added a vector-based DSF implmentation

.cproject

@@ -317,6 +317,7 @@
 </target>
 <target name="clean" path="wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>clean</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -476,7 +477,6 @@
 </target>
 <target name="testBayesTree.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testBayesTree.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -484,6 +484,7 @@
 </target>
 <target name="testSymbolicBayesNet.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testSymbolicBayesNet.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -491,7 +492,6 @@
 </target>
 <target name="testSymbolicFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testSymbolicFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -683,7 +683,6 @@
 </target>
 <target name="testGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -739,6 +738,7 @@
 </target>
 <target name="testSimulated2D.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testSimulated2D.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -786,7 +786,6 @@
 </target>
 <target name="testErrors.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testErrors.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -794,7 +793,6 @@
 </target>
 <target name="testDSF.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testDSF.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -810,7 +808,6 @@
 </target>
 <target name="testConstraintOptimizer.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testConstraintOptimizer.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -818,6 +815,7 @@
 </target>
 <target name="testBTree.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testBTree.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -825,12 +823,19 @@
 </target>
 <target name="testSimulated2DOriented.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testSimulated2DOriented.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
 <runAllBuilders>true</runAllBuilders>
 </target>
+<target name="testDSFVector.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+<buildCommand>make</buildCommand>
+<buildArguments/>
+<buildTarget>testDSFVector.run</buildTarget>
+<stopOnError>true</stopOnError>
+<useDefaultCommand>true</useDefaultCommand>
+<runAllBuilders>true</runAllBuilders>
+</target>
 <target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
 <buildArguments>-j2</buildArguments>

cpp/DSF.h

@@ -110,7 +110,7 @@ namespace gtsam {
 		}
 
 		// get the nodes in the tree with the given label
-		Set set(const Label& label) {
+		Set set(const Label& label) const {
 			Set set;
 			BOOST_FOREACH(const KeyLabel& pair, (Tree)*this) {
 				if (pair.second == label || findSet(pair.second) == label)

cpp/DSFVector.cpp

@@ -0,0 +1,58 @@
+/*
+ * DSFVector.cpp
+ *
+ *   Created on: Jun 25, 2010
+ *       Author: nikai
+ *  Description: a faster implementation for DSF, which uses vector rather than btree.
+ *               As a result, the size of the forest is prefixed.
+ */
+
+#include "DSFVector.h"
+
+using namespace std;
+
+namespace gtsam {
+
+	/* ************************************************************************* */
+	DSFVector::DSFVector (const size_t numNodes) {
+		resize(numNodes);
+		int index = 0;
+		for(iterator it = begin(); it!=end(); it++, index++)
+			*it = index;
+	}
+
+	/* ************************************************************************* */
+	size_t DSFVector::findSet(const size_t& key) const {
+		size_t parent = at(key);
+		return parent == key ? key : findSet(parent);
+	}
+
+	/* ************************************************************************* */
+	std::set<size_t> DSFVector::set(const std::size_t& label) const {
+		std::set<size_t> set;
+		size_t key = 0;
+		std::vector<std::size_t>::const_iterator it = begin();
+		for (; it != end(); it++, key++) {
+			if (*it == label || findSet(*it) == label)
+				set.insert(key);
+		}
+		return set;
+	}
+
+	/* ************************************************************************* */
+	void DSFVector::makeUnionInPlace(const std::size_t& i1, const std::size_t& i2)  {
+		at(findSet(i2)) = findSet(i1);
+	}
+
+	/* ************************************************************************* */
+	std::map<size_t, std::set<size_t> > DSFVector::sets() const {
+		std::map<size_t, std::set<size_t> > sets;
+		size_t key = 0;
+		std::vector<std::size_t>::const_iterator it = begin();
+		for (; it != end(); it++, key++) {
+			sets[findSet(*it)].insert(key);
+		}
+		return sets;
+	}
+
+}

cpp/DSFVector.h

@@ -0,0 +1,41 @@
+/*
+ * DSFVector.h
+ *
+ *   Created on: Jun 25, 2010
+ *       Author: nikai
+ *  Description: a faster implementation for DSF, which uses vector rather than btree.
+ *               As a result, the size of the forest is prefixed.
+ */
+
+#pragma once
+
+#include <vector>
+#include <map>
+#include <set>
+
+namespace gtsam {
+
+	/**
+	 * A fast impelementation of disjoint set forests
+	 */
+	class DSFVector : protected std::vector<std::size_t> {
+	private:
+
+	public:
+		// constructor
+		DSFVector(const std::size_t numNodes);
+
+		// find the label of the set in which {key} lives
+		size_t findSet(const size_t& key) const;
+
+		// the in-place version of makeUnion
+		void makeUnionInPlace(const std::size_t& i1, const std::size_t& i2);
+
+		// get the nodes in the tree with the given label
+		std::set<size_t> set(const std::size_t& label) const;
+
+		// return all sets, i.e. a partition of all elements
+		std::map<size_t, std::set<size_t> > sets() const;
+	};
+
+}

cpp/Makefile.am

@@ -40,15 +40,17 @@ testMatrix_LDADD   = libgtsam.la
 # The header files will be installed in ~/include/gtsam
 headers = gtsam.h Value.h Testable.h Factor.h Conditional.h 
 headers += Ordering.h IndexTable.h numericalDerivative.h
-headers += BTree.h DSF.h
+headers += BTree.h DSF.h DSFVector.h
-sources += Ordering.cpp smallExample.cpp 
+sources += Ordering.cpp smallExample.cpp DSFVector.cpp
-check_PROGRAMS += testOrdering testBTree testDSF
+check_PROGRAMS += testOrdering testBTree testDSF testDSFVector
 testOrdering_SOURCES = testOrdering.cpp
 testOrdering_LDADD   = libgtsam.la
 testBTree_SOURCES    = testBTree.cpp
 testBTree_LDADD		   = libgtsam.la
 testDSF_SOURCES    = testDSF.cpp
 testDSF_LDADD      = libgtsam.la
+testDSFVector_SOURCES    = testDSFVector.cpp
+testDSFVector_LDADD      = libgtsam.la
 
 # Symbolic Inference
 headers += SymbolicConditional.h

cpp/SymbolicFactor.h

@@ -99,6 +99,10 @@ namespace gtsam {
 			return keys_.empty();
 		}
 
+		/** get the size of the factor */
+		std::size_t size() const {
+			return keys_.size();
+		}
 
 	};
 

cpp/testDSFVector.cpp

@@ -0,0 +1,109 @@
+/*
+ * testDSF.cpp
+ *
+ *   Created on: June 25, 2010
+ *       Author: nikai
+ *  Description: unit tests for DSF
+ */
+
+#include <iostream>
+#include <boost/assign/std/list.hpp>
+#include <boost/assign/std/set.hpp>
+using namespace boost::assign;
+#include <CppUnitLite/TestHarness.h>
+
+#include "DSFVector.h"
+#include "Key.h"
+
+using namespace std;
+using namespace gtsam;
+
+/* ************************************************************************* */
+TEST(DSFVectorVector, findSet) {
+	DSFVector dsf(3);
+	CHECK(dsf.findSet(0) != dsf.findSet(2));
+}
+
+/* ************************************************************************* */
+TEST(DSFVectorVector, makeUnionInPlace) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,2);
+	CHECK(dsf.findSet(0) == dsf.findSet(2));
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, makeUnion2) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(2,0);
+	CHECK(dsf.findSet(0) == dsf.findSet(2));
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, makeUnion3) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,1);
+	dsf.makeUnionInPlace(1,2);
+	CHECK(dsf.findSet(0) == dsf.findSet(2));
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, sets) {
+	DSFVector dsf(2);
+	dsf.makeUnionInPlace(0,1);
+	map<size_t, set<size_t> > sets = dsf.sets();
+	LONGS_EQUAL(1, sets.size());
+
+	set<size_t> expected; expected += 0, 1;
+	CHECK(expected == sets[dsf.findSet(0)]);
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, sets2) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,1);
+	dsf.makeUnionInPlace(1,2);
+	map<size_t, set<size_t> > sets = dsf.sets();
+	LONGS_EQUAL(1, sets.size());
+
+	set<size_t> expected; expected += 0, 1, 2;
+	CHECK(expected == sets[dsf.findSet(0)]);
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, sets3) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,1);
+	map<size_t, set<size_t> > sets = dsf.sets();
+	LONGS_EQUAL(2, sets.size());
+
+	set<size_t> expected; expected += 0, 1;
+	CHECK(expected == sets[dsf.findSet(0)]);
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, set) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,1);
+	set<size_t> set = dsf.set(0);
+	LONGS_EQUAL(2, set.size());
+
+	std::set<size_t> expected; expected += 0, 1;
+	CHECK(expected == set);
+}
+
+/* ************************************************************************* */
+TEST(DSFVector, set2) {
+	DSFVector dsf(3);
+	dsf.makeUnionInPlace(0,1);
+	dsf.makeUnionInPlace(1,2);
+	set<size_t> set = dsf.set(0);
+	LONGS_EQUAL(3, set.size());
+
+	std::set<size_t> expected; expected += 0, 1, 2;
+	CHECK(expected == set);
+}
+
+/* ************************************************************************* */
+int main() { TestResult tr; return TestRegistry::runAllTests(tr);}
+/* ************************************************************************* */
+