Replaced the old Numerical Python by the new NumPy.

Switched from C++ to plain C.
Added checks for malloc's to see if the memory allocation was successful.
From the user viewpoint, all changes should be transparent.

Bio/KDTree/KDTree.h

@@ -1,125 +1,15 @@
-#include <vector>
-#include <algorithm>
-#include <math.h>
-#include <stdlib.h>
-using namespace std;
-
-#define INF 1000000
-#undef NDEBUG
-
-
-float KDTREE_dist(float *coord1, float *coord2, int dim);
-
-class DataPoint
-{
-	private:
-		long int _index;
-		float *_coord;
-	public:
-		static int dim;
-		// needed for vector & sort
-		// T(); T(const T&); ~T(); T& operator=(const T&);
-		friend int operator<(const DataPoint &self, const DataPoint &other);
-		friend int operator==(const DataPoint &self, const DataPoint &other);
-		// end needed for vector
-		static int current_dim;
-		void set_data(long int index, float *coord);
-		float* get_coord(void);
-		long int get_index(void);
-};
-
-class Node
-{
-	private:
-		Node *_left;
-		Node *_right;
-		float _cut_value;
-		int _cut_dim;
-		long int _start, _end;
-	public:
-		Node(float cut_value, int cut_dim, long int start, long int end);
-		~Node();
-		void set_right_node(Node *node);
-		void set_left_node(Node *node);
-		Node *get_right_node(void);
-		Node *get_left_node(void);
-		long int get_index(void);
-		float get_cut_value(void);
-		int get_cut_dim(void);
-		int is_leaf(void);
-		int is_bucket(void);
-		long int get_start(void);
-		long int get_end(void);
-};
-
-class Region
-{
-	private:
-		float *_left;
-		float *_right;
-	public:
-		static int dim;
-		Region(float *left=NULL, float *right=NULL);
-		~Region();
-		Region *intersect_right(float split_coord, int current_dim);
-		Region *intersect_left(float split_coord, int current_dim);
-		float *get_right(void);
-		float *get_left(void);
-		int encloses(float *coord);
-		int test_intersection(Region *query_region, float radius=0);
-		void print(void);
-};
-
-class KDTree
-{
-	private:
-		vector<DataPoint> _data_point_list;
-		vector<long int> _index_list;
-		vector<float> _radius_list;
-		vector<long int> _neighbor_index_list;
-		vector<float> _neighbor_radius_list;
-		Node *_root;
-		Region *_query_region;
-		long int _count;
-		long int _neighbor_count;
-		float _radius;
-		float _radius_sq;
-		float _neighbor_radius;
-		float _neighbor_radius_sq;
-		float *_center_coord;
-		float *_coords;
-		int _bucket_size;
-		// Methods
-		Node *_build_tree(long int offset_begin=0, long int offset_end=0, int depth=0);
-		void _report_subtree(Node *node);
-		void _report_point(long int index, float *coord);
-		void _test_region(Node *node, Region *region, int depth); 
-		void _set_query_region(float *left, float *right);
-		void _add_point(long int index, float *coord);
-		void _search(Region *region=NULL, Node *node=NULL, int depth=0);
-		void _neighbor_search_pairs(Node *left, Region *left_region, Node *right, Region *right_region, int depth);
-		void _neighbor_search(Node *root, Region *region, int depth);
-		void _search_neighbors_between_buckets(Node *node1, Node *node2);
-		void _search_neighbors_in_bucket(Node *node);
-		void _test_neighbors(DataPoint &p1, DataPoint &p2);
-	public:
-		int dim;
-		KDTree(int dim, int bucket_size);
-		~KDTree();
-		void set_data(float *coords, long int nr_points);
-		// single neighbor search 
-		void search_center_radius(float *coord, float radius);
-		long int get_count(void);
-		void copy_indices(long int *indices);
-		void copy_radii(float *radii);
-		// all neighbor search
-		long int neighbor_get_count(void);
-		void neighbor_search(float neighbor_radius);
-		void neighbor_simple_search(float neighbor_radius);
-		void neighbor_copy_indices(long int *indices);
-		void neighbor_copy_radii(float *radii);
-};
-
+#include "Neighbor.h"
 
+struct KDTree;
 
+struct KDTree* KDTree_init(int dim, int bucket_size);
+void KDTree_destroy(struct KDTree* tree);
+int KDTree_set_data(struct KDTree* tree, float *coords, long int nr_points);
+long int KDTree_get_count(struct KDTree* tree);
+long int KDTree_neighbor_get_count(struct KDTree* tree);
+int KDTree_search_center_radius(struct KDTree* tree, float *coord, float radius);
+void KDTree_copy_indices(struct KDTree* tree, long *indices);
+void KDTree_copy_radii(struct KDTree* tree, float *radii);
 
+struct Neighbor* KDTree_neighbor_search(struct KDTree* tree, float neighbor_radius);
+struct Neighbor* KDTree_neighbor_simple_search(struct KDTree* tree, float radius);