1 | /*********************************************************************** |
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2 | * Software License Agreement (BSD License) |
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3 | * |
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4 | * Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved. |
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5 | * Copyright 2008-2009 David G. Lowe (lowe@cs.ubc.ca). All rights reserved. |
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6 | * |
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7 | * THE BSD LICENSE |
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8 | * |
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9 | * Redistribution and use in source and binary forms, with or without |
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10 | * modification, are permitted provided that the following conditions |
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11 | * are met: |
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12 | * |
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13 | * 1. Redistributions of source code must retain the above copyright |
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14 | * notice, this list of conditions and the following disclaimer. |
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15 | * 2. Redistributions in binary form must reproduce the above copyright |
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16 | * notice, this list of conditions and the following disclaimer in the |
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17 | * documentation and/or other materials provided with the distribution. |
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18 | * |
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19 | * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR |
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20 | * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES |
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21 | * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. |
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22 | * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, |
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23 | * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT |
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24 | * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, |
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25 | * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY |
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26 | * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT |
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27 | * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF |
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28 | * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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29 | *************************************************************************/ |
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30 | |
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31 | /*********************************************************************** |
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32 | * Author: Vincent Rabaud |
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33 | *************************************************************************/ |
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34 | |
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35 | #ifndef FLANN_LSH_TABLE_H_ |
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36 | #define FLANN_LSH_TABLE_H_ |
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37 | |
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38 | #include <algorithm> |
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39 | #include <iostream> |
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40 | #include <iomanip> |
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41 | #include <limits.h> |
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42 | // TODO as soon as we use C++0x, use the code in USE_UNORDERED_MAP |
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43 | #if USE_UNORDERED_MAP |
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44 | #include <unordered_map> |
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45 | #else |
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46 | #include <map> |
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47 | #endif |
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48 | #include <math.h> |
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49 | #include <stddef.h> |
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50 | |
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51 | #include "flann/util/dynamic_bitset.h" |
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52 | #include "flann/util/matrix.h" |
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53 | |
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54 | namespace flann |
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55 | { |
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56 | |
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57 | namespace lsh |
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58 | { |
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59 | |
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60 | //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
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61 | |
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62 | /** What is stored in an LSH bucket |
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63 | */ |
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64 | typedef uint32_t FeatureIndex; |
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65 | /** The id from which we can get a bucket back in an LSH table |
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66 | */ |
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67 | typedef unsigned int BucketKey; |
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68 | |
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69 | /** A bucket in an LSH table |
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70 | */ |
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71 | typedef std::vector<FeatureIndex> Bucket; |
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72 | |
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73 | //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
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74 | |
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75 | /** POD for stats about an LSH table |
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76 | */ |
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77 | struct LshStats |
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78 | { |
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79 | std::vector<unsigned int> bucket_sizes_; |
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80 | size_t n_buckets_; |
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81 | size_t bucket_size_mean_; |
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82 | size_t bucket_size_median_; |
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83 | size_t bucket_size_min_; |
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84 | size_t bucket_size_max_; |
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85 | size_t bucket_size_std_dev; |
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86 | /** Each contained vector contains three value: beginning/end for interval, number of elements in the bin |
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87 | */ |
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88 | std::vector<std::vector<unsigned int> > size_histogram_; |
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89 | }; |
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90 | |
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91 | /** Overload the << operator for LshStats |
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92 | * @param out the streams |
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93 | * @param stats the stats to display |
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94 | * @return the streams |
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95 | */ |
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96 | inline std::ostream& operator <<(std::ostream& out, const LshStats& stats) |
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97 | { |
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98 | size_t w = 20; |
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99 | out << "Lsh Table Stats:\n" << std::setw(w) << std::setiosflags(std::ios::right) << "N buckets : " |
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100 | << stats.n_buckets_ << "\n" << std::setw(w) << std::setiosflags(std::ios::right) << "mean size : " |
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101 | << std::setiosflags(std::ios::left) << stats.bucket_size_mean_ << "\n" << std::setw(w) |
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102 | << std::setiosflags(std::ios::right) << "median size : " << stats.bucket_size_median_ << "\n" << std::setw(w) |
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103 | << std::setiosflags(std::ios::right) << "min size : " << std::setiosflags(std::ios::left) |
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104 | << stats.bucket_size_min_ << "\n" << std::setw(w) << std::setiosflags(std::ios::right) << "max size : " |
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105 | << std::setiosflags(std::ios::left) << stats.bucket_size_max_; |
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106 | |
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107 | // Display the histogram |
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108 | out << std::endl << std::setw(w) << std::setiosflags(std::ios::right) << "histogram : " |
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109 | << std::setiosflags(std::ios::left); |
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110 | for (std::vector<std::vector<unsigned int> >::const_iterator iterator = stats.size_histogram_.begin(), end = |
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111 | stats.size_histogram_.end(); iterator != end; ++iterator) out << (*iterator)[0] << "-" << (*iterator)[1] << ": " << (*iterator)[2] << ", "; |
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112 | |
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113 | return out; |
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114 | } |
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115 | |
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116 | |
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117 | //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
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118 | |
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119 | /** Lsh hash table. As its key is a sub-feature, and as usually |
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120 | * the size of it is pretty small, we keep it as a continuous memory array. |
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121 | * The value is an index in the corpus of features (we keep it as an unsigned |
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122 | * int for pure memory reasons, it could be a size_t) |
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123 | */ |
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124 | template<typename ElementType> |
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125 | class LshTable |
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126 | { |
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127 | public: |
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128 | /** A container of all the feature indices. Optimized for space |
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129 | */ |
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130 | #if USE_UNORDERED_MAP |
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131 | typedef std::unordered_map<BucketKey, Bucket> BucketsSpace; |
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132 | #else |
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133 | typedef std::map<BucketKey, Bucket> BucketsSpace; |
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134 | #endif |
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135 | |
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136 | /** A container of all the feature indices. Optimized for speed |
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137 | */ |
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138 | typedef std::vector<Bucket> BucketsSpeed; |
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139 | |
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140 | /** Default constructor |
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141 | */ |
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142 | LshTable() |
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143 | { |
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144 | } |
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145 | |
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146 | /** Default constructor |
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147 | * Create the mask and allocate the memory |
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148 | * @param feature_size is the size of the feature (considered as a ElementType[]) |
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149 | * @param key_size is the number of bits that are turned on in the feature |
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150 | */ |
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151 | LshTable(unsigned int /*feature_size*/, unsigned int /*key_size*/) |
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152 | { |
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153 | std::cerr << "LSH is not implemented for that type" << std::endl; |
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154 | throw; |
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155 | } |
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156 | |
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157 | /** Add a feature to the table |
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158 | * @param value the value to store for that feature |
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159 | * @param feature the feature itself |
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160 | */ |
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161 | void add(unsigned int value, const ElementType* feature) |
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162 | { |
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163 | // Add the value to the corresponding bucket |
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164 | BucketKey key = getKey(feature); |
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165 | |
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166 | switch (speed_level_) { |
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167 | case kArray: |
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168 | // That means we get the buckets from an array |
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169 | buckets_speed_[key].push_back(value); |
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170 | break; |
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171 | case kBitsetHash: |
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172 | // That means we can check the bitset for the presence of a key |
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173 | key_bitset_.set(key); |
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174 | buckets_space_[key].push_back(value); |
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175 | break; |
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176 | case kHash: |
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177 | { |
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178 | // That means we have to check for the hash table for the presence of a key |
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179 | buckets_space_[key].push_back(value); |
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180 | break; |
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181 | } |
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182 | } |
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183 | } |
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184 | |
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185 | /** Add a set of features to the table |
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186 | * @param dataset the values to store |
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187 | */ |
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188 | void add(Matrix<ElementType> dataset) |
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189 | { |
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190 | #if USE_UNORDERED_MAP |
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191 | if (!use_speed_) buckets_space_.rehash((buckets_space_.size() + dataset.rows) * 1.2); |
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192 | #endif |
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193 | // Add the features to the table |
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194 | for (unsigned int i = 0; i < dataset.rows; ++i) add(i, dataset[i]); |
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195 | // Now that the table is full, optimize it for speed/space |
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196 | optimize(); |
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197 | } |
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198 | |
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199 | /** Get a bucket given the key |
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200 | * @param key |
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201 | * @return |
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202 | */ |
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203 | inline const Bucket* getBucketFromKey(BucketKey key) const |
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204 | { |
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205 | // Generate other buckets |
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206 | switch (speed_level_) { |
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207 | case kArray: |
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208 | // That means we get the buckets from an array |
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209 | return &buckets_speed_[key]; |
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210 | break; |
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211 | case kBitsetHash: |
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212 | // That means we can check the bitset for the presence of a key |
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213 | if (key_bitset_.test(key)) return &buckets_space_.find(key)->second; |
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214 | else return 0; |
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215 | break; |
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216 | case kHash: |
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217 | { |
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218 | // That means we have to check for the hash table for the presence of a key |
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219 | BucketsSpace::const_iterator bucket_it, bucket_end = buckets_space_.end(); |
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220 | bucket_it = buckets_space_.find(key); |
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221 | // Stop here if that bucket does not exist |
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222 | if (bucket_it == bucket_end) return 0; |
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223 | else return &bucket_it->second; |
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224 | break; |
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225 | } |
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226 | } |
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227 | return 0; |
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228 | } |
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229 | |
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230 | /** Compute the sub-signature of a feature |
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231 | */ |
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232 | size_t getKey(const ElementType* /*feature*/) const |
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233 | { |
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234 | std::cerr << "LSH is not implemented for that type" << std::endl; |
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235 | throw; |
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236 | return 1; |
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237 | } |
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238 | |
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239 | /** Get statistics about the table |
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240 | * @return |
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241 | */ |
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242 | LshStats getStats() const; |
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243 | |
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244 | private: |
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245 | /** defines the speed fo the implementation |
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246 | * kArray uses a vector for storing data |
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247 | * kBitsetHash uses a hash map but checks for the validity of a key with a bitset |
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248 | * kHash uses a hash map only |
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249 | */ |
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250 | enum SpeedLevel |
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251 | { |
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252 | kArray, kBitsetHash, kHash |
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253 | }; |
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254 | |
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255 | /** Initialize some variables |
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256 | */ |
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257 | void initialize(size_t key_size) |
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258 | { |
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259 | speed_level_ = kHash; |
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260 | key_size_ = key_size; |
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261 | } |
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262 | |
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263 | /** Optimize the table for speed/space |
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264 | */ |
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265 | void optimize() |
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266 | { |
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267 | // If we are already using the fast storage, no need to do anything |
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268 | if (speed_level_ == kArray) return; |
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269 | |
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270 | // Use an array if it will be more than half full |
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271 | if (buckets_space_.size() > (unsigned int)((1 << key_size_) / 2)) { |
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272 | speed_level_ = kArray; |
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273 | // Fill the array version of it |
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274 | buckets_speed_.resize(1 << key_size_); |
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275 | for (BucketsSpace::const_iterator key_bucket = buckets_space_.begin(); key_bucket != buckets_space_.end(); ++key_bucket) buckets_speed_[key_bucket->first] = key_bucket->second; |
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276 | |
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277 | // Empty the hash table |
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278 | buckets_space_.clear(); |
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279 | return; |
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280 | } |
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281 | |
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282 | // If the bitset is going to use less than 10% of the RAM of the hash map (at least 1 size_t for the key and two |
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283 | // for the vector) or less than 512MB (key_size_ <= 30) |
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284 | if (((std::max(buckets_space_.size(), buckets_speed_.size()) * CHAR_BIT * 3 * sizeof(BucketKey)) / 10 |
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285 | >= size_t(1 << key_size_)) || (key_size_ <= 32)) { |
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286 | speed_level_ = kBitsetHash; |
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287 | key_bitset_.resize(1 << key_size_); |
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288 | key_bitset_.reset(); |
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289 | // Try with the BucketsSpace |
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290 | for (BucketsSpace::const_iterator key_bucket = buckets_space_.begin(); key_bucket != buckets_space_.end(); ++key_bucket) key_bitset_.set(key_bucket->first); |
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291 | } |
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292 | else { |
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293 | speed_level_ = kHash; |
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294 | key_bitset_.clear(); |
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295 | } |
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296 | } |
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297 | |
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298 | /** The vector of all the buckets if they are held for speed |
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299 | */ |
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300 | BucketsSpeed buckets_speed_; |
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301 | |
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302 | /** The hash table of all the buckets in case we cannot use the speed version |
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303 | */ |
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304 | BucketsSpace buckets_space_; |
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305 | |
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306 | /** What is used to store the data */ |
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307 | SpeedLevel speed_level_; |
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308 | |
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309 | /** If the subkey is small enough, it will keep track of which subkeys are set through that bitset |
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310 | * That is just a speedup so that we don't look in the hash table (which can be mush slower that checking a bitset) |
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311 | */ |
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312 | DynamicBitset key_bitset_; |
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313 | |
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314 | /** The size of the sub-signature in bits |
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315 | */ |
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316 | unsigned int key_size_; |
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317 | |
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318 | // Members only used for the unsigned char specialization |
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319 | /** The mask to apply to a feature to get the hash key |
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320 | * Only used in the unsigned char case |
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321 | */ |
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322 | std::vector<size_t> mask_; |
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323 | }; |
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324 | |
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325 | //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
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326 | // Specialization for unsigned char |
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327 | |
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328 | template<> |
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329 | inline LshTable<unsigned char>::LshTable(unsigned int feature_size, unsigned int subsignature_size) |
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330 | { |
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331 | initialize(subsignature_size); |
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332 | // Allocate the mask |
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333 | mask_ = std::vector<size_t>((size_t)ceil((float)(feature_size * sizeof(char)) / (float)sizeof(size_t)), 0); |
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334 | |
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335 | // A bit brutal but fast to code |
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336 | std::vector<size_t> indices(feature_size * CHAR_BIT); |
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337 | for (size_t i = 0; i < feature_size * CHAR_BIT; ++i) indices[i] = i; |
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338 | std::random_shuffle(indices.begin(), indices.end()); |
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339 | |
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340 | // Generate a random set of order of subsignature_size_ bits |
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341 | for (unsigned int i = 0; i < key_size_; ++i) { |
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342 | size_t index = indices[i]; |
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343 | |
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344 | // Set that bit in the mask |
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345 | size_t divisor = CHAR_BIT * sizeof(size_t); |
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346 | size_t idx = index / divisor; //pick the right size_t index |
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347 | mask_[idx] |= size_t(1) << (index % divisor); //use modulo to find the bit offset |
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348 | } |
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349 | |
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350 | // Set to 1 if you want to display the mask for debug |
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351 | #if 0 |
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352 | { |
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353 | size_t bcount = 0; |
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354 | BOOST_FOREACH(size_t mask_block, mask_){ |
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355 | out << std::setw(sizeof(size_t) * CHAR_BIT / 4) << std::setfill('0') << std::hex << mask_block |
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356 | << std::endl; |
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357 | bcount += __builtin_popcountll(mask_block); |
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358 | } |
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359 | out << "bit count : " << std::dec << bcount << std::endl; |
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360 | out << "mask size : " << mask_.size() << std::endl; |
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361 | return out; |
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362 | } |
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363 | #endif |
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364 | } |
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365 | |
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366 | /** Return the Subsignature of a feature |
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367 | * @param feature the feature to analyze |
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368 | */ |
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369 | template<> |
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370 | inline size_t LshTable<unsigned char>::getKey(const unsigned char* feature) const |
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371 | { |
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372 | // no need to check if T is dividable by sizeof(size_t) like in the Hamming |
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373 | // distance computation as we have a mask |
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374 | const size_t* feature_block_ptr = reinterpret_cast<const size_t*> (feature); |
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375 | |
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376 | // Figure out the subsignature of the feature |
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377 | // Given the feature ABCDEF, and the mask 001011, the output will be |
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378 | // 000CEF |
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379 | size_t subsignature = 0; |
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380 | size_t bit_index = 1; |
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381 | |
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382 | for (std::vector<size_t>::const_iterator pmask_block = mask_.begin(); pmask_block != mask_.end(); ++pmask_block) { |
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383 | // get the mask and signature blocks |
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384 | size_t feature_block = *feature_block_ptr; |
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385 | size_t mask_block = *pmask_block; |
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386 | while (mask_block) { |
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387 | // Get the lowest set bit in the mask block |
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388 | size_t lowest_bit = mask_block & (-(ptrdiff_t)mask_block); |
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389 | // Add it to the current subsignature if necessary |
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390 | subsignature += (feature_block & lowest_bit) ? bit_index : 0; |
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391 | // Reset the bit in the mask block |
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392 | mask_block ^= lowest_bit; |
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393 | // increment the bit index for the subsignature |
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394 | bit_index <<= 1; |
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395 | } |
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396 | // Check the next feature block |
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397 | ++feature_block_ptr; |
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398 | } |
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399 | return subsignature; |
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400 | } |
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401 | |
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402 | template<> |
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403 | inline LshStats LshTable<unsigned char>::getStats() const |
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404 | { |
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405 | LshStats stats; |
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406 | stats.bucket_size_mean_ = 0; |
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407 | if ((buckets_speed_.empty()) && (buckets_space_.empty())) { |
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408 | stats.n_buckets_ = 0; |
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409 | stats.bucket_size_median_ = 0; |
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410 | stats.bucket_size_min_ = 0; |
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411 | stats.bucket_size_max_ = 0; |
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412 | return stats; |
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413 | } |
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414 | |
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415 | if (!buckets_speed_.empty()) { |
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416 | for (BucketsSpeed::const_iterator pbucket = buckets_speed_.begin(); pbucket != buckets_speed_.end(); ++pbucket) { |
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417 | stats.bucket_sizes_.push_back(pbucket->size()); |
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418 | stats.bucket_size_mean_ += pbucket->size(); |
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419 | } |
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420 | stats.bucket_size_mean_ /= buckets_speed_.size(); |
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421 | stats.n_buckets_ = buckets_speed_.size(); |
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422 | } |
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423 | else { |
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424 | for (BucketsSpace::const_iterator x = buckets_space_.begin(); x != buckets_space_.end(); ++x) { |
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425 | stats.bucket_sizes_.push_back(x->second.size()); |
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426 | stats.bucket_size_mean_ += x->second.size(); |
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427 | } |
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428 | stats.bucket_size_mean_ /= buckets_space_.size(); |
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429 | stats.n_buckets_ = buckets_space_.size(); |
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430 | } |
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431 | |
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432 | std::sort(stats.bucket_sizes_.begin(), stats.bucket_sizes_.end()); |
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433 | |
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434 | // BOOST_FOREACH(int size, stats.bucket_sizes_) |
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435 | // std::cout << size << " "; |
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436 | // std::cout << std::endl; |
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437 | stats.bucket_size_median_ = stats.bucket_sizes_[stats.bucket_sizes_.size() / 2]; |
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438 | stats.bucket_size_min_ = stats.bucket_sizes_.front(); |
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439 | stats.bucket_size_max_ = stats.bucket_sizes_.back(); |
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440 | |
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441 | // TODO compute mean and std |
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442 | /*float mean, stddev; |
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443 | stats.bucket_size_mean_ = mean; |
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444 | stats.bucket_size_std_dev = stddev;*/ |
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445 | |
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446 | // Include a histogram of the buckets |
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447 | unsigned int bin_start = 0; |
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448 | unsigned int bin_end = 20; |
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449 | bool is_new_bin = true; |
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450 | for (std::vector<unsigned int>::iterator iterator = stats.bucket_sizes_.begin(), end = stats.bucket_sizes_.end(); iterator |
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451 | != end; ) |
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452 | if (*iterator < bin_end) { |
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453 | if (is_new_bin) { |
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454 | stats.size_histogram_.push_back(std::vector<unsigned int>(3, 0)); |
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455 | stats.size_histogram_.back()[0] = bin_start; |
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456 | stats.size_histogram_.back()[1] = bin_end - 1; |
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457 | is_new_bin = false; |
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458 | } |
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459 | ++stats.size_histogram_.back()[2]; |
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460 | ++iterator; |
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461 | } |
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462 | else { |
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463 | bin_start += 20; |
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464 | bin_end += 20; |
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465 | is_new_bin = true; |
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466 | } |
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467 | |
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468 | return stats; |
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469 | } |
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470 | |
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471 | // End the two namespaces |
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472 | } |
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473 | } |
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474 | |
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475 | //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
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476 | |
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477 | #endif /* FLANN_LSH_TABLE_H_ */ |
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