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Merge pull request #17639 from pemmanuelviel:pev--binary-kmeans
Pev binary kmeans * Ongoing work transposing kmeans clustering method for bitfields: the computeClustering method Ongoing work transposing kmeans clustering method for bitfields: interface computeBitfieldClustering Fix genericity of computeNodeStatistics Ongoing work transposing kmeans clustering method for bitfields: adapt computeNodeStatistics() Ongoing work transposing kmeans clustering method for bitfields: adapt findNN() method Ongoing work transposing kmeans clustering method for bitfields: allow kmeans with Hamming distance Ongoing work transposing kmeans clustering method for bitfields: adapt distances code Ongoing work transposing kmeans clustering method for bitfields: adapt load/save code Ongoing work transposing kmeans clustering method for bitfields: adapt kmeans hierarchicalClustring() PivotType -> CentersType Renaming Fix type casting for ARM SIMD implementation of Hamming Fix warnings with Win32 compilation Fix warnings with Win64 compilation Fix wrong parenthesis position on rounding * Ensure proper rounding when CentersType is integral
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@ -536,7 +536,7 @@ private:
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@param features The points to be clustered. The matrix must have elements of type
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Distance::ElementType.
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@param centers The centers of the clusters obtained. The matrix must have type
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Distance::ResultType. The number of rows in this matrix represents the number of clusters desired,
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Distance::CentersType. The number of rows in this matrix represents the number of clusters desired,
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however, because of the way the cut in the hierarchical tree is chosen, the number of clusters
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computed will be the highest number of the form (branching-1)\*k+1 that's lower than the number of
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clusters desired, where branching is the tree's branching factor (see description of the
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@ -553,15 +553,15 @@ int hierarchicalClustering(const Mat& features, Mat& centers, const ::cvflann::K
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Distance d = Distance())
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{
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typedef typename Distance::ElementType ElementType;
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typedef typename Distance::ResultType DistanceType;
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typedef typename Distance::CentersType CentersType;
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CV_Assert(features.type() == CvType<ElementType>::type());
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CV_Assert(features.isContinuous());
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::cvflann::Matrix<ElementType> m_features((ElementType*)features.ptr<ElementType>(0), features.rows, features.cols);
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CV_Assert(centers.type() == CvType<DistanceType>::type());
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CV_Assert(centers.type() == CvType<CentersType>::type());
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CV_Assert(centers.isContinuous());
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::cvflann::Matrix<DistanceType> m_centers((DistanceType*)centers.ptr<DistanceType>(0), centers.rows, centers.cols);
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::cvflann::Matrix<CentersType> m_centers((CentersType*)centers.ptr<CentersType>(0), centers.rows, centers.cols);
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return ::cvflann::hierarchicalClustering<Distance>(m_features, m_centers, params, d);
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}
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@ -130,6 +130,9 @@ struct index_creator<False,False,Distance>
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case FLANN_INDEX_LINEAR:
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nnIndex = new LinearIndex<Distance>(dataset, params, distance);
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break;
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case FLANN_INDEX_KMEANS:
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nnIndex = new KMeansIndex<Distance>(dataset, params, distance);
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break;
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case FLANN_INDEX_HIERARCHICAL:
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nnIndex = new HierarchicalClusteringIndex<Distance>(dataset, params, distance);
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break;
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@ -1,4 +1,4 @@
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/***********************************************************************
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/***********************************************************************
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* Software License Agreement (BSD License)
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*
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* Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
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@ -68,6 +68,63 @@ inline float abs<float>(float x) { return fabsf(x); }
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template<>
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inline double abs<double>(double x) { return fabs(x); }
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template<typename TargetType>
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inline TargetType round(float x) { return static_cast<TargetType>(x); }
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template<>
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inline unsigned int round<unsigned int>(float x) { return static_cast<unsigned int>(x + 0.5f); }
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template<>
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inline unsigned short round<unsigned short>(float x) { return static_cast<unsigned short>(x + 0.5f); }
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template<>
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inline unsigned char round<unsigned char>(float x) { return static_cast<unsigned char>(x + 0.5f); }
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template<>
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inline long long round<long long>(float x) { return static_cast<long long>(x + 0.5f); }
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template<>
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inline long round<long>(float x) { return static_cast<long>(x + 0.5f); }
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template<>
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inline int round<int>(float x) { return static_cast<int>(x + 0.5f) - (x<0); }
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template<>
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inline short round<short>(float x) { return static_cast<short>(x + 0.5f) - (x<0); }
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template<>
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inline char round<char>(float x) { return static_cast<char>(x + 0.5f) - (x<0); }
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template<typename TargetType>
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inline TargetType round(double x) { return static_cast<TargetType>(x); }
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template<>
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inline unsigned int round<unsigned int>(double x) { return static_cast<unsigned int>(x + 0.5); }
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template<>
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inline unsigned short round<unsigned short>(double x) { return static_cast<unsigned short>(x + 0.5); }
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template<>
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inline unsigned char round<unsigned char>(double x) { return static_cast<unsigned char>(x + 0.5); }
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template<>
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inline long long round<long long>(double x) { return static_cast<long long>(x + 0.5); }
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template<>
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inline long round<long>(double x) { return static_cast<long>(x + 0.5); }
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template<>
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inline int round<int>(double x) { return static_cast<int>(x + 0.5) - (x<0); }
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template<>
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inline short round<short>(double x) { return static_cast<short>(x + 0.5) - (x<0); }
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template<>
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inline char round<char>(double x) { return static_cast<char>(x + 0.5) - (x<0); }
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template<typename T>
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struct Accumulator { typedef T Type; };
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template<>
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@ -88,13 +145,57 @@ struct Accumulator<int> { typedef float Type; };
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class True
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{
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public:
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static const bool val = true;
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};
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class False
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{
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public:
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static const bool val = false;
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};
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/*
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* This is a "zero iterator". It basically behaves like a zero filled
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* array to all algorithms that use arrays as iterators (STL style).
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* It's useful when there's a need to compute the distance between feature
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* and origin it and allows for better compiler optimisation than using a
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* zero-filled array.
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*/
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template <typename T>
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struct ZeroIterator
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{
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T operator*()
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{
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return 0;
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}
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T operator[](int)
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{
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return 0;
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}
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const ZeroIterator<T>& operator ++()
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{
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return *this;
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}
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ZeroIterator<T> operator ++(int)
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{
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return *this;
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}
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ZeroIterator<T>& operator+=(int)
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{
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return *this;
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}
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};
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/**
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* Squared Euclidean distance functor.
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*
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@ -109,6 +210,7 @@ struct L2_Simple
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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template <typename Iterator1, typename Iterator2>
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ResultType operator()(Iterator1 a, Iterator2 b, size_t size, ResultType /*worst_dist*/ = -1) const
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@ -142,6 +244,7 @@ struct L2
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the squared Euclidean distance between two vectors.
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@ -207,6 +310,7 @@ struct L1
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the Manhattan (L_1) distance between two vectors.
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@ -264,6 +368,7 @@ struct MinkowskiDistance
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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int order;
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@ -328,6 +433,7 @@ struct MaxDistance
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the max distance (L_infinity) between two vectors.
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@ -385,10 +491,12 @@ struct HammingLUT
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typedef unsigned char ElementType;
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typedef int ResultType;
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typedef ElementType CentersType;
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/** this will count the bits in a ^ b
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*/
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ResultType operator()(const unsigned char* a, const unsigned char* b, size_t size) const
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template<typename Iterator2>
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ResultType operator()(const unsigned char* a, const Iterator2 b, size_t size) const
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{
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static const uchar popCountTable[] =
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{
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@ -402,8 +510,31 @@ struct HammingLUT
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3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 4, 5, 5, 6, 5, 6, 6, 7, 5, 6, 6, 7, 6, 7, 7, 8
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};
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ResultType result = 0;
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const unsigned char* b2 = reinterpret_cast<const unsigned char*> (b);
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for (size_t i = 0; i < size; i++) {
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result += popCountTable[a[i] ^ b[i]];
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result += popCountTable[a[i] ^ b2[i]];
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}
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return result;
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}
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ResultType operator()(const unsigned char* a, const ZeroIterator<unsigned char> b, size_t size) const
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{
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(void)b;
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static const uchar popCountTable[] =
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{
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0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
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1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
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1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
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2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
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1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
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2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
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2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7,
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3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 4, 5, 5, 6, 5, 6, 6, 7, 5, 6, 6, 7, 6, 7, 7, 8
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};
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ResultType result = 0;
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for (size_t i = 0; i < size; i++) {
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result += popCountTable[a[i]];
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}
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return result;
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}
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@ -422,17 +553,20 @@ struct Hamming
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typedef T ElementType;
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typedef int ResultType;
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typedef ElementType CentersType;
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template<typename Iterator1, typename Iterator2>
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ResultType operator()(Iterator1 a, Iterator2 b, size_t size, ResultType /*worst_dist*/ = -1) const
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ResultType operator()(const Iterator1 a, const Iterator2 b, size_t size, ResultType /*worst_dist*/ = -1) const
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{
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ResultType result = 0;
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#if defined(__ARM_NEON__) && !defined(__CUDACC__)
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{
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const unsigned char* a2 = reinterpret_cast<const unsigned char*> (a);
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const unsigned char* b2 = reinterpret_cast<const unsigned char*> (b);
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uint32x4_t bits = vmovq_n_u32(0);
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for (size_t i = 0; i < size; i += 16) {
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uint8x16_t A_vec = vld1q_u8 (a + i);
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uint8x16_t B_vec = vld1q_u8 (b + i);
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uint8x16_t A_vec = vld1q_u8 (a2 + i);
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uint8x16_t B_vec = vld1q_u8 (b2 + i);
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uint8x16_t AxorB = veorq_u8 (A_vec, B_vec);
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uint8x16_t bitsSet = vcntq_u8 (AxorB);
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uint16x8_t bitSet8 = vpaddlq_u8 (bitsSet);
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@ -470,6 +604,52 @@ struct Hamming
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#endif
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return result;
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}
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template<typename Iterator1>
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ResultType operator()(const Iterator1 a, ZeroIterator<unsigned char> b, size_t size, ResultType /*worst_dist*/ = -1) const
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{
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(void)b;
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ResultType result = 0;
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#if defined(__ARM_NEON__) && !defined(__CUDACC__)
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{
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const unsigned char* a2 = reinterpret_cast<const unsigned char*> (a);
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uint32x4_t bits = vmovq_n_u32(0);
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for (size_t i = 0; i < size; i += 16) {
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uint8x16_t A_vec = vld1q_u8 (a2 + i);
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uint8x16_t bitsSet = vcntq_u8 (A_vec);
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uint16x8_t bitSet8 = vpaddlq_u8 (bitsSet);
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uint32x4_t bitSet4 = vpaddlq_u16 (bitSet8);
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bits = vaddq_u32(bits, bitSet4);
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}
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uint64x2_t bitSet2 = vpaddlq_u32 (bits);
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result = vgetq_lane_s32 (vreinterpretq_s32_u64(bitSet2),0);
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result += vgetq_lane_s32 (vreinterpretq_s32_u64(bitSet2),2);
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}
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#elif defined(__GNUC__)
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{
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//for portability just use unsigned long -- and use the __builtin_popcountll (see docs for __builtin_popcountll)
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typedef unsigned long long pop_t;
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const size_t modulo = size % sizeof(pop_t);
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const pop_t* a2 = reinterpret_cast<const pop_t*> (a);
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const pop_t* a2_end = a2 + (size / sizeof(pop_t));
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for (; a2 != a2_end; ++a2) result += __builtin_popcountll(*a2);
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if (modulo) {
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//in the case where size is not dividable by sizeof(size_t)
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//need to mask off the bits at the end
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pop_t a_final = 0;
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memcpy(&a_final, a2, modulo);
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result += __builtin_popcountll(a_final);
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}
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}
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#else // NO NEON and NOT GNUC
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HammingLUT lut;
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result = lut(reinterpret_cast<const unsigned char*> (a), b, size);
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#endif
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return result;
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}
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};
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template<typename T>
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@ -480,6 +660,7 @@ struct Hamming2
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typedef T ElementType;
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typedef int ResultType;
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typedef ElementType CentersType;
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/** This is popcount_3() from:
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* http://en.wikipedia.org/wiki/Hamming_weight */
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@ -500,7 +681,7 @@ struct Hamming2
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#endif
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template <typename Iterator1, typename Iterator2>
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ResultType operator()(Iterator1 a, Iterator2 b, size_t size, ResultType /*worst_dist*/ = -1) const
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ResultType operator()(const Iterator1 a, const Iterator2 b, size_t size, ResultType /*worst_dist*/ = -1) const
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{
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#ifdef FLANN_PLATFORM_64_BIT
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const uint64_t* pa = reinterpret_cast<const uint64_t*>(a);
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@ -526,6 +707,31 @@ struct Hamming2
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return result;
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}
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template <typename Iterator1>
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ResultType operator()(const Iterator1 a, ZeroIterator<unsigned char> b, size_t size, ResultType /*worst_dist*/ = -1) const
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{
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(void)b;
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#ifdef FLANN_PLATFORM_64_BIT
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const uint64_t* pa = reinterpret_cast<const uint64_t*>(a);
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ResultType result = 0;
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size /= long_word_size_;
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for(size_t i = 0; i < size; ++i ) {
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result += popcnt64(*pa);
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++pa;
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}
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#else
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const uint32_t* pa = reinterpret_cast<const uint32_t*>(a);
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ResultType result = 0;
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size /= long_word_size_;
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for(size_t i = 0; i < size; ++i ) {
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result += popcnt32(*pa);
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++pa;
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}
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#endif
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return result;
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}
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private:
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#ifdef FLANN_PLATFORM_64_BIT
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static const size_t long_word_size_ = sizeof(uint64_t)/sizeof(unsigned char);
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@ -546,6 +752,7 @@ struct HistIntersectionDistance
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the histogram intersection distance
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@ -601,6 +808,7 @@ struct HellingerDistance
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the Hellinger distance
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@ -650,6 +858,7 @@ struct ChiSquareDistance
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the chi-square distance
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@ -704,6 +913,7 @@ struct KL_Divergence
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typedef T ElementType;
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typedef typename Accumulator<T>::Type ResultType;
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typedef ResultType CentersType;
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/**
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* Compute the Kullback-Leibler divergence
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@ -749,46 +959,6 @@ struct KL_Divergence
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};
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/*
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* This is a "zero iterator". It basically behaves like a zero filled
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* array to all algorithms that use arrays as iterators (STL style).
|
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* It's useful when there's a need to compute the distance between feature
|
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* and origin it and allows for better compiler optimisation than using a
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* zero-filled array.
|
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*/
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template <typename T>
|
||||
struct ZeroIterator
|
||||
{
|
||||
|
||||
T operator*()
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
T operator[](int)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
const ZeroIterator<T>& operator ++()
|
||||
{
|
||||
return *this;
|
||||
}
|
||||
|
||||
ZeroIterator<T> operator ++(int)
|
||||
{
|
||||
return *this;
|
||||
}
|
||||
|
||||
ZeroIterator<T>& operator+=(int)
|
||||
{
|
||||
return *this;
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
|
||||
/*
|
||||
* Depending on processed distances, some of them are already squared (e.g. L2)
|
||||
* and some are not (e.g.Hamming). In KMeans++ for instance we want to be sure
|
||||
@ -849,6 +1019,58 @@ typename Distance::ResultType ensureSquareDistance( typename Distance::ResultTyp
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* ...a template to tell the user if the distance he is working with is actually squared
|
||||
*/
|
||||
|
||||
template <typename Distance, typename ElementType>
|
||||
struct isSquareDist
|
||||
{
|
||||
bool operator()() { return false; }
|
||||
};
|
||||
|
||||
|
||||
template <typename ElementType>
|
||||
struct isSquareDist<L2_Simple<ElementType>, ElementType>
|
||||
{
|
||||
bool operator()() { return true; }
|
||||
};
|
||||
|
||||
template <typename ElementType>
|
||||
struct isSquareDist<L2<ElementType>, ElementType>
|
||||
{
|
||||
bool operator()() { return true; }
|
||||
};
|
||||
|
||||
|
||||
template <typename ElementType>
|
||||
struct isSquareDist<MinkowskiDistance<ElementType>, ElementType>
|
||||
{
|
||||
bool operator()() { return true; }
|
||||
};
|
||||
|
||||
template <typename ElementType>
|
||||
struct isSquareDist<HellingerDistance<ElementType>, ElementType>
|
||||
{
|
||||
bool operator()() { return true; }
|
||||
};
|
||||
|
||||
template <typename ElementType>
|
||||
struct isSquareDist<ChiSquareDistance<ElementType>, ElementType>
|
||||
{
|
||||
bool operator()() { return true; }
|
||||
};
|
||||
|
||||
|
||||
template <typename Distance>
|
||||
bool isSquareDistance()
|
||||
{
|
||||
typedef typename Distance::ElementType ElementType;
|
||||
|
||||
isSquareDist<Distance, ElementType> dummy;
|
||||
return dummy();
|
||||
}
|
||||
|
||||
/*
|
||||
* ...and a template to ensure the user that he will process the normal distance,
|
||||
* and not squared distance, without losing processing time calling sqrt(ensureSquareDistance)
|
||||
|
||||
@ -282,7 +282,7 @@ private:
|
||||
* of the form (branching-1)*K+1 smaller than clusters.rows).
|
||||
*/
|
||||
template <typename Distance>
|
||||
int hierarchicalClustering(const Matrix<typename Distance::ElementType>& points, Matrix<typename Distance::ResultType>& centers,
|
||||
int hierarchicalClustering(const Matrix<typename Distance::ElementType>& points, Matrix<typename Distance::CentersType>& centers,
|
||||
const KMeansIndexParams& params, Distance d = Distance())
|
||||
{
|
||||
KMeansIndex<Distance> kmeans(points, params, d);
|
||||
|
||||
@ -49,6 +49,8 @@
|
||||
#include "saving.h"
|
||||
#include "logger.h"
|
||||
|
||||
#define BITS_PER_CHAR 8
|
||||
|
||||
|
||||
namespace cvflann
|
||||
{
|
||||
@ -83,6 +85,10 @@ class KMeansIndex : public NNIndex<Distance>
|
||||
public:
|
||||
typedef typename Distance::ElementType ElementType;
|
||||
typedef typename Distance::ResultType DistanceType;
|
||||
typedef typename Distance::CentersType CentersType;
|
||||
|
||||
typedef typename Distance::is_kdtree_distance is_kdtree_distance;
|
||||
typedef typename Distance::is_vector_space_distance is_vector_space_distance;
|
||||
|
||||
|
||||
|
||||
@ -272,12 +278,14 @@ public:
|
||||
return FLANN_INDEX_KMEANS;
|
||||
}
|
||||
|
||||
template<class CentersContainerType>
|
||||
class KMeansDistanceComputer : public cv::ParallelLoopBody
|
||||
{
|
||||
public:
|
||||
KMeansDistanceComputer(Distance _distance, const Matrix<ElementType>& _dataset,
|
||||
const int _branching, const int* _indices, const Matrix<double>& _dcenters, const size_t _veclen,
|
||||
std::vector<int> &_new_centroids, std::vector<DistanceType> &_sq_dists)
|
||||
const int _branching, const int* _indices, const CentersContainerType& _dcenters,
|
||||
const size_t _veclen, std::vector<int> &_new_centroids,
|
||||
std::vector<DistanceType> &_sq_dists)
|
||||
: distance(_distance)
|
||||
, dataset(_dataset)
|
||||
, branching(_branching)
|
||||
@ -315,7 +323,7 @@ public:
|
||||
const Matrix<ElementType>& dataset;
|
||||
const int branching;
|
||||
const int* indices;
|
||||
const Matrix<double>& dcenters;
|
||||
const CentersContainerType& dcenters;
|
||||
const size_t veclen;
|
||||
std::vector<int> &new_centroids;
|
||||
std::vector<DistanceType> &sq_dists;
|
||||
@ -429,8 +437,16 @@ public:
|
||||
root_ = pool_.allocate<KMeansNode>();
|
||||
std::memset(root_, 0, sizeof(KMeansNode));
|
||||
|
||||
computeNodeStatistics(root_, indices_, (int)size_);
|
||||
computeClustering(root_, indices_, (int)size_, branching_,0);
|
||||
if(is_kdtree_distance::val || is_vector_space_distance::val)
|
||||
{
|
||||
computeNodeStatistics(root_, indices_, (unsigned int)size_);
|
||||
computeClustering(root_, indices_, (int)size_, branching_,0);
|
||||
}
|
||||
else
|
||||
{
|
||||
computeBitfieldNodeStatistics(root_, indices_, (unsigned int)size_);
|
||||
computeBitfieldClustering(root_, indices_, (int)size_, branching_,0);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -515,7 +531,7 @@ public:
|
||||
* numClusters = number of clusters to have in the clustering computed
|
||||
* Returns: number of cluster centers
|
||||
*/
|
||||
int getClusterCenters(Matrix<DistanceType>& centers)
|
||||
int getClusterCenters(Matrix<CentersType>& centers)
|
||||
{
|
||||
int numClusters = centers.rows;
|
||||
if (numClusters<1) {
|
||||
@ -530,7 +546,7 @@ public:
|
||||
Logger::info("Clusters requested: %d, returning %d\n",numClusters, clusterCount);
|
||||
|
||||
for (int i=0; i<clusterCount; ++i) {
|
||||
DistanceType* center = clusters[i]->pivot;
|
||||
CentersType* center = clusters[i]->pivot;
|
||||
for (size_t j=0; j<veclen_; ++j) {
|
||||
centers[i][j] = center[j];
|
||||
}
|
||||
@ -555,7 +571,7 @@ private:
|
||||
/**
|
||||
* The cluster center.
|
||||
*/
|
||||
DistanceType* pivot;
|
||||
CentersType* pivot;
|
||||
/**
|
||||
* The cluster radius.
|
||||
*/
|
||||
@ -615,7 +631,7 @@ private:
|
||||
{
|
||||
node = pool_.allocate<KMeansNode>();
|
||||
load_value(stream, *node);
|
||||
node->pivot = new DistanceType[veclen_];
|
||||
node->pivot = new CentersType[veclen_];
|
||||
load_value(stream, *(node->pivot), (int)veclen_);
|
||||
if (node->childs==NULL) {
|
||||
int indices_offset;
|
||||
@ -652,32 +668,31 @@ private:
|
||||
* indices = array of indices of the points belonging to the node
|
||||
* indices_length = number of indices in the array
|
||||
*/
|
||||
void computeNodeStatistics(KMeansNodePtr node, int* indices, int indices_length)
|
||||
void computeNodeStatistics(KMeansNodePtr node, int* indices, unsigned int indices_length)
|
||||
{
|
||||
|
||||
DistanceType radius = 0;
|
||||
DistanceType variance = 0;
|
||||
DistanceType* mean = new DistanceType[veclen_];
|
||||
memoryCounter_ += int(veclen_*sizeof(DistanceType));
|
||||
CentersType* mean = new CentersType[veclen_];
|
||||
memoryCounter_ += int(veclen_*sizeof(CentersType));
|
||||
|
||||
memset(mean,0,veclen_*sizeof(DistanceType));
|
||||
memset(mean,0,veclen_*sizeof(CentersType));
|
||||
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
for (unsigned int i=0; i<indices_length; ++i) {
|
||||
ElementType* vec = dataset_[indices[i]];
|
||||
for (size_t j=0; j<veclen_; ++j) {
|
||||
mean[j] += vec[j];
|
||||
}
|
||||
variance += distance_(vec, ZeroIterator<ElementType>(), veclen_);
|
||||
}
|
||||
float length = static_cast<float>(indices_length);
|
||||
for (size_t j=0; j<veclen_; ++j) {
|
||||
mean[j] /= indices_length;
|
||||
mean[j] = cvflann::round<CentersType>( mean[j] / static_cast<double>(indices_length) );
|
||||
}
|
||||
variance /= indices_length;
|
||||
variance /= static_cast<DistanceType>( length );
|
||||
variance -= distance_(mean, ZeroIterator<ElementType>(), veclen_);
|
||||
|
||||
DistanceType tmp = 0;
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
tmp = distance_(mean, dataset_[indices[i]], veclen_);
|
||||
DistanceType radius = 0;
|
||||
for (unsigned int i=0; i<indices_length; ++i) {
|
||||
DistanceType tmp = distance_(mean, dataset_[indices[i]], veclen_);
|
||||
if (tmp>radius) {
|
||||
radius = tmp;
|
||||
}
|
||||
@ -689,6 +704,70 @@ private:
|
||||
}
|
||||
|
||||
|
||||
void computeBitfieldNodeStatistics(KMeansNodePtr node, int* indices,
|
||||
unsigned int indices_length)
|
||||
{
|
||||
const unsigned int accumulator_veclen = static_cast<unsigned int>(
|
||||
veclen_*sizeof(CentersType)*BITS_PER_CHAR);
|
||||
|
||||
unsigned long long variance = 0ull;
|
||||
CentersType* mean = new CentersType[veclen_];
|
||||
memoryCounter_ += int(veclen_*sizeof(CentersType));
|
||||
unsigned int* mean_accumulator = new unsigned int[accumulator_veclen];
|
||||
|
||||
memset(mean_accumulator, 0, accumulator_veclen);
|
||||
|
||||
for (unsigned int i=0; i<indices_length; ++i) {
|
||||
variance += static_cast<unsigned long long>( ensureSquareDistance<Distance>(
|
||||
distance_(dataset_[indices[i]], ZeroIterator<ElementType>(), veclen_)));
|
||||
unsigned char* vec = (unsigned char*)dataset_[indices[i]];
|
||||
for (size_t k=0, l=0; k<accumulator_veclen; k+=BITS_PER_CHAR, ++l) {
|
||||
mean_accumulator[k] += (vec[l]) & 0x01;
|
||||
mean_accumulator[k+1] += (vec[l]>>1) & 0x01;
|
||||
mean_accumulator[k+2] += (vec[l]>>2) & 0x01;
|
||||
mean_accumulator[k+3] += (vec[l]>>3) & 0x01;
|
||||
mean_accumulator[k+4] += (vec[l]>>4) & 0x01;
|
||||
mean_accumulator[k+5] += (vec[l]>>5) & 0x01;
|
||||
mean_accumulator[k+6] += (vec[l]>>6) & 0x01;
|
||||
mean_accumulator[k+7] += (vec[l]>>7) & 0x01;
|
||||
}
|
||||
}
|
||||
double cnt = static_cast<double>(indices_length);
|
||||
unsigned char* char_mean = (unsigned char*)mean;
|
||||
for (size_t k=0, l=0; k<accumulator_veclen; k+=BITS_PER_CHAR, ++l) {
|
||||
char_mean[l] = static_cast<unsigned char>(
|
||||
(((int)(0.5 + (double)(mean_accumulator[k]) / cnt)))
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+1]) / cnt))<<1)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+2]) / cnt))<<2)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+3]) / cnt))<<3)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+4]) / cnt))<<4)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+5]) / cnt))<<5)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+6]) / cnt))<<6)
|
||||
| (((int)(0.5 + (double)(mean_accumulator[k+7]) / cnt))<<7));
|
||||
}
|
||||
variance = static_cast<unsigned long long>(
|
||||
0.5 + static_cast<double>(variance) / static_cast<double>(indices_length));
|
||||
variance -= static_cast<unsigned long long>(
|
||||
ensureSquareDistance<Distance>(
|
||||
distance_(mean, ZeroIterator<ElementType>(), veclen_)));
|
||||
|
||||
DistanceType radius = 0;
|
||||
for (unsigned int i=0; i<indices_length; ++i) {
|
||||
DistanceType tmp = distance_(mean, dataset_[indices[i]], veclen_);
|
||||
if (tmp>radius) {
|
||||
radius = tmp;
|
||||
}
|
||||
}
|
||||
|
||||
node->variance = static_cast<DistanceType>(variance);
|
||||
node->radius = radius;
|
||||
node->pivot = mean;
|
||||
|
||||
delete[] mean_accumulator;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* The method responsible with actually doing the recursive hierarchical
|
||||
* clustering
|
||||
@ -737,7 +816,6 @@ private:
|
||||
cv::AutoBuffer<int> belongs_to_buf(indices_length);
|
||||
int* belongs_to = belongs_to_buf.data();
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
|
||||
DistanceType sq_dist = distance_(dataset_[indices[i]], dataset_[centers_idx[0]], veclen_);
|
||||
belongs_to[i] = 0;
|
||||
for (int j=1; j<branching; ++j) {
|
||||
@ -791,7 +869,7 @@ private:
|
||||
std::vector<DistanceType> sq_dists(indices_length);
|
||||
|
||||
// reassign points to clusters
|
||||
KMeansDistanceComputer invoker(distance_, dataset_, branching, indices, dcenters, veclen_, new_centroids, sq_dists);
|
||||
KMeansDistanceComputer<Matrix<double> > invoker(distance_, dataset_, branching, indices, dcenters, veclen_, new_centroids, sq_dists);
|
||||
parallel_for_(cv::Range(0, (int)indices_length), invoker);
|
||||
|
||||
for (int i=0; i < (int)indices_length; ++i) {
|
||||
@ -834,13 +912,13 @@ private:
|
||||
|
||||
}
|
||||
|
||||
DistanceType** centers = new DistanceType*[branching];
|
||||
CentersType** centers = new CentersType*[branching];
|
||||
|
||||
for (int i=0; i<branching; ++i) {
|
||||
centers[i] = new DistanceType[veclen_];
|
||||
memoryCounter_ += (int)(veclen_*sizeof(DistanceType));
|
||||
centers[i] = new CentersType[veclen_];
|
||||
memoryCounter_ += (int)(veclen_*sizeof(CentersType));
|
||||
for (size_t k=0; k<veclen_; ++k) {
|
||||
centers[i][k] = (DistanceType)dcenters[i][k];
|
||||
centers[i][k] = (CentersType)dcenters[i][k];
|
||||
}
|
||||
}
|
||||
|
||||
@ -858,7 +936,7 @@ private:
|
||||
if (belongs_to[i]==c) {
|
||||
DistanceType d = distance_(dataset_[indices[i]], ZeroIterator<ElementType>(), veclen_);
|
||||
variance += d;
|
||||
mean_radius += sqrt(d);
|
||||
mean_radius += static_cast<DistanceType>( sqrt(d) );
|
||||
std::swap(indices[i],indices[end]);
|
||||
std::swap(belongs_to[i],belongs_to[end]);
|
||||
end++;
|
||||
@ -883,6 +961,204 @@ private:
|
||||
|
||||
|
||||
|
||||
void computeBitfieldClustering(KMeansNodePtr node, int* indices,
|
||||
int indices_length, int branching, int level)
|
||||
{
|
||||
node->size = indices_length;
|
||||
node->level = level;
|
||||
|
||||
if (indices_length < branching) {
|
||||
node->indices = indices;
|
||||
std::sort(node->indices,node->indices+indices_length);
|
||||
node->childs = NULL;
|
||||
return;
|
||||
}
|
||||
|
||||
cv::AutoBuffer<int> centers_idx_buf(branching);
|
||||
int* centers_idx = centers_idx_buf.data();
|
||||
int centers_length;
|
||||
(this->*chooseCenters)(branching, indices, indices_length, centers_idx, centers_length);
|
||||
|
||||
if (centers_length<branching) {
|
||||
node->indices = indices;
|
||||
std::sort(node->indices,node->indices+indices_length);
|
||||
node->childs = NULL;
|
||||
return;
|
||||
}
|
||||
|
||||
const unsigned int accumulator_veclen = static_cast<unsigned int>(
|
||||
veclen_*sizeof(ElementType)*BITS_PER_CHAR);
|
||||
cv::AutoBuffer<unsigned int> dcenters_buf(branching*accumulator_veclen);
|
||||
Matrix<unsigned int> dcenters(dcenters_buf.data(), branching, accumulator_veclen);
|
||||
|
||||
CentersType** centers = new CentersType*[branching];
|
||||
|
||||
for (int i=0; i<branching; ++i) {
|
||||
centers[i] = new CentersType[veclen_];
|
||||
memoryCounter_ += (int)(veclen_*sizeof(CentersType));
|
||||
}
|
||||
|
||||
std::vector<DistanceType> radiuses(branching);
|
||||
cv::AutoBuffer<int> count_buf(branching);
|
||||
int* count = count_buf.data();
|
||||
for (int i=0; i<branching; ++i) {
|
||||
radiuses[i] = 0;
|
||||
count[i] = 0;
|
||||
}
|
||||
|
||||
// assign points to clusters
|
||||
cv::AutoBuffer<int> belongs_to_buf(indices_length);
|
||||
int* belongs_to = belongs_to_buf.data();
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
|
||||
DistanceType dist = distance_(dataset_[indices[i]], dataset_[centers_idx[0]], veclen_);
|
||||
belongs_to[i] = 0;
|
||||
for (int j=1; j<branching; ++j) {
|
||||
DistanceType new_dist = distance_(dataset_[indices[i]], dataset_[centers_idx[j]], veclen_);
|
||||
if (dist>new_dist) {
|
||||
belongs_to[i] = j;
|
||||
dist = new_dist;
|
||||
}
|
||||
}
|
||||
if (dist>radiuses[belongs_to[i]]) {
|
||||
radiuses[belongs_to[i]] = dist;
|
||||
}
|
||||
count[belongs_to[i]]++;
|
||||
}
|
||||
|
||||
bool converged = false;
|
||||
int iteration = 0;
|
||||
while (!converged && iteration<iterations_) {
|
||||
converged = true;
|
||||
iteration++;
|
||||
|
||||
// compute the new cluster centers
|
||||
for (int i=0; i<branching; ++i) {
|
||||
memset(dcenters[i],0,sizeof(unsigned int)*accumulator_veclen);
|
||||
radiuses[i] = 0;
|
||||
}
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
unsigned char* vec = (unsigned char*)dataset_[indices[i]];
|
||||
unsigned int* dcenter = dcenters[belongs_to[i]];
|
||||
for (size_t k=0, l=0; k<accumulator_veclen; k+=BITS_PER_CHAR, ++l) {
|
||||
dcenter[k] += (vec[l]) & 0x01;
|
||||
dcenter[k+1] += (vec[l]>>1) & 0x01;
|
||||
dcenter[k+2] += (vec[l]>>2) & 0x01;
|
||||
dcenter[k+3] += (vec[l]>>3) & 0x01;
|
||||
dcenter[k+4] += (vec[l]>>4) & 0x01;
|
||||
dcenter[k+5] += (vec[l]>>5) & 0x01;
|
||||
dcenter[k+6] += (vec[l]>>6) & 0x01;
|
||||
dcenter[k+7] += (vec[l]>>7) & 0x01;
|
||||
}
|
||||
}
|
||||
for (int i=0; i<branching; ++i) {
|
||||
double cnt = static_cast<double>(count[i]);
|
||||
unsigned int* dcenter = dcenters[i];
|
||||
unsigned char* charCenter = (unsigned char*)centers[i];
|
||||
for (size_t k=0, l=0; k<accumulator_veclen; k+=BITS_PER_CHAR, ++l) {
|
||||
charCenter[l] = static_cast<unsigned char>(
|
||||
(((int)(0.5 + (double)(dcenter[k]) / cnt)))
|
||||
| (((int)(0.5 + (double)(dcenter[k+1]) / cnt))<<1)
|
||||
| (((int)(0.5 + (double)(dcenter[k+2]) / cnt))<<2)
|
||||
| (((int)(0.5 + (double)(dcenter[k+3]) / cnt))<<3)
|
||||
| (((int)(0.5 + (double)(dcenter[k+4]) / cnt))<<4)
|
||||
| (((int)(0.5 + (double)(dcenter[k+5]) / cnt))<<5)
|
||||
| (((int)(0.5 + (double)(dcenter[k+6]) / cnt))<<6)
|
||||
| (((int)(0.5 + (double)(dcenter[k+7]) / cnt))<<7));
|
||||
}
|
||||
}
|
||||
|
||||
std::vector<int> new_centroids(indices_length);
|
||||
std::vector<DistanceType> dists(indices_length);
|
||||
|
||||
// reassign points to clusters
|
||||
KMeansDistanceComputer<ElementType**> invoker(distance_, dataset_, branching, indices, centers, veclen_, new_centroids, dists);
|
||||
parallel_for_(cv::Range(0, (int)indices_length), invoker);
|
||||
|
||||
for (int i=0; i < indices_length; ++i) {
|
||||
DistanceType dist(dists[i]);
|
||||
int new_centroid(new_centroids[i]);
|
||||
if (dist > radiuses[new_centroid]) {
|
||||
radiuses[new_centroid] = dist;
|
||||
}
|
||||
if (new_centroid != belongs_to[i]) {
|
||||
count[belongs_to[i]]--;
|
||||
count[new_centroid]++;
|
||||
belongs_to[i] = new_centroid;
|
||||
converged = false;
|
||||
}
|
||||
}
|
||||
|
||||
for (int i=0; i<branching; ++i) {
|
||||
// if one cluster converges to an empty cluster,
|
||||
// move an element into that cluster
|
||||
if (count[i]==0) {
|
||||
int j = (i+1)%branching;
|
||||
while (count[j]<=1) {
|
||||
j = (j+1)%branching;
|
||||
}
|
||||
|
||||
for (int k=0; k<indices_length; ++k) {
|
||||
if (belongs_to[k]==j) {
|
||||
// for cluster j, we move the furthest element from the center to the empty cluster i
|
||||
if ( distance_(dataset_[indices[k]], centers[j], veclen_) == radiuses[j] ) {
|
||||
belongs_to[k] = i;
|
||||
count[j]--;
|
||||
count[i]++;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
converged = false;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
// compute kmeans clustering for each of the resulting clusters
|
||||
node->childs = pool_.allocate<KMeansNodePtr>(branching);
|
||||
int start = 0;
|
||||
int end = start;
|
||||
for (int c=0; c<branching; ++c) {
|
||||
int s = count[c];
|
||||
|
||||
unsigned long long variance = 0ull;
|
||||
DistanceType mean_radius =0;
|
||||
for (int i=0; i<indices_length; ++i) {
|
||||
if (belongs_to[i]==c) {
|
||||
DistanceType d = distance_(dataset_[indices[i]], ZeroIterator<ElementType>(), veclen_);
|
||||
variance += static_cast<unsigned long long>( ensureSquareDistance<Distance>(d) );
|
||||
mean_radius += ensureSimpleDistance<Distance>(d);
|
||||
std::swap(indices[i],indices[end]);
|
||||
std::swap(belongs_to[i],belongs_to[end]);
|
||||
end++;
|
||||
}
|
||||
}
|
||||
mean_radius = static_cast<DistanceType>(
|
||||
0.5f + static_cast<float>(mean_radius) / static_cast<float>(s));
|
||||
variance = static_cast<unsigned long long>(
|
||||
0.5 + static_cast<double>(variance) / static_cast<double>(s));
|
||||
variance -= static_cast<unsigned long long>(
|
||||
ensureSquareDistance<Distance>(
|
||||
distance_(centers[c], ZeroIterator<ElementType>(), veclen_)));
|
||||
|
||||
node->childs[c] = pool_.allocate<KMeansNode>();
|
||||
std::memset(node->childs[c], 0, sizeof(KMeansNode));
|
||||
node->childs[c]->radius = radiuses[c];
|
||||
node->childs[c]->pivot = centers[c];
|
||||
node->childs[c]->variance = static_cast<DistanceType>(variance);
|
||||
node->childs[c]->mean_radius = mean_radius;
|
||||
computeBitfieldClustering(node->childs[c],indices+start, end-start, branching, level+1);
|
||||
start=end;
|
||||
}
|
||||
|
||||
delete[] centers;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Performs one descent in the hierarchical k-means tree. The branches not
|
||||
* visited are stored in a priority queue.
|
||||
@ -905,12 +1181,16 @@ private:
|
||||
DistanceType rsq = node->radius;
|
||||
DistanceType wsq = result.worstDist();
|
||||
|
||||
DistanceType val = bsq-rsq-wsq;
|
||||
DistanceType val2 = val*val-4*rsq*wsq;
|
||||
|
||||
//if (val>0) {
|
||||
if ((val>0)&&(val2>0)) {
|
||||
return;
|
||||
if (isSquareDistance<Distance>())
|
||||
{
|
||||
DistanceType val = bsq-rsq-wsq;
|
||||
if ((val>0) && (val*val > 4*rsq*wsq))
|
||||
return;
|
||||
}
|
||||
else
|
||||
{
|
||||
if (bsq-rsq > wsq)
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
@ -956,7 +1236,8 @@ private:
|
||||
// float* best_center = node->childs[best_index]->pivot;
|
||||
for (int i=0; i<branching_; ++i) {
|
||||
if (i != best_index) {
|
||||
domain_distances[i] -= cb_index_*node->childs[i]->variance;
|
||||
domain_distances[i] -= cvflann::round<DistanceType>(
|
||||
cb_index_*node->childs[i]->variance );
|
||||
|
||||
// float dist_to_border = getDistanceToBorder(node.childs[i].pivot,best_center,q);
|
||||
// if (domain_distances[i]<dist_to_border) {
|
||||
@ -981,12 +1262,16 @@ private:
|
||||
DistanceType rsq = node->radius;
|
||||
DistanceType wsq = result.worstDist();
|
||||
|
||||
DistanceType val = bsq-rsq-wsq;
|
||||
DistanceType val2 = val*val-4*rsq*wsq;
|
||||
|
||||
// if (val>0) {
|
||||
if ((val>0)&&(val2>0)) {
|
||||
return;
|
||||
if (isSquareDistance<Distance>())
|
||||
{
|
||||
DistanceType val = bsq-rsq-wsq;
|
||||
if ((val>0) && (val*val > 4*rsq*wsq))
|
||||
return;
|
||||
}
|
||||
else
|
||||
{
|
||||
if (bsq-rsq > wsq)
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
@ -1024,7 +1309,8 @@ private:
|
||||
DistanceType dist = distance_(q, node->childs[i]->pivot, veclen_);
|
||||
|
||||
int j=0;
|
||||
while (domain_distances[j]<dist && j<i) j++;
|
||||
while (domain_distances[j]<dist && j<i)
|
||||
j++;
|
||||
for (int k=i; k>j; --k) {
|
||||
domain_distances[k] = domain_distances[k-1];
|
||||
sort_indices[k] = sort_indices[k-1];
|
||||
|
||||
Loading…
Reference in New Issue
Block a user