bloom_filter.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/atomics.h>
#include <nvbio/basic/static_vector.h>

namespace nvbio {





template <typename T>
struct inplace_or
{
};

template <>
struct inplace_or<uint32>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint32* word, const uint32 mask) const
    {
        atomic_or( word, mask );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint32& block, const uint32 word, const uint32 mask) const
    {
        block |= mask;
    }
};

template <>
struct inplace_or<uint2>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint2* word, const uint2 mask) const
    {
        atomic_or( &(word->x), mask.x );
        atomic_or( &(word->y), mask.y );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint2& block, const uint32 word, const uint32 mask) const
    {
        if (word == 0) block.x |= mask;
        else           block.y |= mask;
    }
};

template <>
struct inplace_or<uint4>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint4* word, const uint4 mask) const
    {
        atomic_or( &(word->x), mask.x );
        atomic_or( &(word->y), mask.y );
        atomic_or( &(word->z), mask.z );
        atomic_or( &(word->w), mask.w );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint4& block, const uint32 word, const uint32 mask) const
    {
        if      (word == 0) block.x |= mask;
        else if (word == 1) block.y |= mask;
        else if (word == 2) block.z |= mask;
        else                block.w |= mask;
    }
};

template <>
struct inplace_or<uint64>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint64* word, const uint64 mask) const
    {
        atomic_or( word, mask );
    }
};

template <>
struct inplace_or<uint64_2>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint64_2* word, const uint64_2 mask) const
    {
        atomic_or( &(word->x), mask.x );
        atomic_or( &(word->y), mask.y );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint64_2& block, const uint32 word, const uint64 mask) const
    {
        if (word == 0) block.x |= mask;
        else           block.y |= mask;
    }
};

template <>
struct inplace_or<uint64_4>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint64_4* word, const uint64_4 mask) const
    {
        atomic_or( &(word->x), mask.x );
        atomic_or( &(word->y), mask.y );
        atomic_or( &(word->z), mask.z );
        atomic_or( &(word->w), mask.w );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void operator() (uint64_4& block, const uint32 word, const uint64 mask) const
    {
        if      (word == 0) block.x |= mask;
        else if (word == 1) block.y |= mask;
        else if (word == 2) block.z |= mask;
        else                block.w |= mask;
    }
};

template <
    uint32   K,                         // number of hash functions { Hash1 + i * Hash2 | i : 0, ..., K-1 }
    typename Hash1,                     // first hash generator function
    typename Hash2,                     // second hash generator function
    typename Iterator,                  // storage iterator - must dereference to uint32
    typename OrOperator = inplace_or<uint32> >   // OR binary operator
struct bloom_filter
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    bloom_filter(
        const uint64    size,
        Iterator        storage,
        const Hash1     hash1 = Hash1(),
        const Hash2     hash2 = Hash2());

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void insert(const Key key, const OrOperator or_op = OrOperator());

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    bool has(const Key key) const;

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    bool operator[] (const Key key) const { return has( key ); }

    uint64      m_size;
    Iterator    m_storage;
    Hash1       m_hash1;
    Hash2       m_hash2;
};


template <
    typename Hash1,                     // first hash generator function
    typename Hash2,                     // second hash generator function
    typename Iterator,                  // storage iterator - must be one of {uint32|uint2|uint4|uint64|uint64_2|uint64_4}
    typename OrOperator = inplace_or<typename std::iterator_traits<Iterator>::value_type> >   // OR binary operator
struct blocked_bloom_filter
{
    typedef typename std::iterator_traits<Iterator>::value_type block_type;
    typedef typename vector_traits<block_type>::value_type      word_type;

    static const uint32 BLOCK_DIM  = vector_traits<block_type>::DIM;
    static const uint32 BLOCK_SIZE = sizeof(block_type)*8u;
    static const uint32 WORD_SIZE  = sizeof(word_type)*8u;

    typedef StaticVector<word_type,BLOCK_DIM>                   vector_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    blocked_bloom_filter(
        const uint32    k,
        const uint64    size,
        Iterator        storage,
        const Hash1     hash1 = Hash1(),
        const Hash2     hash2 = Hash2());

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    void insert(const Key key, const OrOperator or_op = OrOperator());

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE 
    bool has(const Key key) const;

    template <typename Key>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    bool operator[] (const Key key) const { return has( key ); }

    uint32          m_k;
    uint64          m_size;
    Iterator        m_storage;
    Hash1           m_hash1;
    Hash2           m_hash2;
};

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
uint32 optimal_bloom_filter_hashes(const float bits_per_key)
{
    return uint32( bits_per_key * logf(2.0) ) + 1u;
}

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
float optimal_bloom_filter_bits_per_key(const float fp_rate)
{
    return -logf(fp_rate) / (logf(2.0f)*logf(2.0f));
}

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
float optimal_bloom_filter_bits_per_key(const uint32 K)
{
    return float(K) / logf(2.0f);
}

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
void optimal_bloom_filter_parameters(const float fp_rate, uint32* K, float* bits_per_key)
{
    *bits_per_key = optimal_bloom_filter_bits_per_key( fp_rate );

    *K = optimal_bloom_filter_hashes( *bits_per_key );
}

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
float optimal_bloom_filter_fp_rate(const uint32 K, const float bits_per_key)
{
    return powf( 1.0f - expf( -float(K) / bits_per_key ), float(K) );
}


} // namespace nvbio

#include <nvbio/basic/bloom_filter_inl.h>