code used in my phd

.gitignore

@@ -0,0 +1 @@
+.svn*

CMakeLists.txt

@@ -0,0 +1,49 @@
+cmake_minimum_required (VERSION 2.6) 
+project (clustering)
+
+IF(CMAKE_SIZEOF_VOID_P EQUAL 4)
+    SET(LIB_SUFFIX "")
+ELSE(CMAKE_SIZEOF_VOID_P EQUAL 4)
+    SET(LIB_SUFFIX 64)
+ENDIF(CMAKE_SIZEOF_VOID_P EQUAL 4)
+
+SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+
+find_package(Eigen2 REQUIRED)
+include_directories(${Eigen2_INCLUDE_DIR})
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+      "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+      FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+
+if(CMAKE_BUILD_TYPE MATCHES "Debug")
+	set(LIB_NAME clusteringd)
+else(CMAKE_BUILD_TYPE MATCHES "Debug")
+	set(LIB_NAME clustering)
+endif(CMAKE_BUILD_TYPE MATCHES "Debug")
+
+file(GLOB LIB_PUBLIC_HEADERS "${CMAKE_SOURCE_DIR}/*.h")
+file(GLOB LIB_SOURCES "${CMAKE_SOURCE_DIR}/*.cpp")
+
+#add_library (${LIB_NAME}-s STATIC ${LIB_PUBLIC_HEADERS} ${LIB_SOURCES})
+add_library (${LIB_NAME} SHARED ${LIB_PUBLIC_HEADERS} ${LIB_SOURCES})
+
+install(
+    TARGETS ${LIB_NAME}
+    LIBRARY DESTINATION lib${LIB_SUFFIX}
+)
+
+#install(
+#    TARGETS ${LIB_NAME}-s
+#    ARCHIVE DESTINATION lib${LIB_SUFFIX}
+#)
+
+install(
+    FILES ${LIB_PUBLIC_HEADERS}
+    DESTINATION include/${LIB_NAME}
+)

ClusterRotate.cpp

@@ -0,0 +1,77 @@
+/*
+ * ClusterRotate.cpp
+ *
+ *  Created on: 04-Mar-2009
+ *      Author: sbutler
+ */
+
+#include "ClusterRotate.h"
+
+#include <map>
+#include <Eigen/Array>
+
+ClusterRotate::ClusterRotate(int method):
+	mMethod(method),
+	mMaxQuality(0)
+{
+
+}
+
+std::vector<std::vector<int> > ClusterRotate::cluster(Eigen::MatrixXd& X) {
+	mMaxQuality = 0;
+	std::vector<std::vector<int> > clusters;
+	Eigen::MatrixXd vecRot;
+	Eigen::MatrixXd vecIn = X.block(0,0,X.rows(),2);
+	Evrot* e = NULL;
+	for (int g=2; g <= X.cols(); g++) {
+		// make it incremental (used already aligned vectors)
+		if( g > 2 ) {
+			vecIn.resize(X.rows(),g);
+			vecIn.block(0,0,vecIn.rows(),g-1) = e->getRotatedEigenVectors();
+			vecIn.block(0,g-1,X.rows(),1) = X.block(0,g-1,X.rows(),1);
+			delete e;
+		}
+		//perform the rotation for the current number of dimensions
+		e = new Evrot(vecIn, mMethod);
+
+		//save max quality
+		if (e->getQuality() > mMaxQuality) {
+			mMaxQuality = e->getQuality();
+		}
+		//save cluster data for max cluster or if we're near the max cluster (so prefer more clusters)
+		if ((e->getQuality() > mMaxQuality) || (mMaxQuality - e->getQuality() <= 0.001)) {
+			clusters = e->getClusters();
+			vecRot = e->getRotatedEigenVectors();
+		}
+	}
+
+	Eigen::MatrixXd clusterCentres = Eigen::MatrixXd::Zero(clusters.size(),vecRot.cols());
+	for (unsigned int i=0; i < clusters.size(); i++) {
+		for (unsigned int j=0; j < clusters[i].size(); j++) {
+			//sum points within cluster
+			clusterCentres.row(i) += vecRot.row(clusters[i][j]);
+		}
+	}
+	for (unsigned int i=0; i < clusters.size(); i++) {
+		//find average point within cluster
+		clusterCentres.row(i) = clusterCentres.row(i) / clusters[i].size();
+	}
+
+	//order clustered points by (ascending) distance to cluster centre
+	for (unsigned int i=0; i < clusters.size(); i++) {
+		std::multimap<double,int> clusterDistance;
+		for (unsigned int j=0; j < clusters[i].size(); j++) {
+			double d2 = (vecRot.row(clusters[i][j]) - clusterCentres.row(i)).squaredNorm();
+			clusterDistance.insert(std::make_pair(d2, clusters[i][j]));
+		}
+		//the map will be sorted based on the key so just loop through it
+		//to get set of data indices sorted on the distance to cluster
+		clusters[i].clear();
+		for (std::multimap<double,int>::iterator it = clusterDistance.begin(); it != clusterDistance.end(); it++) {
+			clusters[i].push_back(it->second);
+		}
+	}
+
+	return clusters;
+}
+

ClusterRotate.h

@@ -0,0 +1,32 @@
+/*
+ * ClusterRotate.h
+ *
+ *  Created on: 04-Mar-2009
+ *      Author: sbutler
+ */
+
+#ifndef CLUSTERROTATE_H_
+#define CLUSTERROTATE_H_
+
+#include <Eigen/Core>
+#include <vector>
+
+#include "Evrot.h"
+
+class ClusterRotate {
+
+public:
+	ClusterRotate(int method = 1);
+	virtual ~ClusterRotate() { }
+
+	std::vector<std::vector<int> > cluster(Eigen::MatrixXd& X);
+	double getMaxQuality() { return mMaxQuality; };
+
+protected:
+
+	int mMethod;
+	double mMaxQuality;
+
+};
+
+#endif /* CLUSTERROTATE_H_ */