Add similaritys

app/src/DnaStore.cpp

@@ -16,7 +16,7 @@
 #define DATA_FILE_NAME "DATA.bin"
 #define VECTOR_FILE_NAME "VECTOR.bin"
 #define GEN_FILE_PATTRN "gen/%04d.bin"
-#define HOST_NAME "petrovv.com"
+#define HOST_NAME "localhost"
 
 void DnaStore::load(DnaManagerData *data)
 {

shared/inc/values/Dna.hpp

@@ -9,8 +9,6 @@
 #define MAX_DEPTH 8
 #define MAX_POSIBLE_DEPTH 11
 static_assert(MAX_DEPTH <= MAX_POSIBLE_DEPTH);
-static_assert(180 == sizeof(Dna));
-constexpr int SIZE_OF_DNA = sizeof(Dna);
 
 struct Branch
 {

shared/inc/values/Similarity.hpp

@@ -3,14 +3,14 @@
 
 namespace Similarity
 {
-  // float euclidean_distance(Dna *d1, Dna *d2); direct distance betwen vector. wont give 0 and 1
+  float euclidean_distance(Dna *d1, Dna *d2);// direct distance betwen vector. wont give 0 and 1
-  // float dot_product(Dna *d1, Dna *d2); doent return betwen 0 to 1
+  // float dot_product(Dna *d1, Dna *d2); // doent return betwen 0 to 1
-  // float cosine_similarity(Dna *d1, Dna *d2);
+  float cosine_similarity(Dna *d1, Dna *d2);
-  // float cosine_similarity_int(Dna *d1, Dna *d2);
+  float cosine_similarity_int(Dna *d1, Dna *d2);
   float hamming_distance(Dna *d1, Dna *d2);
   float hamming_distance_without_seeds(Dna *d1, Dna *d2);
   // float jaccard_index(Dna *d1, Dna *d2); // primerja unio genov naprimer gleda ce je gen za nebo isti z genom za barvo za liste, to nerabimo
-  // float levenshtein_distance(Dna *d1, Dna *d2); // odstranjen ker mi vrne iste podatke kot hamming distance ki je bolj enostaven za izracun
+  float levenshtein_distance(Dna *d1, Dna *d2); // odstranjen ker mi vrne iste podatke kot hamming distance ki je bolj enostaven za izracun
   // float needleman_wunsch(Dna *d1, Dna *d2); used for bioinformatics and aligment. Dont need its aligned alredy
 
   typedef float(simil_func)(Dna *d1, Dna *d2);

shared/src/values/Similarity.cpp

@@ -1,56 +1,72 @@
 #include "values/Similarity.hpp"
 #include <cmath>
+#include <algorithm>
+#include <numeric>
+#include <raylib.h>
 
 namespace Similarity
 {
+
+  float euclidean_distance(Dna *d1, Dna *d2)
+  {
+    uint8_t *a = (uint8_t *)d1;
+    uint8_t *b = (uint8_t *)d2;
+    float sum = 0.0f;
+    for (size_t i = 0; i < sizeof(Dna); ++i) {
+        float diff = static_cast<float>(a[i]) - static_cast<float>(b[i]);
+        sum += diff * diff;
+    }
+
+    float distance = std::sqrt(sum);
+    float max_distance = 255.0f * std::sqrt(static_cast<float>(sizeof(Dna)));
+    return distance / max_distance;
+  }
+
   // todo: use int8_t insted of uint8_t and map data
   // 0 -> -128
   // 255 -> 127
   // int8_t = uint8_t - 128
-  // float cosine_similarity(Dna *d1, Dna *d2)
+  float cosine_similarity(Dna *d1, Dna *d2)
-  // {
+  {
-  //   uint8_t *d1a = (uint8_t *)d1;
+    uint8_t *d1a = (uint8_t *)d1;
-  //   uint8_t *d2a = (uint8_t *)d2;
+    uint8_t *d2a = (uint8_t *)d2;
 
-  //   float mag1 = 0.0f;
+    float mag1 = 0.0f;
-  //   float mag2 = 0.0f;
+    float mag2 = 0.0f;
-  //   float dot_prod = 0.0f;
+    float dot_prod = 0.0f;
-  //   for (size_t i = 0; i < sizeof(Dna); i++)
+    for (size_t i = 0; i < sizeof(Dna); i++)
-  //   {
+    {
-  //     dot_prod += d1a[i] * d2a[i];
+      dot_prod += d1a[i] * d2a[i];
-  //     mag1 += d1a[i] * d1a[i];
+      mag1 += d1a[i] * d1a[i];
-  //     mag2 += d2a[i] * d2a[i];
+      mag2 += d2a[i] * d2a[i];
-  //   }
+    }
-  //   mag1 = sqrt(mag1);
+    mag1 = sqrt(mag1);
-  //   mag2 = sqrt(mag2);
+    mag2 = sqrt(mag2);
 
-  //   return dot_prod / (mag1 * mag2);
+    return dot_prod / (mag1 * mag2);
-  // }
+  }
 
-  // float cosine_similarity_int(Dna *d1, Dna *d2)
+  float cosine_similarity_int(Dna *d1, Dna *d2)
-  // {
+  {
-  //   auto map = [](uint8_t a) -> int8_t
+    auto map = [](uint8_t a) -> int8_t
-  //   { return a - 128; };
+    { return a - 128; };
-
+    uint8_t *d1a = (uint8_t *)d1;
-  //   uint8_t *d1a = (uint8_t *)d1;
+    uint8_t *d2a = (uint8_t *)d2;
-  //   uint8_t *d2a = (uint8_t *)d2;
+    float mag1 = 0.0f;
-
+    float mag2 = 0.0f;
-  //   float mag1 = 0.0f;
+    float dot_prod = 0.0f;
-  //   float mag2 = 0.0f;
+    for (size_t i = 0; i < sizeof(Dna); i++)
-  //   float dot_prod = 0.0f;
+    {
-  //   for (size_t i = 0; i < sizeof(Dna); i++)
+      int8_t a = map(d1a[i]);
-  //   {
+      int8_t b = map(d2a[i]);
-  //     int8_t a = map(d1a[i]);
+      dot_prod += a * b;
-  //     int8_t b = map(d2a[i]);
+      mag1 += a * a;
-  //     dot_prod += a * b;
+      mag2 += b * b;
-  //     mag1 += a * a;
+    }
-  //     mag2 += b * b;
+    mag1 = sqrt(mag1);
-  //   }
+    mag2 = sqrt(mag2);
-  //   mag1 = sqrt(mag1);
+    return dot_prod / (mag1 * mag2);
-  //   mag2 = sqrt(mag2);
+  }
-
-  //   return dot_prod / (mag1 * mag2);
-  // }
 
   float hamming_distance(Dna *d1, Dna *d2)
   {
@@ -99,4 +115,40 @@ namespace Similarity
     float average_similarity = total_similarity / num_pairs;
     return average_similarity * 100.0f;
   }
+
+  float levenshtein_distance(Dna *d1, Dna *d2)
+  {
+    size_t len = sizeof(Dna);
+    uint8_t *a = (uint8_t *)d1;
+    uint8_t *b = (uint8_t *)d2;
+
+    // Create a distance matrix
+    std::vector<std::vector<uint32_t>> dp(len + 1, std::vector<uint32_t>(len + 1, 0));
+
+    // Initialize the first row and column
+    for (size_t i = 0; i <= len; ++i)
+    {
+      dp[i][0] = i;
+    }
+    for (size_t j = 0; j <= len; ++j)
+    {
+      dp[0][j] = j;
+    }
+
+    // Fill the distance matrix
+    for (size_t i = 1; i <= len; ++i)
+    {
+      for (size_t j = 1; j <= len; ++j)
+      {
+        uint32_t cost = (a[i - 1] == b[j - 1]) ? 0 : 1;
+        dp[i][j] = std::min({
+            dp[i - 1][j] + 1,       // deletion
+            dp[i][j - 1] + 1,       // insertion
+            dp[i - 1][j - 1] + cost // substitution
+        });
+      }
+    }
+    return 1 - (dp[len][len] / float (len + len));
+  }
+
 }

view/inc/Vapp.hpp

@@ -14,7 +14,7 @@ enum DrawingStage
   done,
 };
 
-constexpr int numberOfFunc = 2;
+constexpr int numberOfFunc = 6;
 
 class Vapp
 {

view/src/Vapp.cpp

@@ -11,7 +11,7 @@ const char select_user_id[] = "SELECT USER_ID FROM user_table GROUP BY USER_ID;"
 
 constexpr int sizeOfCanvas = 1000;
 
-void Vapp::init(char* filename)
+void Vapp::init(char *filename)
 {
   bigTexture = LoadRenderTexture(sizeOfCanvas * 4, sizeOfCanvas * 4);
   treeTexture = LoadRenderTexture(sizeOfCanvas, sizeOfCanvas);
@@ -100,8 +100,12 @@ void Vapp::update()
     break;
   case DrawingStage::calSim:
 
-    simil[0] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+    simil[0] = Similarity::calc_similarity(manager.vector, Similarity::euclidean_distance);
-    simil[1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
+    simil[1] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity);
+    simil[2] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity_int);
+    simil[3] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+    simil[4] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
+    simil[5] = Similarity::calc_similarity(manager.vector, Similarity::levenshtein_distance);
     stageOfDrawing = DrawingStage::done;
     break;
 
@@ -173,13 +177,35 @@ void Vapp::draw()
   if (showStats)
   {
     ImGui::Begin("Status", &showStats);
-    ImGui::LabelText("##sim1", "hamming_distance: %f", simil[0]);
+    ImGui::LabelText("##sim1", "euclidean_distance: %f", simil[0]);
-    ImGui::LabelText("##sim2", "hamming_distance_without_seeds: %f", simil[1]);
+    ImGui::LabelText("##sim2", "cosine_similarity: %f", simil[1]);
+    ImGui::LabelText("##sim3", "cosine_similarity_int: %f", simil[2]);
+    ImGui::LabelText("##sim4", "hamming_distance: %f", simil[3]);
+    ImGui::LabelText("##sim5", "hamming_distance_without_seeds: %f", simil[4]);
+    ImGui::LabelText("##sim6", "levenshtein_distance: %f", simil[5]);
 
     const ImGuiTableFlags flags = ImGuiTableFlags_NoHostExtendX | ImGuiTableFlags_SizingFixedFit | ImGuiTableFlags_Resizable | ImGuiTableFlags_BordersOuter | ImGuiTableFlags_BordersV | ImGuiTableFlags_ContextMenuInBody;
     const int columns = numberOfFunc + 1;
     if (ImGui::BeginTable("table1", columns, flags))
     {
+
+      ImGui::TableNextRow();
+
+      ImGui::TableSetColumnIndex(0);
+      ImGui::Text("index");
+      ImGui::TableSetColumnIndex(1);
+      ImGui::Text("euclidean_distance");
+      ImGui::TableSetColumnIndex(2);
+      ImGui::Text("cosine_similarity");
+      ImGui::TableSetColumnIndex(3);
+      ImGui::Text("cosine_similarity_int");
+      ImGui::TableSetColumnIndex(4);
+      ImGui::Text("hamming_distance");
+      ImGui::TableSetColumnIndex(5);
+      ImGui::Text("hamming_distance_without_seeds");
+      ImGui::TableSetColumnIndex(6);
+      ImGui::Text("levenshtein_distance");
+
       for (int row = 0; row < similTable.size(); row++)
       {
         ImGui::TableNextRow();
@@ -277,7 +303,7 @@ void Vapp::setUpTable()
       UiUnit unit = DnaManager::next(&manager);
       if ((unit.index != pos))
       {
-        // DOTO: SET ERROR
+        // TODO: SET ERROR
         TraceLog(LOG_ERROR, "LOADING DNA");
         sql::finalize(get_gen_stmt);
         return;
@@ -290,9 +316,13 @@ void Vapp::setUpTable()
     {
       similTable.emplace_back();
       int s = similTable.size() - 1;
-      similTable[s][0] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
-      similTable[s][1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
 
+      similTable[s][0] = Similarity::calc_similarity(manager.vector, Similarity::euclidean_distance);
+      similTable[s][1] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity);
+      similTable[s][2] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity_int);
+      similTable[s][3] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+      similTable[s][4] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
+      similTable[s][5] = Similarity::calc_similarity(manager.vector, Similarity::levenshtein_distance);
       DnaManager::newGen(&manager);
     }
     else