From 8f26e69f4628d1ca0bed4826a7829b9be95f1013 Mon Sep 17 00:00:00 2001
From: TheBloodthirster <13606074505@163.com>
Date: Fri, 28 Aug 2020 18:02:58 +0800
Subject: [PATCH] update kmeans (#3489)

Signed-off-by: hjp <13606074505@163.com>
---
 .../src/index/thirdparty/faiss/Clustering.cpp | 139 ++++++++++++++++--
 core/src/index/thirdparty/faiss/Clustering.h  |  31 ++++
 2 files changed, 157 insertions(+), 13 deletions(-)
 mode change 100644 => 100755 core/src/index/thirdparty/faiss/Clustering.cpp
 mode change 100644 => 100755 core/src/index/thirdparty/faiss/Clustering.h

diff --git a/core/src/index/thirdparty/faiss/Clustering.cpp b/core/src/index/thirdparty/faiss/Clustering.cpp
old mode 100644
new mode 100755
index eba243d1..017fb199
--- a/core/src/index/thirdparty/faiss/Clustering.cpp
+++ b/core/src/index/thirdparty/faiss/Clustering.cpp
@@ -20,6 +20,7 @@
 #include <faiss/utils/random.h>
 #include <faiss/utils/distances.h>
 #include <faiss/impl/FaissAssert.h>
+#include <faiss/FaissHook.h>
 #include <faiss/IndexFlat.h>
 
 namespace faiss {
@@ -258,11 +259,115 @@ int split_clusters (size_t d, size_t k, size_t n,
     return nsplit;
 
 }
+};
+KmeansType kmeans_type = KmeansType::KMEANS;
 
+void Clustering::kmeans_algorithm(std::vector<int>& centroids_index, int64_t random_seed,
+                                  size_t n_input_centroids, size_t d, size_t k,
+                                  idx_t nx, const uint8_t *x_in)
+{
+    // centroids with random points from the dataset
+    rand_perm (centroids_index.data(), nx, random_seed);
+}
 
+void Clustering::kmeans_plus_plus_algorithm(std::vector<int>& centroids_index, int64_t random_seed,
+                                            size_t n_input_centroids, size_t d,
+                                            size_t k, idx_t nx, const uint8_t *x_in)
+{
+    FAISS_THROW_IF_NOT_MSG (
+       n_input_centroids == 0,
+       "Kmeans plus plus only support the provided input centroids number of zero"
+    );
 
-};
+    size_t thread_max_num = omp_get_max_threads();
+    auto x = reinterpret_cast<const float*>(x_in);
+
+    // The square of distance to current centroid
+    std::vector<float> dx_distance(nx, 1.0 / 0.0);
+    std::vector<float> pre_sum(nx);
+
+    // task of each thread when calculate P(x)
+    std::vector<size_t> task(thread_max_num, nx);
+    size_t step = (nx + thread_max_num - 1) / thread_max_num;
+    for (size_t i = 0; i + 1 < thread_max_num; i++) {
+        task[i] = (i + 1) * step;
+    }
+
+    // Record the centroids that has been calculated
+    // Input :
+    // nx : int -> nb of points
+    // d : size_t -> nb of dimensions
+    // k : size_t -> nb of centroids
+    // x : unsigned char -> data : the x[i*d] means the i-th point's d-th value
+    // Output:
+    // centroids : array -> the cluster centers
+
+    // 1. get the pre-n-input-centroids: if equal to 0, 
+    //   then should get the first random start point
+    RandomGenerator rng (random_seed);
+    //if (n_input_centroids == 0) {}
+    size_t first_center;
+    first_center = static_cast<size_t>(rng.rand_int64() % nx);
+    centroids_index[0] = first_center;
+    
+    // 2. use the first few centroids to calculate the next centroid,and already has first random start point
+    //size_t current_centroids = n_input_centroids == 0 ? 1 : n_input_centroids;
+    size_t current_centroids = 1;
+    // For every epoch there is i-th centroids,and we want to calculate the i+1 centroid
+    for (size_t i = current_centroids; i < k; i++) {
+        auto last_centroids_data = x + centroids_index[i - 1] * d;
+        // for every point
+        #pragma omp parallel for
+        for (size_t point_it = 0; point_it < nx; point_it++) {
+            float distance_of_point_and_centroid = 0;
+            distance_of_point_and_centroid = fvec_L2sqr((x + point_it * d), last_centroids_data, d);
+            if (distance_of_point_and_centroid < dx_distance[point_it]) {
+                dx_distance[point_it] = distance_of_point_and_centroid;
+            }
+        }
+
+        //calculate P(x)
+        #pragma omp parallel for
+        for (size_t point_it = 0; point_it < thread_max_num; point_it++) {
+            size_t left = point_it == 0 ? 0 : task[point_it - 1];
+            size_t right = task[point_it];
+            // cout <<"Thread = "<< omp_get_thread_num() <<" left = "<<left<<" right = "<<right << endl;
+            pre_sum[left] = dx_distance[left];
+            for (size_t j = left + 1; j < right; j++) {
+                pre_sum[j] = pre_sum[j - 1] + dx_distance[j];
+            }
+        }
+        float sum = 0.0;
+        for (size_t point_it = 0; point_it < thread_max_num; point_it++) {
+            sum += pre_sum[task[point_it] - 1];
+        }
 
+        // the random num is [0,sum]
+        float choose_centroid_random = rng.rand_double() * sum;
+
+        size_t task_i = 0;
+        for (task_i = 0; task_i < thread_max_num; task_i++) {
+            auto task_pre_sum = pre_sum[task[task_i] - 1];
+            if (choose_centroid_random - task_pre_sum <= 0) {
+                break;
+            }
+            choose_centroid_random -= task_pre_sum;
+        }
+
+        size_t left = task_i == 0 ? 0 : task[task_i - 1];
+        size_t right = task[task_i];
+
+        //find the next centroid using Binary search and the left is what we want
+        while(left < right) {
+            size_t mid = left + (right - left) / 2;
+            if (pre_sum[mid] < choose_centroid_random)
+                left = mid + 1;
+            else
+                right = mid;
+        }
+        centroids_index[i] = left;
+    }
+}   
 
 void Clustering::train_encoded (idx_t nx, const uint8_t *x_in,
                                 const Index * codec, Index & index,
@@ -384,23 +489,31 @@ void Clustering::train_encoded (idx_t nx, const uint8_t *x_in,
             printf("Outer iteration %d / %d\n", redo, nredo);
         }
 
-        // initialize (remaining) centroids with random points from the dataset
-        centroids.resize (d * k);
-        std::vector<int> perm (nx);
-
-        rand_perm (perm.data(), nx, seed + 1 + redo * 15486557L);
+        {
+            int64_t random_seed = seed + 1 + redo * 15486557L;
+            std::vector<int> centroids_index(nx);
 
-        if (!codec) {
-            for (int i = n_input_centroids; i < k ; i++) {
-                memcpy (&centroids[i * d], x + perm[i] * line_size, line_size);
+            if (KmeansType::KMEANS == kmeans_type) {
+                //Use classic kmeans algorithm
+                kmeans_algorithm(centroids_index, random_seed, n_input_centroids, d, k, nx, x_in);
+            } else if (KmeansType::KMEANS_PLUSPLUS == kmeans_type) {
+                //Use kmeans++ algorithm
+                kmeans_plus_plus_algorithm(centroids_index, random_seed, n_input_centroids, d, k, nx, x_in);
             }
-        } else {
-            for (int i = n_input_centroids; i < k ; i++) {
-                codec->sa_decode (1, x + perm[i] * line_size, &centroids[i * d]);
+
+            centroids.resize(d * k);
+            if (!codec) {
+                for (int i = n_input_centroids; i < k; i++) {
+                    memcpy(&centroids[i * d], x + centroids_index[i] * line_size, line_size);
+                }
+            } else {
+                for (int i = n_input_centroids; i < k; i++) {
+                    codec->sa_decode(1, x + centroids_index[i] * line_size, &centroids[i * d]);
+                }
             }
         }
 
-        post_process_centroids ();
+        post_process_centroids();
 
         // prepare the index
 
diff --git a/core/src/index/thirdparty/faiss/Clustering.h b/core/src/index/thirdparty/faiss/Clustering.h
old mode 100644
new mode 100755
index 46410af7..e4818860
--- a/core/src/index/thirdparty/faiss/Clustering.h
+++ b/core/src/index/thirdparty/faiss/Clustering.h
@@ -15,6 +15,19 @@
 
 namespace faiss {
 
+/**
+ * The algorithm of Kmeans Type
+ */
+enum KmeansType
+{
+    KMEANS,
+    KMEANS_PLUSPLUS,
+    KMEANS_TWO,
+};
+
+//The default algorithm use the KMEANS_PLUSPLUS
+extern KmeansType kmeans_type;
+
 
 /** Class for the clustering parameters. Can be passed to the
  * constructor of the Clustering object.
@@ -87,6 +100,24 @@ struct Clustering: ClusteringParameters {
     virtual void train (idx_t n, const float * x, faiss::Index & index,
                         const float *x_weights = nullptr);
 
+    /**
+     * @brief Kmeans algorithm
+     * 
+     * @param centroids_index   [out] centroids index
+     * @param random_seed       seed for the random number generator
+     * @param n_input_centroids the number of centroids that user input
+     * @param d                 dimension
+     * @param k                 number of centroids
+     * @param nx                size of data
+     * @param x_in              data of point
+     */
+    void kmeans_algorithm(std::vector<int>& centroids_index, int64_t random_seed,
+                          size_t n_input_centroids, size_t d, size_t k,
+                          idx_t nx, const uint8_t *x_in);
+
+    void kmeans_plus_plus_algorithm(std::vector<int>& centroids_index, int64_t random_seed,
+                                    size_t n_input_centroids, size_t d, size_t k,
+                                    idx_t nx, const uint8_t *x_in);
 
     /** run with encoded vectors
      *
-- 
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