Distance.cpp

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/*
 * this program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2006-2009 Christian Gehl
 * Written (W) 2006-2009 Soeren Sonnenburg
 * Copyright (C) 2006-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#include <shogun/lib/config.h>
#include <shogun/lib/common.h>
#include <shogun/io/SGIO.h>
#include <shogun/io/File.h>
#include <shogun/lib/Time.h>
#include <shogun/lib/Signal.h>
#include <shogun/base/Parallel.h>
#include <shogun/base/Parameter.h>

#include <shogun/distance/Distance.h>
#include <shogun/features/Features.h>

#include <string.h>
#include <unistd.h>

#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif

using namespace shogun;

template <class T> struct D_THREAD_PARAM
{
    CDistance* distance;
    int32_t start;
    int32_t end;
    int32_t total_start;
    int32_t total_end;
    int32_t m;
    int32_t n;
    T* result;
    bool symmetric;
    bool verbose;
};

CDistance::CDistance() : CSGObject()
{
    init();
}


CDistance::CDistance(CFeatures* p_lhs, CFeatures* p_rhs) : CSGObject()
{
    init();
    init(p_lhs, p_rhs);
}

CDistance::~CDistance()
{
    SG_FREE(precomputed_matrix);
    precomputed_matrix=NULL;

    remove_lhs_and_rhs();
}

bool CDistance::init(CFeatures* l, CFeatures* r)
{
    //make sure features were indeed supplied
    ASSERT(l)
    ASSERT(r)

    //make sure features are compatible
    ASSERT(l->get_feature_class()==r->get_feature_class())
    ASSERT(l->get_feature_type()==r->get_feature_type())

    //remove references to previous features
    remove_lhs_and_rhs();

    //increase reference counts
    SG_REF(l);
    SG_REF(r);

    lhs=l;
    rhs=r;

    num_lhs=l->get_num_vectors();
    num_rhs=r->get_num_vectors();

    SG_FREE(precomputed_matrix);
    precomputed_matrix=NULL ;

    return true;
}

void CDistance::load(CFile* loader)
{
    SG_SET_LOCALE_C;
    SG_RESET_LOCALE;
}

void CDistance::save(CFile* writer)
{
    SG_SET_LOCALE_C;
    SG_RESET_LOCALE;
}

void CDistance::remove_lhs_and_rhs()
{
    SG_UNREF(rhs);
    rhs = NULL;
    num_rhs=0;

    SG_UNREF(lhs);
    lhs = NULL;
    num_lhs=0;
}

void CDistance::remove_lhs()
{
    SG_UNREF(lhs);
    lhs = NULL;
    num_lhs=0;
}

void CDistance::remove_rhs()
{
    SG_UNREF(rhs);
    rhs = NULL;
    num_rhs=0;
}

CFeatures* CDistance::replace_rhs(CFeatures* r)
{
    //make sure features were indeed supplied
    ASSERT(r)

    //make sure features are compatible
    ASSERT(lhs->get_feature_class()==r->get_feature_class())
    ASSERT(lhs->get_feature_type()==r->get_feature_type())

    //remove references to previous rhs features
    CFeatures* tmp=rhs;

    rhs=r;
    num_rhs=r->get_num_vectors();

    SG_FREE(precomputed_matrix);
    precomputed_matrix=NULL ;

    // return old features including reference count
    return tmp;
}

CFeatures* CDistance::replace_lhs(CFeatures* l)
{
    //make sure features were indeed supplied
    ASSERT(l)

    //make sure features are compatible
    ASSERT(rhs->get_feature_class()==l->get_feature_class())
    ASSERT(rhs->get_feature_type()==l->get_feature_type())

    //remove references to previous rhs features
    CFeatures* tmp=lhs;

    lhs=l;
    num_lhs=l->get_num_vectors();

    SG_FREE(precomputed_matrix);
    precomputed_matrix=NULL ;

    // return old features including reference count
    return tmp;
}

float64_t CDistance::distance(int32_t idx_a, int32_t idx_b)
{
    REQUIRE(idx_a >= 0 && idx_b >= 0, "In CDistance::distance(int32_t,int32_t), idx_a and "
            "idx_b must be positive, %d and %d given instead\n", idx_a, idx_b)

    ASSERT(lhs)
    ASSERT(rhs)

    if (lhs==rhs)
    {
        int32_t num_vectors = lhs->get_num_vectors();

        if (idx_a>=num_vectors)
            idx_a=2*num_vectors-1-idx_a;

        if (idx_b>=num_vectors)
            idx_b=2*num_vectors-1-idx_b;
    }

    REQUIRE(idx_a < lhs->get_num_vectors() && idx_b < rhs->get_num_vectors(),
            "In CDistance::distance(int32_t,int32_t), idx_a and idx_b must be less than "
            "the number of vectors, but %d >= %d or %d >= %d\n",
            idx_a, lhs->get_num_vectors(), idx_b, rhs->get_num_vectors())

    if (precompute_matrix && (precomputed_matrix==NULL) && (lhs==rhs))
        do_precompute_matrix() ;

    if (precompute_matrix && (precomputed_matrix!=NULL))
    {
        if (idx_a>=idx_b)
            return precomputed_matrix[idx_a*(idx_a+1)/2+idx_b] ;
        else
            return precomputed_matrix[idx_b*(idx_b+1)/2+idx_a] ;
    }

    return compute(idx_a, idx_b);
}

void CDistance::do_precompute_matrix()
{
    int32_t num_left=lhs->get_num_vectors();
    int32_t num_right=rhs->get_num_vectors();
    SG_INFO("precomputing distance matrix (%ix%i)\n", num_left, num_right)

    ASSERT(num_left==num_right)
    ASSERT(lhs==rhs)
    int32_t num=num_left;

    SG_FREE(precomputed_matrix);
    precomputed_matrix=SG_MALLOC(float32_t, num*(num+1)/2);

    for (int32_t i=0; i<num; i++)
    {
        SG_PROGRESS(i*i,0,num*num)
        for (int32_t j=0; j<=i; j++)
            precomputed_matrix[i*(i+1)/2+j] = compute(i,j) ;
    }

    SG_PROGRESS(num*num,0,num*num)
    SG_DONE()
}

void CDistance::init()
{
    precomputed_matrix = NULL;
    precompute_matrix = false;
    lhs = NULL;
    rhs = NULL;
    num_lhs=0;
    num_rhs=0;

    m_parameters->add((CSGObject**) &lhs, "lhs",
                      "Feature vectors to occur on left hand side.");
    m_parameters->add((CSGObject**) &rhs, "rhs",
                      "Feature vectors to occur on right hand side.");
}

template <class T> void* CDistance::get_distance_matrix_helper(void* p)
{
    D_THREAD_PARAM<T>* params= (D_THREAD_PARAM<T>*) p;
    int32_t i_start=params->start;
    int32_t i_end=params->end;
    CDistance* k=params->distance;
    T* result=params->result;
    bool symmetric=params->symmetric;
    int32_t n=params->n;
    int32_t m=params->m;
    bool verbose=params->verbose;
    int64_t total_start=params->total_start;
    int64_t total_end=params->total_end;
    int64_t total=total_start;

    for (int32_t i=i_start; i<i_end; i++)
    {
        int32_t j_start=0;

        if (symmetric)
            j_start=i;

        for (int32_t j=j_start; j<n; j++)
        {
            float64_t v=k->distance(i,j);
            result[i+j*m]=v;

            if (symmetric && i!=j)
                result[j+i*m]=v;

            if (verbose)
            {
                total++;

                if (symmetric && i!=j)
                    total++;

                if (total%100 == 0)
                    SG_OBJ_PROGRESS(k, total, total_start, total_end)

                if (CSignal::cancel_computations())
                    break;
            }
        }

    }

    return NULL;
}

template <class T>
SGMatrix<T> CDistance::get_distance_matrix()
{
    T* result = NULL;

    REQUIRE(has_features(), "no features assigned to distance\n")

    int32_t m=get_num_vec_lhs();
    int32_t n=get_num_vec_rhs();

    int64_t total_num = int64_t(m)*n;

    // if lhs == rhs and sizes match assume k(i,j)=k(j,i)
    bool symmetric= (lhs && lhs==rhs && m==n);

    SG_DEBUG("returning distance matrix of size %dx%d\n", m, n)

        result=SG_MALLOC(T, total_num);

    int32_t num_threads=parallel->get_num_threads();
    if (num_threads < 2)
    {
        D_THREAD_PARAM<T> params;
        params.distance=this;
        params.result=result;
        params.start=0;
        params.end=m;
        params.total_start=0;
        params.total_end=total_num;
        params.n=n;
        params.m=m;
        params.symmetric=symmetric;
        params.verbose=true;
        get_distance_matrix_helper<T>((void*) &params);
    }
    else
    {
        pthread_t* threads = SG_MALLOC(pthread_t, num_threads-1);
        D_THREAD_PARAM<T>* params = SG_MALLOC(D_THREAD_PARAM<T>, num_threads);
        int64_t step= total_num/num_threads;

        int32_t t;

        num_threads--;
        for (t=0; t<num_threads; t++)
        {
            params[t].distance = this;
            params[t].result = result;
            params[t].start = compute_row_start(t*step, n, symmetric);
            params[t].end = compute_row_start((t+1)*step, n, symmetric);
            params[t].total_start=t*step;
            params[t].total_end=(t+1)*step;
            params[t].n=n;
            params[t].m=m;
            params[t].symmetric=symmetric;
            params[t].verbose=false;

            int code=pthread_create(&threads[t], NULL,
                    CDistance::get_distance_matrix_helper<T>, (void*)&params[t]);

            if (code != 0)
            {
                SG_WARNING("Thread creation failed (thread %d of %d) "
                        "with error:'%s'\n",t, num_threads, strerror(code));
                num_threads=t;
                break;
            }
        }

        params[t].distance = this;
        params[t].result = result;
        params[t].start = compute_row_start(t*step, n, symmetric);
        params[t].end = m;
        params[t].total_start=t*step;
        params[t].total_end=total_num;
        params[t].n=n;
        params[t].m=m;
        params[t].symmetric=symmetric;
        params[t].verbose=true;
        get_distance_matrix_helper<T>(&params[t]);

        for (t=0; t<num_threads; t++)
        {
            if (pthread_join(threads[t], NULL) != 0)
                SG_WARNING("pthread_join of thread %d/%d failed\n", t, num_threads)
        }

        SG_FREE(params);
        SG_FREE(threads);
    }

    SG_DONE()

    return SGMatrix<T>(result,m,n,true);
}

template SGMatrix<float64_t> CDistance::get_distance_matrix<float64_t>();
template SGMatrix<float32_t> CDistance::get_distance_matrix<float32_t>();

template void* CDistance::get_distance_matrix_helper<float64_t>(void* p);
template void* CDistance::get_distance_matrix_helper<float32_t>(void* p);