SHOGUN v0.9.0
|
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) 2009 Soeren Sonnenburg 00008 * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society 00009 */ 00010 00011 #include "features/ExplicitSpecFeatures.h" 00012 #include "lib/io.h" 00013 00014 using namespace shogun; 00015 00016 CExplicitSpecFeatures::CExplicitSpecFeatures(void) :CDotFeatures() 00017 { 00018 SG_UNSTABLE("CExplicitSpecFeatures::CExplicitSpecFeatures(void)", 00019 "\n"); 00020 00021 use_normalization = false; 00022 num_strings = 0; 00023 alphabet_size = 0; 00024 00025 spec_size = 0; 00026 k_spectrum = NULL; 00027 } 00028 00029 00030 CExplicitSpecFeatures::CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize) : CDotFeatures() 00031 { 00032 ASSERT(str); 00033 00034 use_normalization=normalize; 00035 num_strings = str->get_num_vectors(); 00036 spec_size = str->get_num_symbols(); 00037 00038 obtain_kmer_spectrum(str); 00039 00040 SG_DEBUG("SPEC size=%d, num_str=%d\n", spec_size, num_strings); 00041 } 00042 00043 CExplicitSpecFeatures::CExplicitSpecFeatures(const CExplicitSpecFeatures& orig) : CDotFeatures(orig), 00044 num_strings(orig.num_strings), alphabet_size(orig.alphabet_size), spec_size(orig.spec_size) 00045 { 00046 k_spectrum= new float64_t*[num_strings]; 00047 for (int32_t i=0; i<num_strings; i++) 00048 k_spectrum[i]=CMath::clone_vector(k_spectrum[i], spec_size); 00049 } 00050 00051 CExplicitSpecFeatures::~CExplicitSpecFeatures() 00052 { 00053 delete_kmer_spectrum(); 00054 } 00055 00056 float64_t CExplicitSpecFeatures::dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2) 00057 { 00058 ASSERT(df); 00059 ASSERT(df->get_feature_type() == get_feature_type()); 00060 ASSERT(df->get_feature_class() == get_feature_class()); 00061 CExplicitSpecFeatures* sf = (CExplicitSpecFeatures*) df; 00062 00063 ASSERT(vec_idx1 < num_strings); 00064 ASSERT(vec_idx2 < sf->num_strings); 00065 float64_t* vec1=k_spectrum[vec_idx1]; 00066 float64_t* vec2=sf->k_spectrum[vec_idx2]; 00067 00068 return CMath::dot(vec1, vec2, spec_size); 00069 } 00070 00071 float64_t CExplicitSpecFeatures::dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len) 00072 { 00073 ASSERT(vec2_len == spec_size); 00074 ASSERT(vec_idx1 < num_strings); 00075 float64_t* vec1=k_spectrum[vec_idx1]; 00076 float64_t result=0; 00077 00078 for (int32_t i=0; i<spec_size; i++) 00079 result+=vec1[i]*vec2[i]; 00080 00081 return result; 00082 } 00083 00084 void CExplicitSpecFeatures::add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val) 00085 { 00086 ASSERT(vec2_len == spec_size); 00087 ASSERT(vec_idx1 < num_strings); 00088 float64_t* vec1=k_spectrum[vec_idx1]; 00089 00090 if (abs_val) 00091 { 00092 for (int32_t i=0; i<spec_size; i++) 00093 vec2[i]+=alpha*CMath::abs(vec1[i]); 00094 } 00095 else 00096 { 00097 for (int32_t i=0; i<spec_size; i++) 00098 vec2[i]+=alpha*vec1[i]; 00099 } 00100 } 00101 00102 void CExplicitSpecFeatures::obtain_kmer_spectrum(CStringFeatures<uint16_t>* str) 00103 { 00104 k_spectrum= new float64_t*[num_strings]; 00105 00106 for (int32_t i=0; i<num_strings; i++) 00107 { 00108 k_spectrum[i]=new float64_t[spec_size]; 00109 memset(k_spectrum[i], 0, sizeof(float64_t)*spec_size); 00110 00111 int32_t len=0; 00112 bool free_fv; 00113 uint16_t* fv=str->get_feature_vector(i, len, free_fv); 00114 00115 for (int32_t j=0; j<len; j++) 00116 k_spectrum[i][fv[j]]++; 00117 00118 str->free_feature_vector(fv, i, free_fv); 00119 00120 if (use_normalization) 00121 { 00122 float64_t n=0; 00123 for (int32_t j=0; j<spec_size; j++) 00124 n+=CMath::sq(k_spectrum[i][j]); 00125 00126 n=CMath::sqrt(n); 00127 00128 for (int32_t j=0; j<spec_size; j++) 00129 k_spectrum[i][j]/=n; 00130 } 00131 } 00132 } 00133 00134 void CExplicitSpecFeatures::delete_kmer_spectrum() 00135 { 00136 for (int32_t i=0; i<num_strings; i++) 00137 delete[] k_spectrum[i]; 00138 00139 delete[] k_spectrum; 00140 k_spectrum=NULL; 00141 } 00142 00143 CFeatures* CExplicitSpecFeatures::duplicate() const 00144 { 00145 return new CExplicitSpecFeatures(*this); 00146 }