DiffusionMaps.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) 2011 Sergey Lisitsyn
 * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
 */

#include <shogun/converter/DiffusionMaps.h>
#include <shogun/converter/EmbeddingConverter.h>
#include <shogun/lib/config.h>
#include <shogun/distance/EuclideanDistance.h>
#include <shogun/lib/tapkee/tapkee_shogun.hpp>

using namespace shogun;

CDiffusionMaps::CDiffusionMaps() :
        CEmbeddingConverter()
{
    m_t = 10;
    m_width = 1.0;
    set_distance(new CEuclideanDistance());

    init();
}

void CDiffusionMaps::init()
{
    SG_ADD(&m_t, "t", "number of steps", MS_AVAILABLE);
    SG_ADD(&m_width, "width", "gaussian kernel width", MS_AVAILABLE);
}

CDiffusionMaps::~CDiffusionMaps()
{
}

void CDiffusionMaps::set_t(int32_t t)
{
    m_t = t;
}

int32_t CDiffusionMaps::get_t() const
{
    return m_t;
}

void CDiffusionMaps::set_width(float64_t width)
{
    m_width = width;
}

float64_t CDiffusionMaps::get_width() const
{
    return m_width;
}

const char* CDiffusionMaps::get_name() const
{
    return "DiffusionMaps";
};

CFeatures* CDiffusionMaps::apply(CFeatures* features)
{
    ASSERT(features)
    // shorthand for simplefeatures
    SG_REF(features);
    // compute distance matrix
    ASSERT(m_distance)
    m_distance->init(features,features);
    CDenseFeatures<float64_t>* embedding = embed_distance(m_distance);
    m_distance->cleanup();
    SG_UNREF(features);
    return (CFeatures*)embedding;
}

CDenseFeatures<float64_t>* CDiffusionMaps::embed_distance(CDistance* distance)
{
    TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
    parameters.n_timesteps = m_t;
    parameters.gaussian_kernel_width = m_width;
    parameters.method = SHOGUN_DIFFUSION_MAPS;
    parameters.target_dimension = m_target_dim;
    parameters.distance = distance;
    return tapkee_embed(parameters);
}