack("<QQQ", data[0:offset])
if length != len(data) - LEGACY_OFFSET:
# This can happen if the data was serialized on Windows, where the units
# were 32bit rather than 64bit.
unit = "L"
unit_size = LEGACY_WINDOWS_UNIT_SIZE
offset = LEGACY_WINDOWS_OFFSET
hcount, length, seed = struct.unpack("<LLL", data[0:offset])
# The length was the number of bytes in memory. But because of the
# platform size issue, the actual serialized bytes is half that.
assert length // 2 == len(data) - offset, "Length is invalid"
# This is the same in either case because the Windows code was written
# without being aware of the difference in size between Windows and
# non-Windows.
decode_len = length // LEGACY_UNIT_SIZE
bloom.hcount = hcount
bloom.length = length
bloom.seed = <uint32_t>seed
# This is tricky - to remove empty space we're going to map bytes into
# containers. On Windows or Linux, length is both the number of actually
# used bits in the bitfield and the number of bytes when the bitfield was
# in memory in the old format. In our output, length will be the bitfield
# length in bits.
buflen = length // KEY_BITS
if length % KEY_BITS > 0:
buflen += 1
contents = struct.unpack(f"<{decode_len}{unit}", data[offset:])
assert buflen > 0, "Tried to allocate an empty buffer"
bloom.bitfield = vector[key_t](buflen, 0)
# Each item in contents provides one actually used byte, so we'll copy it
# into the containers.
for i in range(len(contents)):
block = i // sizeof(key_t)
idx = i % sizeof(key_t)
bloom.bitfield[block] |= contents[i] << (8 * idx)
cdef void bloom_init(BloomStruct* bloom, key_t hcount, key_t length, uint32_t seed) except *:
# size should be a multiple of the container size - round up
if length % KEY_BITS:
length = ((length // KEY_BITS) + 1) * KEY_BITS
bloom.length = length # this is a bit value
bloom.hcount = hcount
buflen = length // KEY_BITS
assert buflen > 0, "Tried to allocate an empty buffer"
bloom.bitfield = vector[key_t](buflen, 0)
bloom.seed = seed
# Instead of calling MurmurHash with a different seed for each hash function, this
# generates two initial hash values and then combines them to create the correct
# number of hashes. This technique is faster than just doing MurmurhHash
# repeatedly and has been shown to work as well as full hashing.
# For details see "Less Hashing, Same Performance: Building a Better Bloom
# Filter", Kirsch & Mitzenmacher.
# https://www.semanticscholar.org/paper/Less-hashing%2C-same-performance%3A-Building-a-better-Kirsch-Mitzenmacher/65c43afbfc064705bdc40d3473f32518e9306429
# The choice of seeds is arbitrary.
cdef void bloom_add(BloomStruct* bloom, key_t item) nogil:
cdef key_t hv
cdef key_t[2] keys
cdef key_t one = 1 # We want this explicitly typed, because bits
hash128_x86(&item, sizeof(key_t), 0, &keys)
for hiter in range(bloom.hcount):
hv = (keys[0] + (hiter * keys[1])) % bloom.length # length is in BITS
bloom.bitfield[hv // KEY_BITS] |= one << (hv % KEY_BITS)
cdef bint bloom_contains(const BloomStruct* bloom, key_t item) nogil:
cdef key_t hv
cdef key_t[2] keys
cdef key_t one = 1 # We want this explicitly typed, because bits
hash128_x86(&item, sizeof(key_t), 0, &keys)
for hiter in range(bloom.hcount):
hv = (keys[0] + (hiter * keys[1])) % bloom.length # length is in BITS
if not (bloom.bitfield[hv // KEY_BITS] & one << (hv % KEY_BITS)):
return False
return True
def pickle_bloom(BloomFilter bloom):
return unpickle_bloom, (bloom.to_bytes(),)
def unpickle_bloom(byte_string):
return BloomFilter().from_bytes(byte_string)
copy_reg.pickle(BloomFilter, pickle_bloom, unpickle_bloom)
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