KD-Tree and Ball tree added in a unified interface

src/shogun/multiclass/tree/BallTree.cpp

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+/*
+ * Copyright (c) The Shogun Machine Learning Toolbox
+ * Written (w) 2014 Parijat Mazumdar
+ * 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 COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
+ *
+ * The views and conclusions contained in the software and documentation are those
+ * of the authors and should not be interpreted as representing official policies,
+ * either expressed or implied, of the Shogun Development Team.
+ */
+
+#include <shogun/multiclass/tree/BallTree.h>
+
+using namespace shogun;
+
+CBallTree::CBallTree(int32_t leaf_size, EDistanceMetric d)
+: CNbodyTree(leaf_size,d)
+{
+}
+
+float64_t CBallTree::min_distsq(bnode_t* node,float64_t* feat, int32_t dim)
+{
+	float64_t dist=0;
+	SGVector<float64_t> center=node->data.center;
+	for (int32_t i=0;i<dim;i++)
+		dist+=add_dim_dist(center[i]-feat[i]);
+
+	return CMath::max(0.0,dist-node->data.radius);
+}
+
+void CBallTree::init_node(bnode_t* node, index_t start, index_t end)
+{
+	SGVector<float64_t> upper_bounds(m_data.num_rows);
+	SGVector<float64_t> lower_bounds(m_data.num_rows);
+
+	SGVector<float64_t> center(m_data.num_rows);
+	for (int32_t i=0;i<m_data.num_rows;i++)
+	{
+		center[i]=m_data(i,vec_id[start]);
+		upper_bounds[i]=m_data(i,vec_id[start]);
+		lower_bounds[i]=m_data(i,vec_id[start]);
+		for (int32_t j=start+1;j<=end;j++)
+		{
+			float64_t data_pt=m_data(i,vec_id[j]);
+			upper_bounds[i]=CMath::max(upper_bounds[i],data_pt);
+			lower_bounds[i]=CMath::min(lower_bounds[i],data_pt);
+			center[i]+=data_pt;
+		}
+
+		center[i]/=(end-start+1.f);
+	}
+
+	float64_t radius=0;
+	for (int32_t i=start;i<=end;i++)
+		radius=CMath::max(distance(vec_id[i],center.vector,center.vlen),radius);
+
+	actual_dists(&radius,1);
+
+	node->data.radius=radius;
+	node->data.center=center;
+	node->data.start_idx=start;
+	node->data.bbox_upper=upper_bounds;
+	node->data.bbox_lower=lower_bounds;	
+	node->data.end_idx=end;
+}

src/shogun/multiclass/tree/BallTree.h

@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) The Shogun Machine Learning Toolbox
+ * Written (w) 2014 Parijat Mazumdar
+ * 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 COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
+ *
+ * The views and conclusions contained in the software and documentation are those
+ * of the authors and should not be interpreted as representing official policies,
+ * either expressed or implied, of the Shogun Development Team.
+ */
+
+
+#ifndef _BALLTREE_H__
+#define _BALLTREE_H__
+
+#include <shogun/lib/config.h>
+
+#include <shogun/multiclass/tree/NbodyTree.h>
+
+namespace shogun
+{
+
+/** @brief This class implements Ball tree.
+ */
+class CBallTree : public CNbodyTree
+{
+public:
+	/** constructor
+	 * 
+	 * @param data data points using which Ball-Tree will be made	 
+	 * @param leaf_size min number of samples in any node
+	 */
+	CBallTree(int32_t leaf_size=1, EDistanceMetric d=DM_EUCLID);
+
+	/** Destructor */
+	~CBallTree() { };
+
+	/** get name
+	 * @return class of the tree 
+	 */
+	virtual const char* get_name() const { return "BallTree"; }
+
+private:
+	/** find squared minimum distance between node and a query vector
+	 * 
+	 * @param node present node
+	 * @param feat query vector
+	 * @param dim dimensions of query vector
+	 * @return squared min distance
+	 */
+	float64_t min_distsq(bnode_t* node,float64_t* feat, int32_t dim);
+
+	/** initialize node
+	 *
+	 * @param node node to be initialized
+	 * @param start start index of index vector
+	 * @param end end index of index vector
+	 */
+	void init_node(bnode_t* node, index_t start, index_t end);
+
+};
+} /* namespace shogun */
+
+#endif /* _BALLTREE_H__ */

src/shogun/multiclass/tree/KDTree.cpp

@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) The Shogun Machine Learning Toolbox
+ * Written (w) 2014 Parijat Mazumdar
+ * 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 COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
+ *
+ * The views and conclusions contained in the software and documentation are those
+ * of the authors and should not be interpreted as representing official policies,
+ * either expressed or implied, of the Shogun Development Team.
+ */
+
+#include <shogun/multiclass/tree/KDTree.h>
+
+using namespace shogun;
+
+CKDTree::CKDTree(int32_t leaf_size, EDistanceMetric d)
+: CNbodyTree(leaf_size,d)
+{
+}
+
+CKDTree::~CKDTree()
+{
+}
+
+float64_t CKDTree::min_distsq(bnode_t* node,float64_t* feat, int32_t dim)
+{
+	float64_t dist=0;
+	for (int32_t i=0;i<dim;i++)
+	{
+		float64_t dim_dist=(node->data.bbox_lower[i]-feat[i])+CMath::abs(feat[i]-node->data.bbox_lower[i]);
+		dim_dist+=(feat[i]-node->data.bbox_upper[i])+CMath::abs(feat[i]-node->data.bbox_upper[i]);		
+		dist+=add_dim_dist(0.5*dim_dist);
+	}
+
+	return dist;
+}
+
+void CKDTree::init_node(bnode_t* node, index_t start, index_t end)
+{
+	SGVector<float64_t> upper_bounds(m_data.num_rows);
+	SGVector<float64_t> lower_bounds(m_data.num_rows);
+
+	for (int32_t i=0;i<m_data.num_rows;i++)
+	{
+		upper_bounds[i]=m_data(i,vec_id[start]);
+		lower_bounds[i]=m_data(i,vec_id[start]);
+		for (int32_t j=start+1;j<=end;j++)
+		{
+			upper_bounds[i]=CMath::max(upper_bounds[i],m_data(i,vec_id[j]));
+			lower_bounds[i]=CMath::min(lower_bounds[i],m_data(i,vec_id[j]));
+		}
+	}
+
+	float64_t radius=0;
+	for (int32_t i=0;i<m_data.num_rows;i++)
+		radius=CMath::max(radius,upper_bounds[i]-lower_bounds[i]);
+
+	node->data.bbox_upper=upper_bounds;
+	node->data.bbox_lower=lower_bounds;
+	node->data.radius=0.5*radius;
+	node->data.start_idx=start;
+	node->data.end_idx=end;
+}

src/shogun/multiclass/tree/KDTree.h

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+/*
+ * Copyright (c) The Shogun Machine Learning Toolbox
+ * Written (w) 2014 Parijat Mazumdar
+ * 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 COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
+ *
+ * The views and conclusions contained in the software and documentation are those
+ * of the authors and should not be interpreted as representing official policies,
+ * either expressed or implied, of the Shogun Development Team.
+ */
+
+
+#ifndef _KDTREE_H__
+#define _KDTREE_H__
+
+#include <shogun/lib/config.h>
+
+#include <shogun/multiclass/tree/NbodyTree.h>
+
+namespace shogun
+{
+
+/** @brief This class implements KD-Tree.
+ */
+class CKDTree : public CNbodyTree
+{
+public:
+	/** constructor
+	 * 
+	 * @param data data points using which KD-Tree will be made	 
+	 * @param leaf_size min number of samples in any node
+	 */
+	CKDTree(int32_t leaf_size=1, EDistanceMetric d=DM_EUCLID);
+
+	/** Destructor */
+	~CKDTree();
+
+	/** get name
+	 * @return class of the tree 
+	 */
+	virtual const char* get_name() const { return "KDTree"; }
+
+private:
+	/** find squared minimum distance between node and a query vector
+	 * 
+	 * @param node present node
+	 * @param feat query vector
+	 * @param dim dimensions of query vector
+	 * @return squared min distance
+	 */
+	float64_t min_distsq(bnode_t* node,float64_t* feat, int32_t dim);
+
+	/** initialize node
+	 *
+	 * @param node node to be initialized
+	 * @param start start index of index vector
+	 * @param end end index of index vector
+	 */
+	void init_node(bnode_t* node, index_t start, index_t end);
+
+};
+} /* namespace shogun */
+
+#endif /* _KDREE_H__ */