tapkee_shogun.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.
 *
 * Copyright (c) 2012-2013 Sergey Lisitsyn
 */

#include <shogun/lib/tapkee/tapkee_shogun.hpp>


#define CUSTOM_UNIFORM_RANDOM_INDEX_FUNCTION shogun::CMath::random()
#define CUSTOM_UNIFORM_RANDOM_FUNCTION shogun::CMath::random(static_cast<tapkee::ScalarType>(0),static_cast<tapkee::ScalarType>(1))
#define CUSTOM_GAUSSIAN_RANDOM_FUNCTION shogun::CMath::normal_random(static_cast<tapkee::ScalarType>(0),static_cast<tapkee::ScalarType>(1))
#define TAPKEE_EIGEN_INCLUDE_FILE <shogun/mathematics/eigen3.h>

#ifdef HAVE_ARPACK
    #define TAPKEE_WITH_ARPACK
#endif
#define TAPKEE_USE_LGPL_COVERTREE
#include <shogun/lib/tapkee/tapkee.hpp>
#include <shogun/lib/tapkee/callbacks/pimpl_callbacks.hpp>

using namespace shogun;

class ShogunLoggerImplementation : public tapkee::LoggerImplementation
{
    virtual void message_info(const std::string& msg)
    {
        SG_SINFO((msg+"\n").c_str())
    }
    virtual void message_warning(const std::string& msg)
    {
        SG_SWARNING((msg+"\n").c_str())
    }
    virtual void message_error(const std::string& msg)
    {
        SG_SERROR((msg+"\n").c_str())
    }
    virtual void message_debug(const std::string& msg)
    {
        SG_SDEBUG((msg+"\n").c_str())
    }
    virtual void message_benchmark(const std::string& msg)
    {
        SG_SINFO((msg+"\n").c_str())
    }
};

struct ShogunFeatureVectorCallback
{
    ShogunFeatureVectorCallback(CDotFeatures* f) : dim(0), features(f) { }
    inline tapkee::IndexType dimension() const
    {
        if (features)
            return (dim = features->get_dim_feature_space());

        return 0;
    }
    inline void vector(int i, tapkee::DenseVector& v) const
    {
        v.setZero();
        features->add_to_dense_vec(1.0,i,v.data(),dim);
    }
    mutable int32_t dim;
    CDotFeatures* features;
};


CDenseFeatures<float64_t>* shogun::tapkee_embed(const shogun::TAPKEE_PARAMETERS_FOR_SHOGUN& parameters)
{
    tapkee::LoggingSingleton::instance().set_logger_impl(new ShogunLoggerImplementation);
    tapkee::LoggingSingleton::instance().enable_benchmark();
    tapkee::LoggingSingleton::instance().enable_info();

    pimpl_kernel_callback<CKernel> kernel_callback(parameters.kernel);
    pimpl_distance_callback<CDistance> distance_callback(parameters.distance);
    ShogunFeatureVectorCallback features_callback(parameters.features);

    tapkee::DimensionReductionMethod method;
#ifdef HAVE_ARPACK
    tapkee::EigenMethod eigen_method = tapkee::Arpack;
#else
    tapkee::EigenMethod eigen_method = tapkee::Dense;
#endif
    tapkee::NeighborsMethod neighbors_method = tapkee::CoverTree;
    size_t N = 0;

    switch (parameters.method)
    {
        case SHOGUN_KERNEL_LOCALLY_LINEAR_EMBEDDING:
        case SHOGUN_LOCALLY_LINEAR_EMBEDDING:
            method = tapkee::KernelLocallyLinearEmbedding;
            N = parameters.kernel->get_num_vec_lhs();
            break;
        case SHOGUN_NEIGHBORHOOD_PRESERVING_EMBEDDING:
            method = tapkee::NeighborhoodPreservingEmbedding;
            N = parameters.kernel->get_num_vec_lhs();
            break;
        case SHOGUN_LOCAL_TANGENT_SPACE_ALIGNMENT:
            method = tapkee::KernelLocalTangentSpaceAlignment;
            N = parameters.kernel->get_num_vec_lhs();
            break;
        case SHOGUN_LINEAR_LOCAL_TANGENT_SPACE_ALIGNMENT:
            method = tapkee::LinearLocalTangentSpaceAlignment;
            N = parameters.kernel->get_num_vec_lhs();
            break;
        case SHOGUN_HESSIAN_LOCALLY_LINEAR_EMBEDDING:
            method = tapkee::HessianLocallyLinearEmbedding;
            N = parameters.kernel->get_num_vec_lhs();
            break;
        case SHOGUN_DIFFUSION_MAPS:
            method = tapkee::DiffusionMap;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_LAPLACIAN_EIGENMAPS:
            method = tapkee::LaplacianEigenmaps;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_LOCALITY_PRESERVING_PROJECTIONS:
            method = tapkee::LocalityPreservingProjections;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_MULTIDIMENSIONAL_SCALING:
            method = tapkee::MultidimensionalScaling;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_LANDMARK_MULTIDIMENSIONAL_SCALING:
            method = tapkee::LandmarkMultidimensionalScaling;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_ISOMAP:
            method = tapkee::Isomap;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_LANDMARK_ISOMAP:
            method = tapkee::LandmarkIsomap;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_STOCHASTIC_PROXIMITY_EMBEDDING:
            method = tapkee::StochasticProximityEmbedding;
            N = parameters.distance->get_num_vec_lhs();
            break;
        case SHOGUN_FACTOR_ANALYSIS:
            method = tapkee::FactorAnalysis;
            N = parameters.features->get_num_vectors();
            break;
        case SHOGUN_TDISTRIBUTED_STOCHASTIC_NEIGHBOR_EMBEDDING:
            method = tapkee::tDistributedStochasticNeighborEmbedding;
            N = parameters.features->get_num_vectors();
            break;
        case SHOGUN_MANIFOLD_SCULPTING:
            method = tapkee::ManifoldSculpting;
            N = parameters.features->get_num_vectors();
            break;
    }

    std::vector<int32_t> indices(N);
    for (size_t i=0; i<N; i++)
        indices[i] = i;

    tapkee::ParametersSet parameters_set =
        (tapkee::keywords::method=method,
         tapkee::keywords::eigen_method=eigen_method,
         tapkee::keywords::neighbors_method=neighbors_method,
         tapkee::keywords::num_neighbors=parameters.n_neighbors,
         tapkee::keywords::diffusion_map_timesteps = parameters.n_timesteps,
         tapkee::keywords::target_dimension = parameters.target_dimension,
         tapkee::keywords::spe_num_updates = parameters.spe_num_updates,
         tapkee::keywords::nullspace_shift = parameters.eigenshift,
         tapkee::keywords::landmark_ratio = parameters.landmark_ratio,
         tapkee::keywords::gaussian_kernel_width = parameters.gaussian_kernel_width,
         tapkee::keywords::spe_tolerance = parameters.spe_tolerance,
         tapkee::keywords::spe_global_strategy = parameters.spe_global_strategy,
         tapkee::keywords::max_iteration = parameters.max_iteration,
         tapkee::keywords::fa_epsilon = parameters.fa_epsilon,
         tapkee::keywords::sne_perplexity = parameters.sne_perplexity,
         tapkee::keywords::sne_theta = parameters.sne_theta,
         tapkee::keywords::squishing_rate = parameters.squishing_rate
         );

    tapkee::TapkeeOutput output = tapkee::embed(indices.begin(),indices.end(),
            kernel_callback,distance_callback,features_callback,parameters_set);
    tapkee::DenseMatrix result_embedding = output.embedding;
    // destroy projecting function
    output.projection.clear();

    SGMatrix<float64_t> feature_matrix(parameters.target_dimension,N);
    // TODO avoid copying
    for (uint32_t i=0; i<N; i++)
    {
        for (uint32_t j=0; j<parameters.target_dimension; j++)
        {
            feature_matrix(j,i) = result_embedding(i,j);
        }
    }
    return new CDenseFeatures<float64_t>(feature_matrix);
}