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[DL-Learner SVN] SF.net SVN: dl-learner:[1257] trunk/src/dl-learner/org/dllearner/scripts
|
From: <ku...@us...> - 2008-09-25 15:49:19
|
Revision: 1257
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1257&view=rev
Author: kurzum
Date: 2008-09-25 15:49:07 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
renamed class, first experiment
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java
Deleted: trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java 2008-09-25 13:40:25 UTC (rev 1256)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java 2008-09-25 15:49:07 UTC (rev 1257)
@@ -1,441 +0,0 @@
-/**
- * Copyright (C) 2007-2008, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-package org.dllearner.scripts;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.SortedSet;
-import java.util.StringTokenizer;
-import java.util.TreeSet;
-
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.FileAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.dllearner.cli.Start;
-import org.dllearner.core.Component;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.core.EvaluatedDescription;
-import org.dllearner.core.KnowledgeSource;
-import org.dllearner.core.LearningAlgorithm;
-import org.dllearner.core.ReasoningService;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.utilities.Files;
-import org.dllearner.utilities.JamonMonitorLogger;
-import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.learn.ConfWriter;
-import org.dllearner.utilities.owl.ReasoningServiceFactory;
-import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
-import org.dllearner.utilities.statistics.SimpleClock;
-import org.dllearner.utilities.statistics.Stat;
-
-import com.jamonapi.MonitorFactory;
-
-public class SemanticBible2 {
-
- private static ReasoningService reasoningService;
-
- private static Logger logger = Logger.getRootLogger();
-
-
- public static String ontologyPath = "examples/semantic_bible/NTNcombined.owl";
- public static String dir = "sembib/";
- public static String sparqldir = dir+"sparql/";
- public static String normaldir = dir+"normal/";
-
- public static String tmpFilename = dir + "tmp.conf";
- static File log = new File(dir+"results+prop.txt");
-
- private static Stat accFragment = new Stat();
- private static Stat accOnOnto = new Stat();
- private static Stat accPosExOnOnto = new Stat();
- private static Stat accNegExOnOnto = new Stat();
- private static Stat timeFragment = new Stat();
- private static Stat nrOfExtractedTriples = new Stat();
- private static Stat dLengthFragment = new Stat();
- private static Stat dDepthFragment = new Stat();
-
- private static Stat timeWhole = new Stat();
- private static Stat accWhole = new Stat();
- private static Stat dLengthWhole = new Stat();
- private static Stat dDepthWhole = new Stat();
-
- private static int normalNoisePercentage = 0;
- private static int normalMaxExecution = 500;
- private static int sparqllMaxExecution = 250;
-
- private static boolean fragHasNot = false;
- private static boolean fragHasAll = false;
- private static boolean fragHasBooleanData = false;
- private static boolean fragHasNrRes = false;
-
- private static boolean wholeHasNot = false;
- private static boolean wholeHasAll = false;
- private static boolean wholeHasBooleanData = false;
- private static boolean wholeHasNrRes = false;
-
-
-
- //private static Class usedReasoner = FastInstanceChecker.class;
-
- private static boolean useSPARQL = true;
-
- /**
- * @param args
- */
- public static void main(String[] args) {
- SimpleClock total = new SimpleClock();
- Files.createFile(log, "");
-
- initLogger();
- logger.warn("Start");
- File tmpFile = new File(tmpFilename);
-
-
- List<File> confs = getFilesContaining(useSPARQL,"ten","all", "99+");
- //analyzeFiles(confs);
-
-
-
- reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
- ComponentManager cm =ComponentManager.getInstance();
- try{
-
-
- for (File f : confs) {
-
- Cache.getDefaultCache().clearCache();
- String fileContent = Files.readFile(f);
-
- SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
- SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
-
-
- StringBuffer sbuf = new StringBuffer(fileContent);
- sbuf.insert(0, sparqlOptions());
- Files.createFile(tmpFile, sbuf.toString());
-
- SimpleClock sc = new SimpleClock();
- Start.main(new String[] { tmpFilename });
- timeFragment.addNumber((double) sc.getTime());
-
- LearningAlgorithm la = cm.getLiveLearningAlgorithms().remove(0);
-
- EvaluatedDescription onFragment =(la.getCurrentlyBestEvaluatedDescription());
-
- accFragment.addNumber(onFragment.getAccuracy());
- dDepthFragment.addNumber((double)onFragment.getDescriptionDepth());
- dLengthFragment.addNumber((double)onFragment.getDescriptionLength());
-
- String desc = onFragment.getDescription().toKBSyntaxString();
-
- fragHasNot = ( fragHasNot || desc.contains("NOT"));
- fragHasAll = (fragHasAll || desc.contains("ALL"));
- fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
- fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
-
- SortedSet<Individual> retrieved = reasoningService.retrieval(onFragment.getDescription());
- EvaluatedDescription onOnto = reEvaluateDescription(
- onFragment.getDescription(), retrieved, posEx, negEx);
-
- accOnOnto.addNumber(onOnto.getAccuracy());
-
- int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
- normalNoisePercentage = 100-tmp;
- accPosExOnOnto.addNumber((double)(onOnto.getCoveredPositives().size()/5));
- double n = (double) (5-onOnto.getCoveredNegatives().size());
- accNegExOnOnto.addNumber(n/5.0);
- SparqlKnowledgeSource s=null;
- for(KnowledgeSource ks : cm.getLiveKnowledgeSources()){
- if (ks instanceof SparqlKnowledgeSource) {
- s = (SparqlKnowledgeSource) ks;
- }
- }
-
- double nrtrip = (double)(s.getNrOfExtractedTriples());
- nrOfExtractedTriples.addNumber(nrtrip);
-
-
-
- cm.freeAllComponents();
- /*************comp**/
- logger.warn("learning normal");
-
- StringBuffer sbufNormal = new StringBuffer();
- sbufNormal.append(normalOptions());
- sbufNormal.append(ConfWriter.listExamples(true, posEx));
- sbufNormal.append(ConfWriter.listExamples(false, negEx));
- //sbufNormal.append(ConfWriter.)
- Files.createFile(tmpFile, sbufNormal.toString());
-
-
- SimpleClock scNormal = new SimpleClock();
- Start.main(new String[] { tmpFilename });
- timeWhole.addNumber((double) scNormal.getTime());
-
- la = cm.getLiveLearningAlgorithms().remove(0);
-
- EvaluatedDescription normalOnOnto =(la.getCurrentlyBestEvaluatedDescription());
- accWhole.addNumber(normalOnOnto.getAccuracy());
- dDepthWhole.addNumber((double)normalOnOnto.getDescriptionDepth());
- dLengthWhole.addNumber((double)normalOnOnto.getDescriptionLength());
-
- fragHasNot = ( fragHasNot || desc.contains("NOT"));
- fragHasAll = (fragHasAll || desc.contains("ALL"));
- fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
- fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
-
- cm.freeAllComponents();
- writeLog();
-
-
- }//end for
- }catch (Exception e) {
- e.printStackTrace();
-
- }
- writeLog();
- total.printAndSet("Finished");
- //logger.warn("Finished");
-
- }
-
- public static void writeLog(){
- String l = "\n\n\n*********************\n";
- l +="COUNT: "+accFragment.getCount()+"\n";
- l +="FRAGMENT: ALL: "+fragHasAll+" BOOL: "+fragHasBooleanData+" NOT: "+fragHasNot+" <>=: "+fragHasNrRes+"\n";
- l +="WHOLE: ALL: "+wholeHasAll+" BOOL: "+wholeHasBooleanData+" NOT: "+wholeHasNot+" <>=: "+wholeHasNrRes+"\n";
-
-
- l+="accFragment\t\t"+accFragment.getMeanAsPercentage()+" +-"+accFragment.getStandardDeviation()+"\n";
- l+="accOnOnto\t\t"+accOnOnto.getMeanAsPercentage()+" +-"+accOnOnto.getStandardDeviation()+"\n";
- l+="accPosExOnOnto\t\t"+accPosExOnOnto.getMeanAsPercentage()+" +-"+accPosExOnOnto.getStandardDeviation()+"\n";
- l+="accNegExOnOnto\t\t"+accNegExOnOnto.getMeanAsPercentage()+" +-"+accNegExOnOnto.getStandardDeviation()+"\n";
- l+="timeFragment\t\t"+timeFragment.getMean()+" +-"+timeFragment.getStandardDeviation()+"\n";
- l+="nrOfExtractedTriples\t\t"+nrOfExtractedTriples.getMean()+" +-"+nrOfExtractedTriples.getStandardDeviation()+"\n";
- l+="dLengthFragment\t\t"+dLengthFragment.getMean()+" +-"+dLengthFragment.getStandardDeviation()+"\n";
- l+="dDepthFragment\t\t"+dDepthFragment.getMean()+" +-"+dDepthFragment.getStandardDeviation()+"\n";
-
- l+="timeWhole\t\t"+timeWhole.getMean()+" +-"+timeWhole.getStandardDeviation()+"\n";
- l+="accWhole\t\t"+accWhole.getMeanAsPercentage()+" +-"+accWhole.getStandardDeviation()+"\n";
- l+="dLengthWhole\t\t"+dLengthWhole.getMean()+" +-"+dLengthWhole.getStandardDeviation()+"\n";
- l+="dDepthWhole\t\t"+dDepthWhole.getMean()+" +-"+dDepthWhole.getStandardDeviation()+"\n";
-
- Files.appendFile(log, l);
-
-// write JaMON report in HTML file
- File jamonlog = new File("sembib/jamon.html");
- Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
- }
-
- public static EvaluatedDescription reEvaluateDescription(Description d, SortedSet<Individual> retrieved ,SortedSet<Individual> posEx ,SortedSet<Individual> negEx ){
- SortedSet<Individual> PosAsPos = new TreeSet<Individual>();
- SortedSet<Individual> PosAsNeg = new TreeSet<Individual>();
- SortedSet<Individual> NegAsPos = new TreeSet<Individual>();
- SortedSet<Individual> NegAsNeg = new TreeSet<Individual>();
-
- // PosAsPos
- PosAsPos.addAll(posEx);
- PosAsPos.retainAll(retrieved);
-
- //System.out.println(PosAsPos);
-
- // PosAsNeg
- PosAsNeg.addAll(posEx);
- PosAsNeg.removeAll(retrieved);
-
- //System.out.println(PosAsNeg);
-
- // NegAsPos
- NegAsPos.addAll(negEx);
- NegAsPos.retainAll(retrieved);
-
- //System.out.println(NegAsPos);
-
- // PosAsNeg
- NegAsNeg.addAll(negEx);
- NegAsNeg.removeAll(retrieved);
-
- //System.out.println(NegAsNeg);
-
-
- return new EvaluatedDescription(d, PosAsPos, PosAsNeg, NegAsPos,NegAsNeg);
-
- }
-
- public static LearningAlgorithm getLearningAlgorithm(){
- ComponentManager cm =ComponentManager.getInstance();
-
- List<Component> comp = cm.getLiveComponents();
- for (Component component : comp) {
- if(component instanceof LearningAlgorithm){
- return (LearningAlgorithm) component;
- }
-
- }
- return null;
- }
-
- public static List<File> getFilesContaining(boolean sparql, String numExamples, String allOrEx, String acc) {
- List<File> ret = new ArrayList<File>();
- //SortedSet<File> ret = new TreeSet<File>();
-
- String actualDir = (sparql)?sparqldir:normaldir;
- logger.warn(actualDir);
- File f = new File(actualDir);
- String[] files = f.list();
- Arrays.sort(files);
- int consistent = 0;
- try{
- for (int i = 0; i < files.length; i++) {
-
- if( files[i].contains(numExamples)
- && files[i].contains(allOrEx)
- && files[i].contains(acc)
- ){
- consistent++;
- ret.add(new File(actualDir+files[i]));
- if(ret.size() != consistent){
- logger.warn("double file: "+files[i]);
- }
- }
-
- }
- }catch (Exception e) {
-
- e.printStackTrace();
- }
- if(consistent != ret.size()){
- logger.warn("double files"+consistent+"::"+ret.size());
- System.exit(0);
- }else{
- logger.warn("all files different");
- }
- return ret;
- }
-
- /*public static void analyzeFiles(List<File> l){
-
- SortedSet<String> differentIndividuals = new TreeSet<String>();
- for ( content : l) {
- differentIndividuals.addAll(getIndividuals(content, true));
- differentIndividuals.addAll(getIndividuals(content, false));
-
- }
- System.out.println("found diff inds "+differentIndividuals.size());
-
- }*/
-
- public static SortedSet<String> getIndividuals(String target, boolean posOrNeg){
- if(posOrNeg){
- return getAllStringsBetween(target, "+\"", "\"");
- }else{
- return getAllStringsBetween(target, "-\"", "\"");
- }
-
- }
-
- public static SortedSet<String> getAllStringsBetween(String target, String start, String end){
- SortedSet<String> ret = new TreeSet<String>();
- StringTokenizer st = new StringTokenizer(target,"\n");
- while(st.hasMoreElements()){
- String line = st.nextToken();
- if(line.contains(start)){
- line = line.substring(line.indexOf(start)+start.length());
- String current = line.substring(0,line.indexOf(end));
- ret.add(current);
- }
- }
-
- return ret;
- }
-
- public static String getCombinedOptions(){
- String s="\n"+
- "algorithm = refexamples;\n"+
- "refexamples.useAllConstructor = true;\n"+
- "refexamples.useNegation = true;\n"+
- "refexamples.useCardinalityRestrictions = true;\n"+
- "refexamples.guaranteeXgoodDescriptions = 1;\n"+
-
- "\n"+
- "reasoner = owlAPIReasoner;\n"+
- //"reasoner = fastInstanceChecker;\n"+
- "owlAPIReasoner.reasonerType = pellet;\n\n"+
- "";
- return s;
- }
-
- public static String sparqlOptions (){
- String s="// SPARQL options\n"+
- "sparql.recursionDepth = 2;\n"+
- "sparql.useLits = true;\n"+
- "sparql.predefinedEndpoint = \"LOCALJOSEKIBIBLE\";\n"+
- "sparql.getPropertyInformation = true;\n"+
- "refexamples.maxExecutionTimeInSeconds = "+sparqllMaxExecution+";\n"+
- "import(\"http://localhost:2020/bible\",\"SPARQL\");\n"+
- getCombinedOptions()+
- "";
- return s;
- }
-
- public static String normalOptions (){
- String s="\n"+
- "import(\"NTNcombined.owl\");\n"+
- "refexamples.maxExecutionTimeInSeconds = "+normalMaxExecution+";\n";
-
- s+="refexamples.noisePercentage = "+normalNoisePercentage+";\n"+
- getCombinedOptions()+
- "";
- return s;
- }
-
-
- private static void initLogger() {
-
- SimpleLayout layout = new SimpleLayout();
- // create logger (a simple logger which outputs
- // its messages to the console)
- FileAppender fileAppender = null;
- try {
- fileAppender = new FileAppender(layout, "log/semBibleLog.txt",
- false);
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- logger.removeAllAppenders();
- logger.addAppender(consoleAppender);
- logger.addAppender(fileAppender);
- logger.setLevel(Level.WARN);
-
-
- }
-
-
-}
Copied: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java (from rev 1255, trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-25 15:49:07 UTC (rev 1257)
@@ -0,0 +1,441 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.scripts;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.StringTokenizer;
+import java.util.TreeSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.cli.Start;
+import org.dllearner.core.Component;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.utilities.Files;
+import org.dllearner.utilities.JamonMonitorLogger;
+import org.dllearner.utilities.datastructures.SetManipulation;
+import org.dllearner.utilities.learn.ConfWriter;
+import org.dllearner.utilities.owl.ReasoningServiceFactory;
+import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
+import org.dllearner.utilities.statistics.SimpleClock;
+import org.dllearner.utilities.statistics.Stat;
+
+import com.jamonapi.MonitorFactory;
+
+public class SemanticBibleComparison {
+
+ private static ReasoningService reasoningService;
+
+ private static Logger logger = Logger.getRootLogger();
+
+
+ public static String ontologyPath = "examples/semantic_bible/NTNcombined.owl";
+ public static String dir = "sembib/";
+ public static String sparqldir = dir+"sparql/";
+ public static String normaldir = dir+"normal/";
+
+ public static String tmpFilename = dir + "tmp.conf";
+ static File log = new File(dir+"results+prop.txt");
+
+ private static Stat accFragment = new Stat();
+ private static Stat accOnOnto = new Stat();
+ private static Stat accPosExOnOnto = new Stat();
+ private static Stat accNegExOnOnto = new Stat();
+ private static Stat timeFragment = new Stat();
+ private static Stat nrOfExtractedTriples = new Stat();
+ private static Stat dLengthFragment = new Stat();
+ private static Stat dDepthFragment = new Stat();
+
+ private static Stat timeWhole = new Stat();
+ private static Stat accWhole = new Stat();
+ private static Stat dLengthWhole = new Stat();
+ private static Stat dDepthWhole = new Stat();
+
+ private static int normalNoisePercentage = 0;
+ private static int normalMaxExecution = 500;
+ private static int sparqllMaxExecution = 250;
+
+ private static boolean fragHasNot = false;
+ private static boolean fragHasAll = false;
+ private static boolean fragHasBooleanData = false;
+ private static boolean fragHasNrRes = false;
+
+ private static boolean wholeHasNot = false;
+ private static boolean wholeHasAll = false;
+ private static boolean wholeHasBooleanData = false;
+ private static boolean wholeHasNrRes = false;
+
+
+
+ //private static Class usedReasoner = FastInstanceChecker.class;
+
+ private static boolean useSPARQL = true;
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ SimpleClock total = new SimpleClock();
+ Files.createFile(log, "");
+
+ initLogger();
+ logger.warn("Start");
+ File tmpFile = new File(tmpFilename);
+
+
+ List<File> confs = getFilesContaining(useSPARQL,"ten","all", "99+");
+ //analyzeFiles(confs);
+
+
+
+ reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
+ ComponentManager cm =ComponentManager.getInstance();
+ try{
+
+
+ for (File f : confs) {
+
+ Cache.getDefaultCache().clearCache();
+ String fileContent = Files.readFile(f);
+
+ SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
+ SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
+
+
+ StringBuffer sbuf = new StringBuffer(fileContent);
+ sbuf.insert(0, sparqlOptions());
+ Files.createFile(tmpFile, sbuf.toString());
+
+ SimpleClock sc = new SimpleClock();
+ Start.main(new String[] { tmpFilename });
+ timeFragment.addNumber((double) sc.getTime());
+
+ LearningAlgorithm la = cm.getLiveLearningAlgorithms().remove(0);
+
+ EvaluatedDescription onFragment =(la.getCurrentlyBestEvaluatedDescription());
+
+ accFragment.addNumber(onFragment.getAccuracy());
+ dDepthFragment.addNumber((double)onFragment.getDescriptionDepth());
+ dLengthFragment.addNumber((double)onFragment.getDescriptionLength());
+
+ String desc = onFragment.getDescription().toKBSyntaxString();
+
+ fragHasNot = ( fragHasNot || desc.contains("NOT"));
+ fragHasAll = (fragHasAll || desc.contains("ALL"));
+ fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
+ fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
+
+ SortedSet<Individual> retrieved = reasoningService.retrieval(onFragment.getDescription());
+ EvaluatedDescription onOnto = reEvaluateDescription(
+ onFragment.getDescription(), retrieved, posEx, negEx);
+
+ accOnOnto.addNumber(onOnto.getAccuracy());
+
+ int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
+ normalNoisePercentage = 100-tmp;
+ accPosExOnOnto.addNumber((double)(onOnto.getCoveredPositives().size()/5));
+ double n = (double) (5-onOnto.getCoveredNegatives().size());
+ accNegExOnOnto.addNumber(n/5.0);
+ SparqlKnowledgeSource s=null;
+ for(KnowledgeSource ks : cm.getLiveKnowledgeSources()){
+ if (ks instanceof SparqlKnowledgeSource) {
+ s = (SparqlKnowledgeSource) ks;
+ }
+ }
+
+ double nrtrip = (double)(s.getNrOfExtractedTriples());
+ nrOfExtractedTriples.addNumber(nrtrip);
+
+
+
+ cm.freeAllComponents();
+ /*************comp**/
+ logger.warn("learning normal");
+
+ StringBuffer sbufNormal = new StringBuffer();
+ sbufNormal.append(normalOptions());
+ sbufNormal.append(ConfWriter.listExamples(true, posEx));
+ sbufNormal.append(ConfWriter.listExamples(false, negEx));
+ //sbufNormal.append(ConfWriter.)
+ Files.createFile(tmpFile, sbufNormal.toString());
+
+
+ SimpleClock scNormal = new SimpleClock();
+ Start.main(new String[] { tmpFilename });
+ timeWhole.addNumber((double) scNormal.getTime());
+
+ la = cm.getLiveLearningAlgorithms().remove(0);
+
+ EvaluatedDescription normalOnOnto =(la.getCurrentlyBestEvaluatedDescription());
+ accWhole.addNumber(normalOnOnto.getAccuracy());
+ dDepthWhole.addNumber((double)normalOnOnto.getDescriptionDepth());
+ dLengthWhole.addNumber((double)normalOnOnto.getDescriptionLength());
+
+ fragHasNot = ( fragHasNot || desc.contains("NOT"));
+ fragHasAll = (fragHasAll || desc.contains("ALL"));
+ fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
+ fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
+
+ cm.freeAllComponents();
+ writeLog();
+
+
+ }//end for
+ }catch (Exception e) {
+ e.printStackTrace();
+
+ }
+ writeLog();
+ total.printAndSet("Finished");
+ //logger.warn("Finished");
+
+ }
+
+ public static void writeLog(){
+ String l = "\n\n\n*********************\n";
+ l +="COUNT: "+accFragment.getCount()+"\n";
+ l +="FRAGMENT: ALL: "+fragHasAll+" BOOL: "+fragHasBooleanData+" NOT: "+fragHasNot+" <>=: "+fragHasNrRes+"\n";
+ l +="WHOLE: ALL: "+wholeHasAll+" BOOL: "+wholeHasBooleanData+" NOT: "+wholeHasNot+" <>=: "+wholeHasNrRes+"\n";
+
+
+ l+="accFragment\t\t"+accFragment.getMeanAsPercentage()+" +-"+accFragment.getStandardDeviation()+"\n";
+ l+="accOnOnto\t\t"+accOnOnto.getMeanAsPercentage()+" +-"+accOnOnto.getStandardDeviation()+"\n";
+ l+="accPosExOnOnto\t\t"+accPosExOnOnto.getMeanAsPercentage()+" +-"+accPosExOnOnto.getStandardDeviation()+"\n";
+ l+="accNegExOnOnto\t\t"+accNegExOnOnto.getMeanAsPercentage()+" +-"+accNegExOnOnto.getStandardDeviation()+"\n";
+ l+="timeFragment\t\t"+timeFragment.getMean()+" +-"+timeFragment.getStandardDeviation()+"\n";
+ l+="nrOfExtractedTriples\t\t"+nrOfExtractedTriples.getMean()+" +-"+nrOfExtractedTriples.getStandardDeviation()+"\n";
+ l+="dLengthFragment\t\t"+dLengthFragment.getMean()+" +-"+dLengthFragment.getStandardDeviation()+"\n";
+ l+="dDepthFragment\t\t"+dDepthFragment.getMean()+" +-"+dDepthFragment.getStandardDeviation()+"\n";
+
+ l+="timeWhole\t\t"+timeWhole.getMean()+" +-"+timeWhole.getStandardDeviation()+"\n";
+ l+="accWhole\t\t"+accWhole.getMeanAsPercentage()+" +-"+accWhole.getStandardDeviation()+"\n";
+ l+="dLengthWhole\t\t"+dLengthWhole.getMean()+" +-"+dLengthWhole.getStandardDeviation()+"\n";
+ l+="dDepthWhole\t\t"+dDepthWhole.getMean()+" +-"+dDepthWhole.getStandardDeviation()+"\n";
+
+ Files.appendFile(log, l);
+
+// write JaMON report in HTML file
+ File jamonlog = new File("sembib/jamon.html");
+ Files.createFile(jamonlog, MonitorFactory.getReport());
+ Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ }
+
+ public static EvaluatedDescription reEvaluateDescription(Description d, SortedSet<Individual> retrieved ,SortedSet<Individual> posEx ,SortedSet<Individual> negEx ){
+ SortedSet<Individual> PosAsPos = new TreeSet<Individual>();
+ SortedSet<Individual> PosAsNeg = new TreeSet<Individual>();
+ SortedSet<Individual> NegAsPos = new TreeSet<Individual>();
+ SortedSet<Individual> NegAsNeg = new TreeSet<Individual>();
+
+ // PosAsPos
+ PosAsPos.addAll(posEx);
+ PosAsPos.retainAll(retrieved);
+
+ //System.out.println(PosAsPos);
+
+ // PosAsNeg
+ PosAsNeg.addAll(posEx);
+ PosAsNeg.removeAll(retrieved);
+
+ //System.out.println(PosAsNeg);
+
+ // NegAsPos
+ NegAsPos.addAll(negEx);
+ NegAsPos.retainAll(retrieved);
+
+ //System.out.println(NegAsPos);
+
+ // PosAsNeg
+ NegAsNeg.addAll(negEx);
+ NegAsNeg.removeAll(retrieved);
+
+ //System.out.println(NegAsNeg);
+
+
+ return new EvaluatedDescription(d, PosAsPos, PosAsNeg, NegAsPos,NegAsNeg);
+
+ }
+
+ public static LearningAlgorithm getLearningAlgorithm(){
+ ComponentManager cm =ComponentManager.getInstance();
+
+ List<Component> comp = cm.getLiveComponents();
+ for (Component component : comp) {
+ if(component instanceof LearningAlgorithm){
+ return (LearningAlgorithm) component;
+ }
+
+ }
+ return null;
+ }
+
+ public static List<File> getFilesContaining(boolean sparql, String numExamples, String allOrEx, String acc) {
+ List<File> ret = new ArrayList<File>();
+ //SortedSet<File> ret = new TreeSet<File>();
+
+ String actualDir = (sparql)?sparqldir:normaldir;
+ logger.warn(actualDir);
+ File f = new File(actualDir);
+ String[] files = f.list();
+ Arrays.sort(files);
+ int consistent = 0;
+ try{
+ for (int i = 0; i < files.length; i++) {
+
+ if( files[i].contains(numExamples)
+ && files[i].contains(allOrEx)
+ && files[i].contains(acc)
+ ){
+ consistent++;
+ ret.add(new File(actualDir+files[i]));
+ if(ret.size() != consistent){
+ logger.warn("double file: "+files[i]);
+ }
+ }
+
+ }
+ }catch (Exception e) {
+
+ e.printStackTrace();
+ }
+ if(consistent != ret.size()){
+ logger.warn("double files"+consistent+"::"+ret.size());
+ System.exit(0);
+ }else{
+ logger.warn("all files different");
+ }
+ return ret;
+ }
+
+ /*public static void analyzeFiles(List<File> l){
+
+ SortedSet<String> differentIndividuals = new TreeSet<String>();
+ for ( content : l) {
+ differentIndividuals.addAll(getIndividuals(content, true));
+ differentIndividuals.addAll(getIndividuals(content, false));
+
+ }
+ System.out.println("found diff inds "+differentIndividuals.size());
+
+ }*/
+
+ public static SortedSet<String> getIndividuals(String target, boolean posOrNeg){
+ if(posOrNeg){
+ return getAllStringsBetween(target, "+\"", "\"");
+ }else{
+ return getAllStringsBetween(target, "-\"", "\"");
+ }
+
+ }
+
+ public static SortedSet<String> getAllStringsBetween(String target, String start, String end){
+ SortedSet<String> ret = new TreeSet<String>();
+ StringTokenizer st = new StringTokenizer(target,"\n");
+ while(st.hasMoreElements()){
+ String line = st.nextToken();
+ if(line.contains(start)){
+ line = line.substring(line.indexOf(start)+start.length());
+ String current = line.substring(0,line.indexOf(end));
+ ret.add(current);
+ }
+ }
+
+ return ret;
+ }
+
+ public static String getCombinedOptions(){
+ String s="\n"+
+ "algorithm = refexamples;\n"+
+ "refexamples.useAllConstructor = true;\n"+
+ "refexamples.useNegation = true;\n"+
+ "refexamples.useCardinalityRestrictions = true;\n"+
+ "refexamples.guaranteeXgoodDescriptions = 1;\n"+
+
+ "\n"+
+ "reasoner = owlAPIReasoner;\n"+
+ //"reasoner = fastInstanceChecker;\n"+
+ "owlAPIReasoner.reasonerType = pellet;\n\n"+
+ "";
+ return s;
+ }
+
+ public static String sparqlOptions (){
+ String s="// SPARQL options\n"+
+ "sparql.recursionDepth = 2;\n"+
+ "sparql.useLits = true;\n"+
+ "sparql.predefinedEndpoint = \"LOCALJOSEKIBIBLE\";\n"+
+ "sparql.getPropertyInformation = true;\n"+
+ "refexamples.maxExecutionTimeInSeconds = "+sparqllMaxExecution+";\n"+
+ "import(\"http://localhost:2020/bible\",\"SPARQL\");\n"+
+ getCombinedOptions()+
+ "";
+ return s;
+ }
+
+ public static String normalOptions (){
+ String s="\n"+
+ "import(\"NTNcombined.owl\");\n"+
+ "refexamples.maxExecutionTimeInSeconds = "+normalMaxExecution+";\n";
+
+ s+="refexamples.noisePercentage = "+normalNoisePercentage+";\n"+
+ getCombinedOptions()+
+ "";
+ return s;
+ }
+
+
+ private static void initLogger() {
+
+ SimpleLayout layout = new SimpleLayout();
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ FileAppender fileAppender = null;
+ try {
+ fileAppender = new FileAppender(layout, "log/semBibleLog.txt",
+ false);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.addAppender(fileAppender);
+ logger.setLevel(Level.WARN);
+
+
+ }
+
+
+}
Property changes on: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
___________________________________________________________________
Added: svn:mergeinfo
+
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