SHOGUN
v3.2.0
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00001 /* 00002 * This program is free software; you can redistribute it and/or modify 00003 * it under the terms of the GNU General Public License as published by 00004 * the Free Software Foundation; either version 3 of the License, or 00005 * (at your option) any later version. 00006 * 00007 * Written (W) 2011 Sergey Lisitsyn 00008 * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society 00009 */ 00010 00011 #include <shogun/converter/DiffusionMaps.h> 00012 #include <shogun/converter/EmbeddingConverter.h> 00013 #include <shogun/lib/config.h> 00014 #ifdef HAVE_EIGEN3 00015 #include <shogun/distance/EuclideanDistance.h> 00016 #include <shogun/lib/tapkee/tapkee_shogun.hpp> 00017 00018 using namespace shogun; 00019 00020 CDiffusionMaps::CDiffusionMaps() : 00021 CEmbeddingConverter() 00022 { 00023 m_t = 10; 00024 m_width = 1.0; 00025 set_distance(new CEuclideanDistance()); 00026 00027 init(); 00028 } 00029 00030 void CDiffusionMaps::init() 00031 { 00032 SG_ADD(&m_t, "t", "number of steps", MS_AVAILABLE); 00033 SG_ADD(&m_width, "width", "gaussian kernel width", MS_AVAILABLE); 00034 } 00035 00036 CDiffusionMaps::~CDiffusionMaps() 00037 { 00038 } 00039 00040 void CDiffusionMaps::set_t(int32_t t) 00041 { 00042 m_t = t; 00043 } 00044 00045 int32_t CDiffusionMaps::get_t() const 00046 { 00047 return m_t; 00048 } 00049 00050 void CDiffusionMaps::set_width(float64_t width) 00051 { 00052 m_width = width; 00053 } 00054 00055 float64_t CDiffusionMaps::get_width() const 00056 { 00057 return m_width; 00058 } 00059 00060 const char* CDiffusionMaps::get_name() const 00061 { 00062 return "DiffusionMaps"; 00063 }; 00064 00065 CFeatures* CDiffusionMaps::apply(CFeatures* features) 00066 { 00067 ASSERT(features) 00068 // shorthand for simplefeatures 00069 SG_REF(features); 00070 // compute distance matrix 00071 ASSERT(m_distance) 00072 m_distance->init(features,features); 00073 CDenseFeatures<float64_t>* embedding = embed_distance(m_distance); 00074 m_distance->cleanup(); 00075 SG_UNREF(features); 00076 return (CFeatures*)embedding; 00077 } 00078 00079 CDenseFeatures<float64_t>* CDiffusionMaps::embed_distance(CDistance* distance) 00080 { 00081 TAPKEE_PARAMETERS_FOR_SHOGUN parameters; 00082 parameters.n_timesteps = m_t; 00083 parameters.gaussian_kernel_width = m_width; 00084 parameters.method = SHOGUN_DIFFUSION_MAPS; 00085 parameters.target_dimension = m_target_dim; 00086 parameters.distance = distance; 00087 return tapkee_embed(parameters); 00088 } 00089 #endif /* HAVE_EIGEN3 */