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00011 #include <shogun/features/ExplicitSpecFeatures.h>
00012 #include <shogun/io/SGIO.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= SG_MALLOC(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= SG_MALLOC(float64_t*, num_strings);
00105
00106 for (int32_t i=0; i<num_strings; i++)
00107 {
00108 k_spectrum[i]=SG_MALLOC(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 SG_FREE(k_spectrum[i]);
00138
00139 SG_FREE(k_spectrum);
00140 k_spectrum=NULL;
00141 }
00142
00143 CFeatures* CExplicitSpecFeatures::duplicate() const
00144 {
00145 return new CExplicitSpecFeatures(*this);
00146 }