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[DL-Learner SVN] SF.net SVN: dl-learner:[1573] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2009-01-11 07:56:48
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Revision: 1573
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1573&view=rev
Author: jenslehmann
Date: 2009-01-11 07:56:41 +0000 (Sun, 11 Jan 2009)
Log Message:
-----------
EL monitoring
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/utilities/Files.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2009-01-09 15:55:33 UTC (rev 1572)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2009-01-11 07:56:41 UTC (rev 1573)
@@ -465,7 +465,7 @@
@Override
@SuppressWarnings("unchecked")
public ELDescriptionTree clone() {
- Monitor mon = MonitorFactory.start("EL tree clone");
+ Monitor mon = MonitorFactory.start("tree clone");
// clone "global" tree
ELDescriptionTree treeClone = new ELDescriptionTree(rs);
@@ -598,4 +598,16 @@
public int getDepth() {
return maxLevel;
}
+
+ /**
+ * size of tree = number of nodes + sum of cardinality of node labels
+ * @return The tree size.
+ */
+ public int getSize() {
+ int size = nodes.size();
+ for(ELDescriptionNode node : nodes) {
+ size += node.getLabel().size();
+ }
+ return size;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-01-09 15:55:33 UTC (rev 1572)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-01-11 07:56:41 UTC (rev 1573)
@@ -145,7 +145,7 @@
// the position of the node within the tree (needed for getting
// the corresponding node in a cloned tree)
int[] position = v.getCurrentPosition();
- logger.trace(" at position " + Helper.arrayContent(position));
+// logger.trace(" at position " + Helper.arrayContent(position));
// perform operations
refinements.addAll(extendLabel(tree, v, position));
@@ -311,7 +311,9 @@
// System.out.println(mergedTree.toSimulationString());
// we check equivalence by a minimality test (TODO: can we still do this?)
- if(mergedTree.isMinimal()) {
+ boolean minimal = mergedTree.isMinimal();
+ MonitorFactory.add("as.minimal", "boolean", minimal ? 1 : 0);
+ if(minimal) {
logger.trace("Merged tree is minimal, i.e. not equivalent.");
// it is not equivalent, i.e. we found a refinement
refinements.add(mergedTree);
@@ -320,6 +322,7 @@
// perform complex check in merged tree
boolean check = asCheck(wClone);
logger.trace("Result of complex check: " + check);
+ MonitorFactory.add("as.check", "boolean", check ? 1 : 0);
if(check) {
// refine property
Modified: trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-09 15:55:33 UTC (rev 1572)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-11 07:56:41 UTC (rev 1573)
@@ -20,9 +20,16 @@
package org.dllearner.scripts.evaluation;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.net.MalformedURLException;
+import java.text.DecimalFormat;
+import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
import java.util.Random;
import java.util.Set;
@@ -39,8 +46,12 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.refinementoperators.ELDown2;
+import org.dllearner.utilities.Files;
import org.dllearner.utilities.statistics.Stat;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
/**
* An evaluation of the EL refinement operator {@link ELDown2}. It creates
* a set of artificial ontologies with varying complexity and performs
@@ -52,6 +63,7 @@
public class ELOperatorBenchmark {
private static Random rand = new Random(1);
+ private static DecimalFormat df = new DecimalFormat();
public static void main(String[] args) throws ComponentInitException, IOException {
@@ -62,8 +74,14 @@
// logger.removeAllAppenders();
// logger.addAppender(app);
- String example = "/home/jl/ontologien/galen2.owl";
- testOntology(example);
+ // create a directory for log files
+ Date dt = new Date();
+ SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd_HH:mm:ss");
+ String dir = "log/el/" + df.format(dt) + "/";
+ new File(dir).mkdir();
+
+ String example = "/home/jl/promotion/ontologien/galen2.owl";
+ testOntology(dir, example, 100, 15);
System.exit(0);
/* TEST ON ARTIFICIAL ONTOLOGIES
@@ -119,30 +137,36 @@
// ELDown2 operator = new ELDown2();
}
- private static void testOntology(String ont) throws MalformedURLException, ComponentInitException {
+ private static void testOntology(String statDir, String ont, int nrOfChains, int chainLength) throws ComponentInitException, IOException {
System.out.print("Reading in " + ont + " ... ");
ComponentManager cm = ComponentManager.getInstance();
// reading ontology into a reasoner
KnowledgeSource source = cm.knowledgeSource(OWLFile.class);
- cm.applyConfigEntry(source, "url", new File(ont).toURI().toURL());
+ File ontFile = new File(ont);
+ cm.applyConfigEntry(source, "url", ontFile.toURI().toURL());
source.init();
ReasonerComponent reasoner = cm.reasoner(OWLAPIReasoner.class, source);
reasoner.init();
System.out.println("done.");
System.out.println();
- int outerLoops = 1000;
- for(int loop = 0; loop < outerLoops; loop++) {
+ // log file name
+ String name = ontFile.getName();
+ String statFileName = name.substring(0, name.lastIndexOf(".")) + ".txt";
+ File statFile = new File(statDir + statFileName);
+ String statString = "";
+ MonitorFactory.reset();
+ for(int loop = 0; loop < nrOfChains; loop++) {
+
// application of operator and statistics recording
- int nrOfApplications = 15;
ELDescriptionTree currTree = new ELDescriptionTree(reasoner, Thing.instance);
ELDown2 operator = new ELDown2(reasoner);
Stat runtime = new Stat();
Stat runtimePerRefinement = new Stat();
- System.out.println("Testing operator (applying it " + nrOfApplications + " times):");
- for(int i=0; i < nrOfApplications; i++) {
+ System.out.println("Testing operator (applying it " + chainLength + " times):");
+ for(int i=0; i < chainLength; i++) {
// System.out.println(currTree.transformToDescription().toKBSyntaxString());
System.out.print("current concept: " + currTree.transformToDescription().toString(reasoner.getBaseURI(), reasoner.getPrefixes()));
// apply operator on current description
@@ -151,16 +175,66 @@
long time = System.nanoTime() - start;
runtime.addNumber(time/1000000d);
runtimePerRefinement.addNumber(time/1000000d/refinements.size());
+ MonitorFactory.add("operator application time", "ms.", time/1000000d);
+ MonitorFactory.add("operator application time per refinement", "ms.", time/1000000d/refinements.size());
+ MonitorFactory.add("refinement count", "count", refinements.size());
+
+ int sizeSum = 0;
+ for(ELDescriptionTree tree : refinements) {
+ sizeSum += tree.getSize();
+ }
+
+ MonitorFactory.add("refinement size", "count", sizeSum/(double)refinements.size());
+ MonitorFactory.add("refinement size increase", "count", (sizeSum-refinements.size()*currTree.getSize())/(double)refinements.size());
+
System.out.println(" [has " + refinements.size() + " refinements]");
// pick a refinement randomly (which is kind of slow for a set, but
// this does not matter here)
int index = rand.nextInt(refinements.size());
currTree = new ArrayList<ELDescriptionTree>(refinements).get(index);
+ MonitorFactory.add("picked refinement size", "count", currTree.getSize());
}
System.out.println("operator time: " + runtime.prettyPrint("ms"));
System.out.println("operator time per refinement: " + runtimePerRefinement.prettyPrint("ms"));
System.out.println();
}
+
+ statString += "file: " + name + "\n";
+ statString += "nr of refinement chains: " + nrOfChains + "\n";
+ statString += "refinement chain length: " + chainLength + "\n\n";
+
+ statString += getMonitorData(MonitorFactory.getMonitor("operator application time", "ms."));
+ statString += getMonitorData(MonitorFactory.getMonitor("operator application time per refinement", "ms."));
+ statString += "\n";
+
+ statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement count", "count"));
+ statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement size", "count"));
+ statString += getMonitorDataCount(MonitorFactory.getMonitor("picked refinement size", "count"));
+ statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement size increase", "count"));
+ statString += "\n";
+
+ statString += getMonitorData(MonitorFactory.getMonitor("extend label", "ms."));
+ statString += getMonitorData(MonitorFactory.getMonitor("refine label", "ms."));
+ statString += getMonitorData(MonitorFactory.getMonitor("refine edge", "ms."));
+ statString += getMonitorData(MonitorFactory.getMonitor("attach tree", "ms."));
+ statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.minimal", "boolean"));
+ statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.check", "boolean"));
+ statString += getMonitorData(MonitorFactory.getMonitor("tree clone", "ms."));
+ statString += getMonitorData(MonitorFactory.getMonitor("simulation update", "ms."));
+
+ Files.createFile(statFile, statString);
}
+
+ private static String getMonitorData(Monitor mon) {
+ return mon.getLabel() + ": av " + df.format(mon.getAvg()) + "ms (stddev " + df.format(mon.getStdDev()) + "ms, min " + df.format(mon.getMin()) + "ms, max " + df.format(mon.getMax()) + "ms, " + df.format(mon.getTotal()/1000) + "s total, " + (int)mon.getHits() + " hits)\n";
+ }
+
+ private static String getMonitorDataCount(Monitor mon) {
+ return mon.getLabel() + ": av " + df.format(mon.getAvg()) + " (stddev " + df.format(mon.getStdDev()) + ", min " + df.format(mon.getMin()) + ", max " + df.format(mon.getMax()) + ", " + df.format(mon.getTotal()) + " total, " + (int)mon.getHits() + " hits)\n";
+ }
+
+ private static String getMonitorDataBoolean(Monitor mon) {
+ return mon.getLabel() + ": " + df.format(mon.getAvg()*100) + "%\n";
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-01-09 15:55:33 UTC (rev 1572)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-01-11 07:56:41 UTC (rev 1573)
@@ -196,7 +196,8 @@
reasoner.init();
System.out.println("Galen loaded.");
- Description input = KBParser.parseConcept("(\"http://www.co-ode.org/ontologies/galen#15.0\" AND (\"http://www.co-ode.org/ontologies/galen#30.0\" AND (EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".\"http://www.co-ode.org/ontologies/galen#5.0\" AND EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".\"http://www.co-ode.org/ontologies/galen#6.0\")))");
+// Description input = KBParser.parseConcept("(\"http://www.co-ode.org/ontologies/galen#15.0\" AND (\"http://www.co-ode.org/ontologies/galen#30.0\" AND (EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".\"http://www.co-ode.org/ontologies/galen#5.0\" AND EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".\"http://www.co-ode.org/ontologies/galen#6.0\")))");
+ Description input = KBParser.parseConcept("(\"http://www.co-ode.org/ontologies/galen#1.0\" AND (\"http://www.co-ode.org/ontologies/galen#10.0\" AND (EXISTS \"http://www.co-ode.org/ontologies/galen#DomainAttribute\".(\"http://www.co-ode.org/ontologies/galen#1.0\" AND (\"http://www.co-ode.org/ontologies/galen#6.0\" AND \"http://www.co-ode.org/ontologies/galen#TopCategory\")) AND EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".(\"http://www.co-ode.org/ontologies/galen#1.0\" AND (\"http://www.co-ode.org/ontologies/galen#TopCategory\" AND EXISTS \"http://www.co-ode.org/ontologies/galen#Attribute\".TOP)))))");
ConceptTransformation.cleanConcept(input);
ELDown2 operator = new ELDown2(reasoner);
Modified: trunk/src/dl-learner/org/dllearner/utilities/Files.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/Files.java 2009-01-09 15:55:33 UTC (rev 1572)
+++ trunk/src/dl-learner/org/dllearner/utilities/Files.java 2009-01-11 07:56:41 UTC (rev 1573)
@@ -178,7 +178,7 @@
if(debug){System.exit(0);}
}
}
-
+
public static void clearFile(File file) {
try{
createFile(file, "");
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