Updated FLANN

modules/flann/include/opencv2/flann/all_indices.h

@@ -27,50 +27,129 @@
  *************************************************************************/
 
 
-#ifndef _OPENCV_ALL_INDICES_H_
-#define _OPENCV_ALL_INDICES_H_
+#ifndef OPENCV_FLANN_ALL_INDICES_H_
+#define OPENCV_FLANN_ALL_INDICES_H_
 
-#include "opencv2/flann/general.h"
+#include "general.h"
 
-#include "opencv2/flann/nn_index.h"
-#include "opencv2/flann/kdtree_index.h"
-#include "opencv2/flann/kmeans_index.h"
-#include "opencv2/flann/composite_index.h"
-#include "opencv2/flann/linear_index.h"
-#include "opencv2/flann/autotuned_index.h"
+#include "nn_index.h"
+#include "kdtree_index.h"
+#include "kdtree_single_index.h"
+#include "kmeans_index.h"
+#include "composite_index.h"
+#include "linear_index.h"
+#include "hierarchical_clustering_index.h"
+#include "lsh_index.h"
+#include "autotuned_index.h"
 
-namespace cvflann 
+
+namespace cvflann
+{
+
+template<typename KDTreeCapability, typename VectorSpace, typename Distance>
+struct index_creator
+{
+    static NNIndex<Distance>* create(const Matrix<typename Distance::ElementType>& dataset, const IndexParams& params, const Distance& distance)
+    {
+        flann_algorithm_t index_type = get_param<flann_algorithm_t>(params, "algorithm");
+
+        NNIndex<Distance>* nnIndex;
+        switch (index_type) {
+        case FLANN_INDEX_LINEAR:
+            nnIndex = new LinearIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_KDTREE_SINGLE:
+            nnIndex = new KDTreeSingleIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_KDTREE:
+            nnIndex = new KDTreeIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_KMEANS:
+            nnIndex = new KMeansIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_COMPOSITE:
+            nnIndex = new CompositeIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_AUTOTUNED:
+            nnIndex = new AutotunedIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_HIERARCHICAL:
+            nnIndex = new HierarchicalClusteringIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_LSH:
+            nnIndex = new LshIndex<Distance>(dataset, params, distance);
+            break;
+        default:
+            throw FLANNException("Unknown index type");
+        }
+
+        return nnIndex;
+    }
+};
+
+template<typename VectorSpace, typename Distance>
+struct index_creator<False,VectorSpace,Distance>
 {
+    static NNIndex<Distance>* create(const Matrix<typename Distance::ElementType>& dataset, const IndexParams& params, const Distance& distance)
+    {
+        flann_algorithm_t index_type = get_param<flann_algorithm_t>(params, "algorithm");
 
-template<typename T>
-NNIndex<T>* create_index_by_type(const Matrix<T>& dataset, const IndexParams& params)
+        NNIndex<Distance>* nnIndex;
+        switch (index_type) {
+        case FLANN_INDEX_LINEAR:
+            nnIndex = new LinearIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_KMEANS:
+            nnIndex = new KMeansIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_HIERARCHICAL:
+            nnIndex = new HierarchicalClusteringIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_LSH:
+            nnIndex = new LshIndex<Distance>(dataset, params, distance);
+            break;
+        default:
+            throw FLANNException("Unknown index type");
+        }
+
+        return nnIndex;
+    }
+};
+
+template<typename Distance>
+struct index_creator<False,False,Distance>
 {
-	flann_algorithm_t index_type = params.getIndexType();
-
-	NNIndex<T>* nnIndex;
-	switch (index_type) {
-	case FLANN_INDEX_LINEAR:
-		nnIndex = new LinearIndex<T>(dataset, (const LinearIndexParams&)params);
-		break;
-	case FLANN_INDEX_KDTREE:
-		nnIndex = new KDTreeIndex<T>(dataset, (const KDTreeIndexParams&)params);
-		break;
-	case FLANN_INDEX_KMEANS:
-		nnIndex = new KMeansIndex<T>(dataset, (const KMeansIndexParams&)params);
-		break;
-	case FLANN_INDEX_COMPOSITE:
-		nnIndex = new CompositeIndex<T>(dataset, (const CompositeIndexParams&) params);
-		break;
-	case FLANN_INDEX_AUTOTUNED:
-		nnIndex = new AutotunedIndex<T>(dataset, (const AutotunedIndexParams&) params);
-		break;
-	default:
-		throw FLANNException("Unknown index type");
-	}
-
-	return nnIndex;
+    static NNIndex<Distance>* create(const Matrix<typename Distance::ElementType>& dataset, const IndexParams& params, const Distance& distance)
+    {
+        flann_algorithm_t index_type = get_param<flann_algorithm_t>(params, "algorithm");
+
+        NNIndex<Distance>* nnIndex;
+        switch (index_type) {
+        case FLANN_INDEX_LINEAR:
+            nnIndex = new LinearIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_HIERARCHICAL:
+            nnIndex = new HierarchicalClusteringIndex<Distance>(dataset, params, distance);
+            break;
+        case FLANN_INDEX_LSH:
+            nnIndex = new LshIndex<Distance>(dataset, params, distance);
+            break;
+        default:
+            throw FLANNException("Unknown index type");
+        }
+
+        return nnIndex;
+    }
+};
+
+template<typename Distance>
+NNIndex<Distance>* create_index_by_type(const Matrix<typename Distance::ElementType>& dataset, const IndexParams& params, const Distance& distance)
+{
+    return index_creator<typename Distance::is_kdtree_distance,
+                         typename Distance::is_vector_space_distance,
+                         Distance>::create(dataset, params,distance);
 }
 
-} //namespace cvflann
+}
 
-#endif /* _OPENCV_ALL_INDICES_H_ */
+#endif /* OPENCV_FLANN_ALL_INDICES_H_ */

modules/flann/include/opencv2/flann/allocator.h

@@ -28,12 +28,13 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_ALLOCATOR_H_
-#define _OPENCV_ALLOCATOR_H_
+#ifndef OPENCV_FLANN_ALLOCATOR_H_
+#define OPENCV_FLANN_ALLOCATOR_H_
 
 #include <stdlib.h>
 #include <stdio.h>
 
+
 namespace cvflann
 {
 
@@ -47,8 +48,8 @@ namespace cvflann
 template <typename T>
 T* allocate(size_t count = 1)
 {
-	T* mem = (T*) ::malloc(sizeof(T)*count);
-	return mem;
+    T* mem = (T*) ::malloc(sizeof(T)*count);
+    return mem;
 }
 
 
@@ -70,118 +71,118 @@ T* allocate(size_t count = 1)
 const size_t     WORDSIZE=16;
 const  size_t     BLOCKSIZE=8192;
 
-class CV_EXPORTS PooledAllocator
+class PooledAllocator
 {
-	/* We maintain memory alignment to word boundaries by requiring that all
-		allocations be in multiples of the machine wordsize.  */
-	  /* Size of machine word in bytes.  Must be power of 2. */
-	/* Minimum number of bytes requested at a time from	the system.  Must be multiple of WORDSIZE. */
+    /* We maintain memory alignment to word boundaries by requiring that all
+        allocations be in multiples of the machine wordsize.  */
+    /* Size of machine word in bytes.  Must be power of 2. */
+    /* Minimum number of bytes requested at a time from	the system.  Must be multiple of WORDSIZE. */
 
 
-	int 	remaining;  /* Number of bytes left in current block of storage. */
-	void*	base;     /* Pointer to base of current block of storage. */
-	void*	loc;      /* Current location in block to next allocate memory. */
-	int 	blocksize;
+    int     remaining;  /* Number of bytes left in current block of storage. */
+    void*   base;     /* Pointer to base of current block of storage. */
+    void*   loc;      /* Current location in block to next allocate memory. */
+    int     blocksize;
 
 
 public:
-	int 	usedMemory;
-	int 	wastedMemory;
-
-	/**
-		Default constructor. Initializes a new pool.
-	*/
-	PooledAllocator(int blocksize = BLOCKSIZE)
-	{
-    	this->blocksize = blocksize;
-		remaining = 0;
-		base = NULL;
-
-		usedMemory = 0;
-		wastedMemory = 0;
-	}
-
-	/**
-	 * Destructor. Frees all the memory allocated in this pool.
-	 */
- 	~PooledAllocator()
-	{
-		void *prev;
-
-		while (base != NULL) {
-			prev = *((void **) base);  /* Get pointer to prev block. */
-			::free(base);
-			base = prev;
-		}
-	}
-
-	/**
-	 * Returns a pointer to a piece of new memory of the given size in bytes
-	 * allocated from the pool.
-	 */
-	void* allocateBytes(int size)
-	{
-		int blocksize;
-
-		/* Round size up to a multiple of wordsize.  The following expression
-			only works for WORDSIZE that is a power of 2, by masking last bits of
-			incremented size to zero.
-		*/
-		size = (size + (WORDSIZE - 1)) & ~(WORDSIZE - 1);
-
-		/* Check whether a new block must be allocated.  Note that the first word
-			of a block is reserved for a pointer to the previous block.
-		*/
-		if (size > remaining) {
-
-			wastedMemory += remaining;
-
-		/* Allocate new storage. */
-			blocksize = (size + sizeof(void*) + (WORDSIZE-1) > BLOCKSIZE) ?
-						size + sizeof(void*) + (WORDSIZE-1) : BLOCKSIZE;
-
-			// use the standard C malloc to allocate memory
-			void* m = ::malloc(blocksize);
-			if (!m) {
+    int     usedMemory;
+    int     wastedMemory;
+
+    /**
+        Default constructor. Initializes a new pool.
+     */
+    PooledAllocator(int blocksize = BLOCKSIZE)
+    {
+        this->blocksize = blocksize;
+        remaining = 0;
+        base = NULL;
+
+        usedMemory = 0;
+        wastedMemory = 0;
+    }
+
+    /**
+     * Destructor. Frees all the memory allocated in this pool.
+     */
+    ~PooledAllocator()
+    {
+        void* prev;
+
+        while (base != NULL) {
+            prev = *((void**) base); /* Get pointer to prev block. */
+            ::free(base);
+            base = prev;
+        }
+    }
+
+    /**
+     * Returns a pointer to a piece of new memory of the given size in bytes
+     * allocated from the pool.
+     */
+    void* allocateMemory(int size)
+    {
+        int blocksize;
+
+        /* Round size up to a multiple of wordsize.  The following expression
+            only works for WORDSIZE that is a power of 2, by masking last bits of
+            incremented size to zero.
+         */
+        size = (size + (WORDSIZE - 1)) & ~(WORDSIZE - 1);
+
+        /* Check whether a new block must be allocated.  Note that the first word
+            of a block is reserved for a pointer to the previous block.
+         */
+        if (size > remaining) {
+
+            wastedMemory += remaining;
+
+            /* Allocate new storage. */
+            blocksize = (size + sizeof(void*) + (WORDSIZE-1) > BLOCKSIZE) ?
+                        size + sizeof(void*) + (WORDSIZE-1) : BLOCKSIZE;
+
+            // use the standard C malloc to allocate memory
+            void* m = ::malloc(blocksize);
+            if (!m) {
                 fprintf(stderr,"Failed to allocate memory.\n");
-                exit(1);
-			}
-
-			/* Fill first word of new block with pointer to previous block. */
-			((void **) m)[0] = base;
-			base = m;
-
-			int shift = 0;
-			//int shift = (WORDSIZE - ( (((size_t)m) + sizeof(void*)) & (WORDSIZE-1))) & (WORDSIZE-1);
-
-			remaining = blocksize - sizeof(void*) - shift;
-			loc = ((char*)m + sizeof(void*) + shift);
-		}
-		void* rloc = loc;
-		loc = (char*)loc + size;
-		remaining -= size;
-
-		usedMemory += size;
-
-		return rloc;
-	}
-
-	/**
-	 * Allocates (using this pool) a generic type T.
-	 *
-	 * Params:
-	 *     count = number of instances to allocate.
-	 * Returns: pointer (of type T*) to memory buffer
-	 */
+                return NULL;
+            }
+
+            /* Fill first word of new block with pointer to previous block. */
+            ((void**) m)[0] = base;
+            base = m;
+
+            int shift = 0;
+            //int shift = (WORDSIZE - ( (((size_t)m) + sizeof(void*)) & (WORDSIZE-1))) & (WORDSIZE-1);
+
+            remaining = blocksize - sizeof(void*) - shift;
+            loc = ((char*)m + sizeof(void*) + shift);
+        }
+        void* rloc = loc;
+        loc = (char*)loc + size;
+        remaining -= size;
+
+        usedMemory += size;
+
+        return rloc;
+    }
+
+    /**
+     * Allocates (using this pool) a generic type T.
+     *
+     * Params:
+     *     count = number of instances to allocate.
+     * Returns: pointer (of type T*) to memory buffer
+     */
     template <typename T>
-	T* allocate(size_t count = 1)
-	{
-		T* mem = (T*) this->allocateBytes((int)(sizeof(T)*count));
-		return mem;
-	}
+    T* allocate(size_t count = 1)
+    {
+        T* mem = (T*) this->allocateMemory((int)(sizeof(T)*count));
+        return mem;
+    }
 
 };
 
-} // namespace cvflann
+}
 
-#endif //_OPENCV_ALLOCATOR_H_
+#endif //OPENCV_FLANN_ALLOCATOR_H_

modules/flann/include/opencv2/flann/any.h

+#ifndef OPENCV_FLANN_ANY_H_
+#define OPENCV_FLANN_ANY_H_
+/*
+ * (C) Copyright Christopher Diggins 2005-2011
+ * (C) Copyright Pablo Aguilar 2005
+ * (C) Copyright Kevlin Henney 2001
+ *
+ * Distributed under the Boost Software License, Version 1.0. (See
+ * accompanying file LICENSE_1_0.txt or copy at
+ * http://www.boost.org/LICENSE_1_0.txt
+ *
+ * Adapted for FLANN by Marius Muja
+ */
+
+
+
+#include <stdexcept>
+#include <ostream>
+
+namespace cdiggins
+{
+
+namespace anyimpl
+{
+
+struct bad_any_cast
+{
+};
+
+struct empty_any
+{
+};
+
+struct base_any_policy
+{
+    virtual void static_delete(void** x) = 0;
+    virtual void copy_from_value(void const* src, void** dest) = 0;
+    virtual void clone(void* const* src, void** dest) = 0;
+    virtual void move(void* const* src, void** dest) = 0;
+    virtual void* get_value(void** src) = 0;
+    virtual size_t get_size() = 0;
+    virtual void print(std::ostream& out, void* const* src) = 0;
+};
+
+template<typename T>
+struct typed_base_any_policy : base_any_policy
+{
+    virtual size_t get_size() { return sizeof(T); }
+
+};
+
+template<typename T>
+struct small_any_policy : typed_base_any_policy<T>
+{
+    virtual void static_delete(void**) { }
+    virtual void copy_from_value(void const* src, void** dest)
+    {
+        new (dest) T(* reinterpret_cast<T const*>(src));
+    }
+    virtual void clone(void* const* src, void** dest) { *dest = *src; }
+    virtual void move(void* const* src, void** dest) { *dest = *src; }
+    virtual void* get_value(void** src) { return reinterpret_cast<void*>(src); }
+    virtual void print(std::ostream& out, void* const* src) { out << *reinterpret_cast<T const*>(src); }
+};
+
+template<typename T>
+struct big_any_policy : typed_base_any_policy<T>
+{
+    virtual void static_delete(void** x)
+    {
+        if (* x) delete (* reinterpret_cast<T**>(x)); *x = NULL;
+    }
+    virtual void copy_from_value(void const* src, void** dest)
+    {
+        *dest = new T(*reinterpret_cast<T const*>(src));
+    }
+    virtual void clone(void* const* src, void** dest)
+    {
+        *dest = new T(**reinterpret_cast<T* const*>(src));
+    }
+    virtual void move(void* const* src, void** dest)
+    {
+        (*reinterpret_cast<T**>(dest))->~T();
+        **reinterpret_cast<T**>(dest) = **reinterpret_cast<T* const*>(src);
+    }
+    virtual void* get_value(void** src) { return *src; }
+    virtual void print(std::ostream& out, void* const* src) { out << *reinterpret_cast<T const*>(*src); }
+};
+
+template<typename T>
+struct choose_policy
+{
+    typedef big_any_policy<T> type;
+};
+
+template<typename T>
+struct choose_policy<T*>
+{
+    typedef small_any_policy<T*> type;
+};
+
+struct any;
+
+/// Choosing the policy for an any type is illegal, but should never happen.
+/// This is designed to throw a compiler error.
+template<>
+struct choose_policy<any>
+{
+    typedef void type;
+};
+
+/// Specializations for small types.
+#define SMALL_POLICY(TYPE) \
+    template<> \
+    struct choose_policy<TYPE> { typedef small_any_policy<TYPE> type; \
+    };
+
+SMALL_POLICY(signed char);
+SMALL_POLICY(unsigned char);
+SMALL_POLICY(signed short);
+SMALL_POLICY(unsigned short);
+SMALL_POLICY(signed int);
+SMALL_POLICY(unsigned int);
+SMALL_POLICY(signed long);
+SMALL_POLICY(unsigned long);
+SMALL_POLICY(float);
+SMALL_POLICY(bool);
+
+#undef SMALL_POLICY
+
+/// This function will return a different policy for each type.
+template<typename T>
+base_any_policy* get_policy()
+{
+    static typename choose_policy<T>::type policy;
+    return &policy;
+}
+} // namespace anyimpl
+
+struct any
+{
+private:
+    // fields
+    anyimpl::base_any_policy* policy;
+    void* object;
+
+public:
+    /// Initializing constructor.
+    template <typename T>
+    any(const T& x)
+        : policy(anyimpl::get_policy<anyimpl::empty_any>()), object(NULL)
+    {
+        assign(x);
+    }
+
+    /// Empty constructor.
+    any()
+        : policy(anyimpl::get_policy<anyimpl::empty_any>()), object(NULL)
+    { }
+
+    /// Special initializing constructor for string literals.
+    any(const char* x)
+        : policy(anyimpl::get_policy<anyimpl::empty_any>()), object(NULL)
+    {
+        assign(x);
+    }
+
+    /// Copy constructor.
+    any(const any& x)
+        : policy(anyimpl::get_policy<anyimpl::empty_any>()), object(NULL)
+    {
+        assign(x);
+    }
+
+    /// Destructor.
+    ~any()
+    {
+        policy->static_delete(&object);
+    }
+
+    /// Assignment function from another any.
+    any& assign(const any& x)
+    {
+        reset();
+        policy = x.policy;
+        policy->clone(&x.object, &object);
+        return *this;
+    }
+
+    /// Assignment function.
+    template <typename T>
+    any& assign(const T& x)
+    {
+        reset();
+        policy = anyimpl::get_policy<T>();
+        policy->copy_from_value(&x, &object);
+        return *this;
+    }
+
+    /// Assignment operator.
+    template<typename T>
+    any& operator=(const T& x)
+    {
+        return assign(x);
+    }
+
+    /// Assignment operator, specialed for literal strings.
+    /// They have types like const char [6] which don't work as expected.
+    any& operator=(const char* x)
+    {
+        return assign(x);
+    }
+
+    /// Utility functions
+    any& swap(any& x)
+    {
+        std::swap(policy, x.policy);
+        std::swap(object, x.object);
+        return *this;
+    }
+
+    /// Cast operator. You can only cast to the original type.
+    template<typename T>
+    T& cast()
+    {
+        if (policy != anyimpl::get_policy<T>()) throw anyimpl::bad_any_cast();
+        T* r = reinterpret_cast<T*>(policy->get_value(&object));
+        return *r;
+    }
+
+    /// Cast operator. You can only cast to the original type.
+    template<typename T>
+    const T& cast() const
+    {
+        if (policy != anyimpl::get_policy<T>()) throw anyimpl::bad_any_cast();
+        T* r = reinterpret_cast<T*>(policy->get_value((void**)&object));
+        return *r;
+    }
+
+    /// Returns true if the any contains no value.
+    bool empty() const
+    {
+        return policy == anyimpl::get_policy<anyimpl::empty_any>();
+    }
+
+    /// Frees any allocated memory, and sets the value to NULL.
+    void reset()
+    {
+        policy->static_delete(&object);
+        policy = anyimpl::get_policy<anyimpl::empty_any>();
+    }
+
+    /// Returns true if the two types are the same.
+    bool compatible(const any& x) const
+    {
+        return policy == x.policy;
+    }
+
+    /// Returns if the type is compatible with the policy
+    template<typename T>
+    bool has_type()
+    {
+        return policy == anyimpl::get_policy<T>();
+    }
+
+    friend std::ostream& operator <<(std::ostream& out, const any& any_val);
+};
+
+inline std::ostream& operator <<(std::ostream& out, const any& any_val)
+{
+    any_val.policy->print(out,&any_val.object);
+    return out;
+}
+
+}
+
+#endif // OPENCV_FLANN_ANY_H_

modules/flann/include/opencv2/flann/composite_index.h

@@ -28,135 +28,167 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_COMPOSITETREE_H_
-#define _OPENCV_COMPOSITETREE_H_
+#ifndef OPENCV_FLANN_COMPOSITE_INDEX_H_
+#define OPENCV_FLANN_COMPOSITE_INDEX_H_
 
-#include "opencv2/flann/general.h"
-#include "opencv2/flann/nn_index.h"
+#include "general.h"
+#include "nn_index.h"
+#include "kdtree_index.h"
+#include "kmeans_index.h"
 
 namespace cvflann
 {
 
-
-struct CompositeIndexParams : public IndexParams {
-	CompositeIndexParams(int trees_ = 4, int branching_ = 32, int iterations_ = 11,
-			flann_centers_init_t centers_init_ = FLANN_CENTERS_RANDOM, float cb_index_ = 0.2 ) :
-		IndexParams(FLANN_INDEX_COMPOSITE),
-		trees(trees_),
-		branching(branching_),
-		iterations(iterations_),
-		centers_init(centers_init_),
-		cb_index(cb_index_) {};
-
-	int trees;                 // number of randomized trees to use (for kdtree)
-	int branching;             // branching factor (for kmeans tree)
-	int iterations;            // max iterations to perform in one kmeans clustering (kmeans tree)
-	flann_centers_init_t centers_init;          // algorithm used for picking the initial cluster centers for kmeans tree
-    float cb_index;            // cluster boundary index. Used when searching the kmeans tree
-
-	void print() const
-	{
-		logger().info("Index type: %d\n",(int)algorithm);
-		logger().info("Trees: %d\n", trees);
-		logger().info("Branching: %d\n", branching);
-		logger().info("Iterations: %d\n", iterations);
-		logger().info("Centres initialisation: %d\n", centers_init);
-		logger().info("Cluster boundary weight: %g\n", cb_index);
-	}
+/**
+ * Index parameters for the CompositeIndex.
+ */
+struct CompositeIndexParams : public IndexParams
+{
+    CompositeIndexParams(int trees = 4, int branching = 32, int iterations = 11,
+                         flann_centers_init_t centers_init = FLANN_CENTERS_RANDOM, float cb_index = 0.2 )
+    {
+        (*this)["algorithm"] = FLANN_INDEX_KMEANS;
+        // number of randomized trees to use (for kdtree)
+        (*this)["trees"] = trees;
+        // branching factor
+        (*this)["branching"] = branching;
+        // max iterations to perform in one kmeans clustering (kmeans tree)
+        (*this)["iterations"] = iterations;
+        // algorithm used for picking the initial cluster centers for kmeans tree
+        (*this)["centers_init"] = centers_init;
+        // cluster boundary index. Used when searching the kmeans tree
+        (*this)["cb_index"] = cb_index;
+    }
 };
 
 
-
-template <typename ELEM_TYPE, typename DIST_TYPE = typename DistType<ELEM_TYPE>::type >
-class CompositeIndex : public NNIndex<ELEM_TYPE>
+/**
+ * This index builds a kd-tree index and a k-means index and performs nearest
+ * neighbour search both indexes. This gives a slight boost in search performance
+ * as some of the neighbours that are missed by one index are found by the other.
+ */
+template <typename Distance>
+class CompositeIndex : public NNIndex<Distance>
 {
-	KMeansIndex<ELEM_TYPE, DIST_TYPE>* kmeans;
-	KDTreeIndex<ELEM_TYPE, DIST_TYPE>* kdtree;
-
-    const Matrix<ELEM_TYPE> dataset;
-
-    const IndexParams& index_params;
-
-	CompositeIndex& operator=(const CompositeIndex&);
-	CompositeIndex(const CompositeIndex&);
 public:
+    typedef typename Distance::ElementType ElementType;
+    typedef typename Distance::ResultType DistanceType;
+
+    /**
+     * Index constructor
+     * @param inputData dataset containing the points to index
+     * @param params Index parameters
+     * @param d Distance functor
+     * @return
+     */
+    CompositeIndex(const Matrix<ElementType>& inputData, const IndexParams& params = CompositeIndexParams(),
+                   Distance d = Distance()) : index_params_(params)
+    {
+        kdtree_index_ = new KDTreeIndex<Distance>(inputData, params, d);
+        kmeans_index_ = new KMeansIndex<Distance>(inputData, params, d);
 
-	CompositeIndex(const Matrix<ELEM_TYPE>& inputData, const CompositeIndexParams& params = CompositeIndexParams() ) :
-		dataset(inputData), index_params(params)
-	{
-		KDTreeIndexParams kdtree_params(params.trees);
-		KMeansIndexParams kmeans_params(params.branching, params.iterations, params.centers_init, params.cb_index);
-
-		kdtree = new KDTreeIndex<ELEM_TYPE, DIST_TYPE>(inputData,kdtree_params);
-		kmeans = new KMeansIndex<ELEM_TYPE, DIST_TYPE>(inputData,kmeans_params);
-
-	}
+    }
 
-	virtual ~CompositeIndex()
-	{
-		delete kdtree;
-		delete kmeans;
-	}
+    CompositeIndex(const CompositeIndex&);
+    CompositeIndex& operator=(const CompositeIndex&);
 
+    virtual ~CompositeIndex()
+    {
+        delete kdtree_index_;
+        delete kmeans_index_;
+    }
 
+    /**
+     * @return The index type
+     */
     flann_algorithm_t getType() const
     {
         return FLANN_INDEX_COMPOSITE;
     }
 
-
+    /**
+     * @return Size of the index
+     */
     size_t size() const
-	{
-		return dataset.rows;
-	}
-
-	size_t veclen() const
-	{
-		return dataset.cols;
-	}
-
+    {
+        return kdtree_index_->size();
+    }
 
-	int usedMemory() const
-	{
-		return kmeans->usedMemory()+kdtree->usedMemory();
-	}
+    /**
+     * \returns The dimensionality of the features in this index.
+     */
+    size_t veclen() const
+    {
+        return kdtree_index_->veclen();
+    }
 
-	void buildIndex()
-	{
-		logger().info("Building kmeans tree...\n");
-		kmeans->buildIndex();
-		logger().info("Building kdtree tree...\n");
-		kdtree->buildIndex();
-	}
+    /**
+     * \returns The amount of memory (in bytes) used by the index.
+     */
+    int usedMemory() const
+    {
+        return kmeans_index_->usedMemory() + kdtree_index_->usedMemory();
+    }
 
+    /**
+     * \brief Builds the index
+     */
+    void buildIndex()
+    {
+        Logger::info("Building kmeans tree...\n");
+        kmeans_index_->buildIndex();
+        Logger::info("Building kdtree tree...\n");
+        kdtree_index_->buildIndex();
+    }
 
+    /**
+     * \brief Saves the index to a stream
+     * \param stream The stream to save the index to
+     */
     void saveIndex(FILE* stream)
     {
-    	kmeans->saveIndex(stream);
-    	kdtree->saveIndex(stream);
+        kmeans_index_->saveIndex(stream);
+        kdtree_index_->saveIndex(stream);
     }
 
-
+    /**
+     * \brief Loads the index from a stream
+     * \param stream The stream from which the index is loaded
+     */
     void loadIndex(FILE* stream)
     {
-    	kmeans->loadIndex(stream);
-    	kdtree->loadIndex(stream);
+        kmeans_index_->loadIndex(stream);
+        kdtree_index_->loadIndex(stream);
     }
 
-	void findNeighbors(ResultSet<ELEM_TYPE>& result, const ELEM_TYPE* vec, const SearchParams& searchParams)
-	{
-		kmeans->findNeighbors(result,vec,searchParams);
-		kdtree->findNeighbors(result,vec,searchParams);
-	}
+    /**
+     * \returns The index parameters
+     */
+    IndexParams getParameters() const
+    {
+        return index_params_;
+    }
+
+    /**
+     * \brief Method that searches for nearest-neighbours
+     */
+    void findNeighbors(ResultSet<DistanceType>& result, const ElementType* vec, const SearchParams& searchParams)
+    {
+        kmeans_index_->findNeighbors(result, vec, searchParams);
+        kdtree_index_->findNeighbors(result, vec, searchParams);
+    }
 
-	const IndexParams* getParameters() const
-	{
-		return &index_params;
-	}
+private:
+    /** The k-means index */
+    KMeansIndex<Distance>* kmeans_index_;
 
+    /** The kd-tree index */
+    KDTreeIndex<Distance>* kdtree_index_;
 
+    /** The index parameters */
+    const IndexParams index_params_;
 };
 
-} // namespace cvflann
+}
 
-#endif //_OPENCV_COMPOSITETREE_H_
+#endif //OPENCV_FLANN_COMPOSITE_INDEX_H_

modules/flann/include/opencv2/flann/config.h

+/***********************************************************************
+ * Software License Agreement (BSD License)
+ *
+ * Copyright 2008-2011  Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
+ * Copyright 2008-2011  David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *************************************************************************/
+
+
+#ifndef OPENCV_FLANN_CONFIG_H_
+#define OPENCV_FLANN_CONFIG_H_
+
+#define FLANN_VERSION "1.6.10"
+
+#endif /* OPENCV_FLANN_CONFIG_H_ */

modules/flann/include/opencv2/flann/defines.h

+/***********************************************************************
+ * Software License Agreement (BSD License)
+ *
+ * Copyright 2008-2011  Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
+ * Copyright 2008-2011  David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *************************************************************************/
+
+
+#ifndef OPENCV_FLANN_DEFINES_H_
+#define OPENCV_FLANN_DEFINES_H_
+
+#include "config.h"
+
+#ifdef WIN32
+/* win32 dll export/import directives */
+ #ifdef FLANN_EXPORTS
+  #define FLANN_EXPORT __declspec(dllexport)
+ #elif defined(FLANN_STATIC)
+  #define FLANN_EXPORT
+ #else
+  #define FLANN_EXPORT __declspec(dllimport)
+ #endif
+#else
+/* unix needs nothing */
+ #define FLANN_EXPORT
+#endif
+
+
+#ifdef __GNUC__
+#define FLANN_DEPRECATED __attribute__ ((deprecated))
+#elif defined(_MSC_VER)
+#define FLANN_DEPRECATED  __declspec(deprecated)
+#else
+#pragma message("WARNING: You need to implement FLANN_DEPRECATED for this compiler")
+#define FLANN_DEPRECATED
+#endif
+
+
+#if __amd64__ || __x86_64__ || _WIN64 || _M_X64
+#define FLANN_PLATFORM_64_BIT
+#else
+#define FLANN_PLATFORM_32_BIT
+#endif
+
+
+#define FLANN_ARRAY_LEN(a) (sizeof(a)/sizeof(a[0]))
+
+/* Nearest neighbour index algorithms */
+enum flann_algorithm_t
+{
+    FLANN_INDEX_LINEAR = 0,
+    FLANN_INDEX_KDTREE = 1,
+    FLANN_INDEX_KMEANS = 2,
+    FLANN_INDEX_COMPOSITE = 3,
+    FLANN_INDEX_KDTREE_SINGLE = 4,
+    FLANN_INDEX_HIERARCHICAL = 5,
+    FLANN_INDEX_LSH = 6,
+    FLANN_INDEX_SAVED = 254,
+    FLANN_INDEX_AUTOTUNED = 255,
+
+    // deprecated constants, should use the FLANN_INDEX_* ones instead
+    LINEAR = 0,
+    KDTREE = 1,
+    KMEANS = 2,
+    COMPOSITE = 3,
+    KDTREE_SINGLE = 4,
+    SAVED = 254,
+    AUTOTUNED = 255
+};
+
+
+
+enum flann_centers_init_t
+{
+    FLANN_CENTERS_RANDOM = 0,
+    FLANN_CENTERS_GONZALES = 1,
+    FLANN_CENTERS_KMEANSPP = 2,
+
+    // deprecated constants, should use the FLANN_CENTERS_* ones instead
+    CENTERS_RANDOM = 0,
+    CENTERS_GONZALES = 1,
+    CENTERS_KMEANSPP = 2
+};
+
+enum flann_log_level_t
+{
+    FLANN_LOG_NONE = 0,
+    FLANN_LOG_FATAL = 1,
+    FLANN_LOG_ERROR = 2,
+    FLANN_LOG_WARN = 3,
+    FLANN_LOG_INFO = 4,
+};
+
+enum flann_distance_t
+{
+    FLANN_DIST_EUCLIDEAN = 1,
+    FLANN_DIST_L2 = 1,
+    FLANN_DIST_MANHATTAN = 2,
+    FLANN_DIST_L1 = 2,
+    FLANN_DIST_MINKOWSKI = 3,
+    FLANN_DIST_MAX   = 4,
+    FLANN_DIST_HIST_INTERSECT   = 5,
+    FLANN_DIST_HELLINGER = 6,
+    FLANN_DIST_CHI_SQUARE = 7,
+    FLANN_DIST_CS         = 7,
+    FLANN_DIST_KULLBACK_LEIBLER  = 8,
+    FLANN_DIST_KL                = 8,
+
+    // deprecated constants, should use the FLANN_DIST_* ones instead
+    EUCLIDEAN = 1,
+    MANHATTAN = 2,
+    MINKOWSKI = 3,
+    MAX_DIST   = 4,
+    HIST_INTERSECT   = 5,
+    HELLINGER = 6,
+    CS         = 7,
+    KL         = 8,
+    KULLBACK_LEIBLER  = 8
+};
+
+enum flann_datatype_t
+{
+    FLANN_INT8 = 0,
+    FLANN_INT16 = 1,
+    FLANN_INT32 = 2,
+    FLANN_INT64 = 3,
+    FLANN_UINT8 = 4,
+    FLANN_UINT16 = 5,
+    FLANN_UINT32 = 6,
+    FLANN_UINT64 = 7,
+    FLANN_FLOAT32 = 8,
+    FLANN_FLOAT64 = 9
+};
+
+const int FLANN_CHECKS_UNLIMITED = -1;
+const int FLANN_CHECKS_AUTOTUNED = -2;
+
+
+#endif /* OPENCV_FLANN_DEFINES_H_ */

modules/flann/include/opencv2/flann/dynamic_bitset.h

+/***********************************************************************
+ * Software License Agreement (BSD License)
+ *
+ * Copyright 2008-2009  Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
+ * Copyright 2008-2009  David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
+ *
+ * THE BSD LICENSE
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *************************************************************************/
+
+/***********************************************************************
+ * Author: Vincent Rabaud
+ *************************************************************************/
+
+#ifndef OPENCV_FLANN_DYNAMIC_BITSET_H_
+#define OPENCV_FLANN_DYNAMIC_BITSET_H_
+
+//#define FLANN_USE_BOOST 1
+#if FLANN_USE_BOOST
+#include <boost/dynamic_bitset.hpp>
+typedef boost::dynamic_bitset<> DynamicBitset;
+#else
+
+#include <limits.h>
+
+#include "dist.h"
+
+/** Class re-implementing the boost version of it
+ * This helps not depending on boost, it also does not do the bound checks
+ * and has a way to reset a block for speed
+ */
+class DynamicBitset
+{
+public:
+    /** @param default constructor
+     */
+    DynamicBitset()
+    {
+    }
+
+    /** @param only constructor we use in our code
+     * @param the size of the bitset (in bits)
+     */
+    DynamicBitset(size_t size)
+    {
+        resize(size);
+        reset();
+    }
+
+    /** Sets all the bits to 0
+     */
+    void clear()
+    {
+        std::fill(bitset_.begin(), bitset_.end(), 0);
+    }
+
+    /** @brief checks if the bitset is empty
+     * @return true if the bitset is empty
+     */
+    bool empty() const
+    {
+        return bitset_.empty();
+    }
+
+    /** @param set all the bits to 0
+     */
+    void reset()
+    {
+        std::fill(bitset_.begin(), bitset_.end(), 0);
+    }
+
+    /** @brief set one bit to 0
+     * @param
+     */
+    void reset(size_t index)
+    {
+        bitset_[index / cell_bit_size_] &= ~(size_t(1) << (index % cell_bit_size_));
+    }
+
+    /** @brief sets a specific bit to 0, and more bits too
+     * This function is useful when resetting a given set of bits so that the
+     * whole bitset ends up being 0: if that's the case, we don't care about setting
+     * other bits to 0
+     * @param
+     */
+    void reset_block(size_t index)
+    {
+        bitset_[index / cell_bit_size_] = 0;
+    }
+
+    /** @param resize the bitset so that it contains at least size bits
+     * @param size
+     */
+    void resize(size_t size)
+    {
+        size_ = size;
+        bitset_.resize(size / cell_bit_size_ + 1);
+    }
+
+    /** @param set a bit to true
+     * @param index the index of the bit to set to 1
+     */
+    void set(size_t index)
+    {
+        bitset_[index / cell_bit_size_] |= size_t(1) << (index % cell_bit_size_);
+    }
+
+    /** @param gives the number of contained bits
+     */
+    size_t size() const
+    {
+        return size_;
+    }
+
+    /** @param check if a bit is set
+     * @param index the index of the bit to check
+     * @return true if the bit is set
+     */
+    bool test(size_t index) const
+    {
+        return (bool)(bitset_[index / cell_bit_size_] & (size_t(1) << (index % cell_bit_size_)));
+    }
+
+private:
+    std::vector<size_t> bitset_;
+    size_t size_;
+    static const unsigned int cell_bit_size_ = CHAR_BIT * sizeof(size_t);
+};
+
+#endif
+
+#endif // OPENCV_FLANN_DYNAMIC_BITSET_H_

modules/flann/include/opencv2/flann/general.h

@@ -28,119 +28,25 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_GENERAL_H_
-#define _OPENCV_GENERAL_H_
-
-#ifdef __cplusplus
+#ifndef OPENCV_FLANN_GENERAL_H_
+#define OPENCV_FLANN_GENERAL_H_
 
+#include "defines.h"
 #include <stdexcept>
 #include <cassert>
-#include "opencv2/flann/object_factory.h"
-#include "opencv2/flann/logger.h"
-
-namespace cvflann {
-
-#undef ARRAY_LEN
-#define ARRAY_LEN(a) (sizeof(a)/sizeof(a[0]))
-
-/* Nearest neighbour index algorithms */
-enum flann_algorithm_t {
-	FLANN_INDEX_LINEAR = 0,
-	FLANN_INDEX_KDTREE = 1,
-	FLANN_INDEX_KMEANS = 2,
-	FLANN_INDEX_COMPOSITE = 3,
-	FLANN_INDEX_SAVED = 254,
-	FLANN_INDEX_AUTOTUNED = 255
-};
-
-enum flann_centers_init_t {
-	FLANN_CENTERS_RANDOM = 0,
-	FLANN_CENTERS_GONZALES = 1,
-	FLANN_CENTERS_KMEANSPP = 2
-};
-
-
-enum flann_distance_t {
-	FLANN_DIST_EUCLIDEAN = 1,
-	FLANN_DIST_L2 = 1,
-	FLANN_DIST_MANHATTAN = 2,
-	FLANN_DIST_L1 = 2,
-	FLANN_DIST_MINKOWSKI = 3,
-	FLANN_DIST_MAX       = 4,
-	FLANN_DIST_HIST_INTERSECT = 5,
-	FLANN_DIST_HELLINGER = 6,
-	FLANN_DIST_CHI_SQUARE = 7,
-	FLANN_DIST_CS         = 7,
-	FLANN_DIST_KULLBACK_LEIBLER        = 8,
-	FLANN_DIST_KL        = 8
-};
-
-enum flann_datatype_t {
-	FLANN_INT8 = 0,
-	FLANN_INT16 = 1,
-	FLANN_INT32 = 2,
-	FLANN_INT64 = 3,
-	FLANN_UINT8 = 4,
-	FLANN_UINT16 = 5,
-	FLANN_UINT32 = 6,
-	FLANN_UINT64 = 7,
-	FLANN_FLOAT32 = 8,
-	FLANN_FLOAT64 = 9
-};
-
-template <typename ELEM_TYPE>
-struct DistType
-{
-	typedef ELEM_TYPE type;
-};
 
-template <>
-struct DistType<unsigned char>
+namespace cvflann
 {
-	typedef float type;
-};
 
-template <>
-struct DistType<int>
+class FLANNException : public std::runtime_error
 {
-	typedef float type;
-};
-
-
-class FLANNException : public std::runtime_error {
- public:
-   FLANNException(const char* message) : std::runtime_error(message) { }
-
-   FLANNException(const std::string& message) : std::runtime_error(message) { }
- };
-
-
-struct CV_EXPORTS IndexParams {
-protected:
-	IndexParams(flann_algorithm_t algorithm_) : algorithm(algorithm_) {};
-	
 public:
-	virtual ~IndexParams() {}
-	virtual flann_algorithm_t getIndexType() const { return algorithm; }
-
-	virtual void print() const = 0;
-
-	flann_algorithm_t algorithm;
-};
-
-
-typedef ObjectFactory<IndexParams, flann_algorithm_t> ParamsFactory;
-CV_EXPORTS ParamsFactory& ParamsFactory_instance();
-
-struct CV_EXPORTS SearchParams {
-	SearchParams(int checks_ = 32) :
-		checks(checks_) {};
+    FLANNException(const char* message) : std::runtime_error(message) { }
 
-	int checks;
+    FLANNException(const std::string& message) : std::runtime_error(message) { }
 };
 
-} // namespace cvflann
+}
 
-#endif
 
-#endif  /* _OPENCV_GENERAL_H_ */
+#endif  /* OPENCV_FLANN_GENERAL_H_ */

modules/flann/include/opencv2/flann/ground_truth.h

@@ -28,39 +28,41 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_GROUND_TRUTH_H_
-#define _OPENCV_GROUND_TRUTH_H_
+#ifndef OPENCV_FLANN_GROUND_TRUTH_H_
+#define OPENCV_FLANN_GROUND_TRUTH_H_
+
+#include "dist.h"
+#include "matrix.h"
 
-#include "opencv2/flann/dist.h"
-#include "opencv2/flann/matrix.h"
 
 namespace cvflann
 {
 
-template <typename T>
-void find_nearest(const Matrix<T>& dataset, T* query, int* matches, int nn, int skip = 0)
+template <typename Distance>
+void find_nearest(const Matrix<typename Distance::ElementType>& dataset, typename Distance::ElementType* query, int* matches, int nn,
+                  int skip = 0, Distance distance = Distance())
 {
+    typedef typename Distance::ElementType ElementType;
+    typedef typename Distance::ResultType DistanceType;
     int n = nn + skip;
 
-    T* query_end = query + dataset.cols;
-
-    long* match = new long[n];
-    T* dists = new T[n];
+    int* match = new int[n];
+    DistanceType* dists = new DistanceType[n];
 
-    dists[0] = (float)flann_dist(query, query_end, dataset[0]);
+    dists[0] = distance(dataset[0], query, dataset.cols);
     match[0] = 0;
     int dcnt = 1;
 
-    for (size_t i=1;i<dataset.rows;++i) {
-        T tmp = (T)flann_dist(query, query_end, dataset[i]);
+    for (size_t i=1; i<dataset.rows; ++i) {
+        DistanceType tmp = distance(dataset[i], query, dataset.cols);
 
         if (dcnt<n) {
-            match[dcnt] = (long)i;
+            match[dcnt] = i;
             dists[dcnt++] = tmp;
         }
         else if (tmp < dists[dcnt-1]) {
             dists[dcnt-1] = tmp;
-            match[dcnt-1] = (long)i;
+            match[dcnt-1] = i;
         }
 
         int j = dcnt-1;
@@ -72,7 +74,7 @@ void find_nearest(const Matrix<T>& dataset, T* query, int* matches, int nn, int
         }
     }
 
-    for (int i=0;i<nn;++i) {
+    for (int i=0; i<nn; ++i) {
         matches[i] = match[i+skip];
     }
 
@@ -81,15 +83,16 @@ void find_nearest(const Matrix<T>& dataset, T* query, int* matches, int nn, int
 }
 
 
-template <typename T>
-void compute_ground_truth(const Matrix<T>& dataset, const Matrix<T>& testset, Matrix<int>& matches, int skip=0)
+template <typename Distance>
+void compute_ground_truth(const Matrix<typename Distance::ElementType>& dataset, const Matrix<typename Distance::ElementType>& testset, Matrix<int>& matches,
+                          int skip=0, Distance d = Distance())
 {
-    for (size_t i=0;i<testset.rows;++i) {
-        find_nearest(dataset, testset[i], matches[i], (int)matches.cols, skip);
+    for (size_t i=0; i<testset.rows; ++i) {
+        find_nearest<Distance>(dataset, testset[i], matches[i], (int)matches.cols, skip, d);
     }
 }
 
 
-} // namespace cvflann
+}
 
-#endif //_OPENCV_GROUND_TRUTH_H_
+#endif //OPENCV_FLANN_GROUND_TRUTH_H_

modules/flann/include/opencv2/flann/hdf5.h

@@ -27,137 +27,207 @@
  *************************************************************************/
 
 
-#ifndef _OPENCV_HDF5_H_
-#define _OPENCV_HDF5_H_
+#ifndef OPENCV_FLANN_HDF5_H_
+#define OPENCV_FLANN_HDF5_H_
 
-#include <H5Cpp.h>
+#include <hdf5.h>
 
-#include "opencv2/flann/matrix.h"
+#include "matrix.h"
 
 
+namespace cvflann
+{
 
-#ifndef H5_NO_NAMESPACE
-    using namespace H5;
-#endif
+namespace
+{
 
-namespace cvflann 
+template<typename T>
+hid_t get_hdf5_type()
 {
+    throw FLANNException("Unsupported type for IO operations");
+}
+
+template<>
+hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
+template<>
+hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
+template<>
+hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
+template<>
+hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
+template<>
+hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
+template<>
+hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
+template<>
+hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
+template<>
+hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
+template<>
+hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
+template<>
+hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
+template<>
+hid_t get_hdf5_type<long double>() { return H5T_NATIVE_LDOUBLE; }
+}
 
 
-namespace {
+#define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
 
 template<typename T>
-PredType get_hdf5_type()
+void save_to_file(const cvflann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
 {
-	throw FLANNException("Unsupported type for IO operations");
-}
 
-template<> PredType get_hdf5_type<char>() { return PredType::NATIVE_CHAR; }
-template<> PredType get_hdf5_type<unsigned char>() { return PredType::NATIVE_UCHAR; }
-template<> PredType get_hdf5_type<short int>() { return PredType::NATIVE_SHORT; }
-template<> PredType get_hdf5_type<unsigned short int>() { return PredType::NATIVE_USHORT; }
-template<> PredType get_hdf5_type<int>() { return PredType::NATIVE_INT; }
-template<> PredType get_hdf5_type<unsigned int>() { return PredType::NATIVE_UINT; }
-template<> PredType get_hdf5_type<long>() { return PredType::NATIVE_LONG; }
-template<> PredType get_hdf5_type<unsigned long>() { return PredType::NATIVE_ULONG; }
-template<> PredType get_hdf5_type<float>() { return PredType::NATIVE_FLOAT; }
-template<> PredType get_hdf5_type<double>() { return PredType::NATIVE_DOUBLE; }
-template<> PredType get_hdf5_type<long double>() { return PredType::NATIVE_LDOUBLE; }
+#if H5Eset_auto_vers == 2
+    H5Eset_auto( H5E_DEFAULT, NULL, NULL );
+#else
+    H5Eset_auto( NULL, NULL );
+#endif
+
+    herr_t status;
+    hid_t file_id;
+    file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+    if (file_id < 0) {
+        file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+    }
+    CHECK_ERROR(file_id,"Error creating hdf5 file.");
+
+    hsize_t     dimsf[2];              // dataset dimensions
+    dimsf[0] = dataset.rows;
+    dimsf[1] = dataset.cols;
+
+    hid_t space_id = H5Screate_simple(2, dimsf, NULL);
+    hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);
+
+    hid_t dataset_id;
+#if H5Dcreate_vers == 2
+    dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+#else
+    dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
+#endif
+
+    if (dataset_id<0) {
+#if H5Dopen_vers == 2
+        dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
+#else
+        dataset_id = H5Dopen(file_id, name.c_str());
+#endif
+    }
+    CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");
+
+    status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.data );
+    CHECK_ERROR(status, "Error writing to dataset");
+
+    H5Sclose(memspace_id);
+    H5Sclose(space_id);
+    H5Dclose(dataset_id);
+    H5Fclose(file_id);
 
 }
 
 
 template<typename T>
-void save_to_file(const cvflann::Matrix<T>& flann_dataset, const std::string& filename, const std::string& name)
+void load_from_file(cvflann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
 {
-	// Try block to detect exceptions raised by any of the calls inside it
-	try
-	{
-		/*
-		 * Turn off the auto-printing when failure occurs so that we can
-		 * handle the errors appropriately
-		 */
-		Exception::dontPrint();
-
-		/*
-		 * Create a new file using H5F_ACC_TRUNC access,
-		 * default file creation properties, and default file
-		 * access properties.
-		 */
-		H5File file( filename, H5F_ACC_TRUNC );
-
-		/*
-		 * Define the size of the array and create the data space for fixed
-		 * size dataset.
-		 */
-		hsize_t     dimsf[2];              // dataset dimensions
-		dimsf[0] = flann_dataset.rows;
-		dimsf[1] = flann_dataset.cols;
-		DataSpace dataspace( 2, dimsf );
-
-		/*
-		 * Create a new dataset within the file using defined dataspace and
-		 * datatype and default dataset creation properties.
-		 */
-		DataSet dataset = file.createDataSet( name, get_hdf5_type<T>(), dataspace );
-
-		/*
-		 * Write the data to the dataset using default memory space, file
-		 * space, and transfer properties.
-		 */
-		dataset.write( flann_dataset.data, get_hdf5_type<T>() );
-	}  // end of try block
-	catch( H5::Exception& error )
-	{
-		error.printError();
-		throw FLANNException(error.getDetailMsg());
-	}
+    herr_t status;
+    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+    CHECK_ERROR(file_id,"Error opening hdf5 file.");
+
+    hid_t dataset_id;
+#if H5Dopen_vers == 2
+    dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
+#else
+    dataset_id = H5Dopen(file_id, name.c_str());
+#endif
+    CHECK_ERROR(dataset_id,"Error opening dataset in file.");
+
+    hid_t space_id = H5Dget_space(dataset_id);
+
+    hsize_t dims_out[2];
+    H5Sget_simple_extent_dims(space_id, dims_out, NULL);
+
+    dataset = cvflann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);
+
+    status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
+    CHECK_ERROR(status, "Error reading dataset");
+
+    H5Sclose(space_id);
+    H5Dclose(dataset_id);
+    H5Fclose(file_id);
 }
 
 
+#ifdef HAVE_MPI
+
+namespace mpi
+{
+/**
+ * Loads a the hyperslice corresponding to this processor from a hdf5 file.
+ * @param flann_dataset Dataset where the data is loaded
+ * @param filename HDF5 file name
+ * @param name Name of dataset inside file
+ */
 template<typename T>
-void load_from_file(cvflann::Matrix<T>& flann_dataset, const std::string& filename, const std::string& name)
+void load_from_file(cvflann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
 {
-	try
-	{
-		Exception::dontPrint();
-
-		H5File file( filename, H5F_ACC_RDONLY );
-		DataSet dataset = file.openDataSet( name );
-
-		/*
-		 * Check the type used by the dataset matches
-		 */
-		if ( !(dataset.getDataType()==get_hdf5_type<T>())) {
-			throw FLANNException("Dataset matrix type does not match the type to be read.");
-		}
-
-		/*
-		 * Get dataspace of the dataset.
-		 */
-		DataSpace dataspace = dataset.getSpace();
-
-		/*
-		 * Get the dimension size of each dimension in the dataspace and
-		 * display them.
-		 */
-		hsize_t dims_out[2];
-		dataspace.getSimpleExtentDims( dims_out, NULL);
-		
-		flann_dataset.rows = dims_out[0];
-		flann_dataset.cols = dims_out[1];
-		flann_dataset.data = new T[flann_dataset.rows*flann_dataset.cols];
-
-		dataset.read( flann_dataset.data, get_hdf5_type<T>() );
-	}  // end of try block
-	catch( H5::Exception &error )
-	{
-		error.printError();
-		throw FLANNException(error.getDetailMsg());
-	}
-}
+    MPI_Comm comm  = MPI_COMM_WORLD;
+    MPI_Info info  = MPI_INFO_NULL;
+
+    int mpi_size, mpi_rank;
+    MPI_Comm_size(comm, &mpi_size);
+    MPI_Comm_rank(comm, &mpi_rank);
+
+    herr_t status;
+
+    hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+    H5Pset_fapl_mpio(plist_id, comm, info);
+    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
+    CHECK_ERROR(file_id,"Error opening hdf5 file.");
+    H5Pclose(plist_id);
+    hid_t dataset_id;
+#if H5Dopen_vers == 2
+    dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
+#else
+    dataset_id = H5Dopen(file_id, name.c_str());
+#endif
+    CHECK_ERROR(dataset_id,"Error opening dataset in file.");
+
+    hid_t space_id = H5Dget_space(dataset_id);
+    hsize_t dims[2];
+    H5Sget_simple_extent_dims(space_id, dims, NULL);
 
+    hsize_t count[2];
+    hsize_t offset[2];
 
-} // namespace cvflann
+    hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
+    hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));
+
+    count[0] = cnt;
+    count[1] = dims[1];
+    offset[0] = mpi_rank*item_cnt;
+    offset[1] = 0;
+
+    hid_t memspace_id = H5Screate_simple(2,count,NULL);
+
+    H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
+
+    dataset.rows = count[0];
+    dataset.cols = count[1];
+    dataset.data = new T[dataset.rows*dataset.cols];
+
+    plist_id = H5Pcreate(H5P_DATASET_XFER);
+    H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+    status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset.data);
+    CHECK_ERROR(status, "Error reading dataset");
+
+    H5Pclose(plist_id);
+    H5Sclose(space_id);
+    H5Sclose(memspace_id);
+    H5Dclose(dataset_id);
+    H5Fclose(file_id);
+}
+}
+#endif // HAVE_MPI
+} // namespace cvflann::mpi
 
-#endif /* _OPENCV_HDF5_H_ */
+#endif /* OPENCV_FLANN_HDF5_H_ */

modules/flann/include/opencv2/flann/linear_index.h

@@ -28,41 +28,40 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_LINEARSEARCH_H_
-#define _OPENCV_LINEARSEARCH_H_
-
-#include "opencv2/flann/general.h"
-#include "opencv2/flann/nn_index.h"
+#ifndef OPENCV_FLANN_LINEAR_INDEX_H_
+#define OPENCV_FLANN_LINEAR_INDEX_H_
 
+#include "general.h"
+#include "nn_index.h"
 
 namespace cvflann
 {
 
-struct CV_EXPORTS LinearIndexParams : public IndexParams {
-	LinearIndexParams() : IndexParams(FLANN_INDEX_LINEAR) {};
-
-	void print() const
-	{
-		logger().info("Index type: %d\n",(int)algorithm);
-	}
+struct LinearIndexParams : public IndexParams
+{
+    LinearIndexParams()
+    {
+        (* this)["algorithm"] = FLANN_INDEX_LINEAR;
+    }
 };
 
-
-template <typename ELEM_TYPE, typename DIST_TYPE = typename DistType<ELEM_TYPE>::type >
-class LinearIndex : public NNIndex<ELEM_TYPE>
+template <typename Distance>
+class LinearIndex : public NNIndex<Distance>
 {
-	const Matrix<ELEM_TYPE> dataset;
-	const LinearIndexParams& index_params;
+public:
 
-	LinearIndex(const LinearIndex&);
-	LinearIndex& operator=(const LinearIndex&);
+    typedef typename Distance::ElementType ElementType;
+    typedef typename Distance::ResultType DistanceType;
 
-public:
 
-	LinearIndex(const Matrix<ELEM_TYPE>& inputData, const LinearIndexParams& params = LinearIndexParams() ) :
-		dataset(inputData), index_params(params)
-	{
-	}
+    LinearIndex(const Matrix<ElementType>& inputData, const IndexParams& params = LinearIndexParams(),
+                Distance d = Distance()) :
+        dataset_(inputData), index_params_(params), distance_(d)
+    {
+    }
+
+    LinearIndex(const LinearIndex&);
+    LinearIndex& operator=(const LinearIndex&);
 
     flann_algorithm_t getType() const
     {
@@ -70,52 +69,64 @@ public:
     }
 
 
-	size_t size() const
-	{
-		return dataset.rows;
-	}
+    size_t size() const
+    {
+        return dataset_.rows;
+    }
 
-	size_t veclen() const
-	{
-		return dataset.cols;
-	}
+    size_t veclen() const
+    {
+        return dataset_.cols;
+    }
 
 
-	int usedMemory() const
-	{
-		return 0;
-	}
+    int usedMemory() const
+    {
+        return 0;
+    }
 
-	void buildIndex()
-	{
-		/* nothing to do here for linear search */
-	}
+    void buildIndex()
+    {
+        /* nothing to do here for linear search */
+    }
 
     void saveIndex(FILE*)
     {
-		/* nothing to do here for linear search */
+        /* nothing to do here for linear search */
     }
 
 
     void loadIndex(FILE*)
     {
-		/* nothing to do here for linear search */
+        /* nothing to do here for linear search */
+
+        index_params_["algorithm"] = getType();
+    }
+
+    void findNeighbors(ResultSet<DistanceType>& resultSet, const ElementType* vec, const SearchParams& /*searchParams*/)
+    {
+        ElementType* data = dataset_.data;
+        for (size_t i = 0; i < dataset_.rows; ++i, data += dataset_.cols) {
+            DistanceType dist = distance_(data, vec, dataset_.cols);
+            resultSet.addPoint(dist, i);
+        }
     }
 
-	void findNeighbors(ResultSet<ELEM_TYPE>& resultSet, const ELEM_TYPE*, const SearchParams&)
-	{
-		for (size_t i=0;i<dataset.rows;++i) {
-			resultSet.addPoint(dataset[i],(int)i);
-		}
-	}
+    IndexParams getParameters() const
+    {
+        return index_params_;
+    }
 
-	const IndexParams* getParameters() const
-	{
-		return &index_params;
-	}
+private:
+    /** The dataset */
+    const Matrix<ElementType> dataset_;
+    /** Index parameters */
+    IndexParams index_params_;
+    /** Index distance */
+    Distance distance_;
 
 };
 
-} // namespace cvflann
+}
 
-#endif // _OPENCV_LINEARSEARCH_H_
+#endif // OPENCV_FLANN_LINEAR_INDEX_H_

modules/flann/include/opencv2/flann/matrix.h

@@ -28,60 +28,58 @@
  * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *************************************************************************/
 
-#ifndef _OPENCV_DATASET_H_
-#define _OPENCV_DATASET_H_
+#ifndef OPENCV_FLANN_DATASET_H_
+#define OPENCV_FLANN_DATASET_H_
 
 #include <stdio.h>
 
-#include "opencv2/flann/general.h"
+#include "general.h"
 
-
-namespace cvflann 
+namespace cvflann
 {
 
 /**
-* Class that implements a simple rectangular matrix stored in a memory buffer and
-* provides convenient matrix-like access using the [] operators.
-*/
+ * Class that implements a simple rectangular matrix stored in a memory buffer and
+ * provides convenient matrix-like access using the [] operators.
+ */
 template <typename T>
-class Matrix {
+class Matrix
+{
 public:
+    typedef T type;
+
     size_t rows;
     size_t cols;
+    size_t stride;
     T* data;
 
-    Matrix() : rows(0), cols(0), data(NULL)
+    Matrix() : rows(0), cols(0), stride(0), data(NULL)
     {
     }
 
-    Matrix(T* data_, long rows_, long cols_) :
-    	 rows(rows_), cols(cols_), data(data_)
-	{
-	}
+    Matrix(T* data_, size_t rows_, size_t cols_, size_t stride_ = 0) :
+        rows(rows_), cols(cols_),  stride(stride_), data(data_)
+    {
+        if (stride==0) stride = cols;
+    }
 
     /**
      * Convenience function for deallocating the storage data.
      */
-    void release()
+    FLANN_DEPRECATED void free()
     {
-        if (data!=NULL) delete[] data;
+        fprintf(stderr, "The cvflann::Matrix<T>::free() method is deprecated "
+                "and it does not do any memory deallocation any more.  You are"
+                "responsible for deallocating the matrix memory (by doing"
+                "'delete[] matrix.data' for example)");
     }
 
-	~Matrix()
-	{
-	}
-
     /**
-    * Operator that return a (pointer to a) row of the data.
-    */
-    T* operator[](size_t index)
-    {
-        return data+index*cols;
-    }
-
+     * Operator that return a (pointer to a) row of the data.
+     */
     T* operator[](size_t index) const
     {
-        return data+index*cols;
+        return data+index*stride;
     }
 };
 
@@ -95,7 +93,7 @@ public:
     flann_datatype_t type;
 
     UntypedMatrix(void* data_, long rows_, long cols_) :
-    	 rows(rows_), cols(cols_), data(data_)
+        rows(rows_), cols(cols_), data(data_)
     {
     }
 
@@ -113,6 +111,6 @@ public:
 
 
 
-} // namespace cvflann
+}
 
-#endif //_OPENCV_DATASET_H_
+#endif //OPENCV_FLANN_DATASET_H_

modules/flann/src/precomp.hpp

@@ -7,6 +7,7 @@
 
 #include "opencv2/flann/dist.h"
 #include "opencv2/flann/index_testing.h"
+#include "opencv2/flann/params.h"
 #include "opencv2/flann/saving.h"
 #include "opencv2/flann/general.h"