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[DL-Learner SVN] SF.net SVN: dl-learner:[3593] trunk/components-core/src/main/java/org/ dllearner/utilities/GreedyCohaerencyExtractor.java
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From: <lor...@us...> - 2012-02-28 13:07:54
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Revision: 3593
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3593&view=rev
Author: lorenz_b
Date: 2012-02-28 13:07:43 +0000 (Tue, 28 Feb 2012)
Log Message:
-----------
Updated algorithm.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 02:25:27 UTC (rev 3592)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 13:07:43 UTC (rev 3593)
@@ -1,9 +1,12 @@
package org.dllearner.utilities;
+import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -14,6 +17,12 @@
import org.apache.commons.collections15.BidiMap;
import org.apache.commons.collections15.bidimap.DualHashBidiMap;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
+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.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
@@ -28,31 +37,37 @@
public class GreedyCohaerencyExtractor {
- private static final double STEP_SIZE = 0.001;
+ private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(JustificationBasedCoherentOntologyExtractor.class);
+
+ private double stepSize = 0.001;
private static final int ALLOWED_UNSATISFIABLE_CLASSES = 5;
private OWLOntologyManager manager;
- private OWLOntology cohaerentOntology;
+ private OWLOntology coherentOntology;
private IncrementalClassifier reasoner;
public GreedyCohaerencyExtractor() {
// TODO Auto-generated constructor stub
}
- public OWLOntology getCoharentOntology(OWLOntology ontology) throws OWLOntologyCreationException{
+ public OWLOntology getCoherentOntology(OWLOntology ontology, String target, double stepSize) throws OWLOntologyCreationException{
+ stepSize = stepSize/100;
BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = getAxiomTypeCount(ontology);
Map<AxiomType<? extends OWLAxiom>, List<OWLAxiom>> axiomType2AxiomsMap = new HashMap<AxiomType<? extends OWLAxiom>, List<OWLAxiom>>();
for(AxiomType<? extends OWLAxiom> type : AxiomType.AXIOM_TYPES){
axiomType2AxiomsMap.put(type, new ArrayList<OWLAxiom>(ontology.getAxioms(type)));
}
- System.out.println(ontology.getLogicalAxiomCount());
- double[] stepSize = new double[axiomType2CountMap.entrySet().size()];
+ //omit annotation axioms here
+ axiomType2AxiomsMap.remove(AxiomType.ANNOTATION_ASSERTION);
+
+ logger.info("Source ontology contains " + ontology.getLogicalAxiomCount() + " logical axioms.");
+ double[] stepSizeArray = new double[axiomType2CountMap.entrySet().size()];
double[] cnt = new double[axiomType2CountMap.entrySet().size()];
AxiomType[] type = new AxiomType[axiomType2CountMap.entrySet().size()];
int i=0;
for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : axiomType2CountMap.entrySet()){
- stepSize[i] = STEP_SIZE * entry.getValue();
+ stepSizeArray[i] = stepSize * entry.getValue();
type[i] = entry.getKey();
cnt[i] = 0;
i++;
@@ -60,71 +75,67 @@
manager = OWLManager.createOWLOntologyManager();
- cohaerentOntology = manager.createOntology();
+ coherentOntology = manager.createOntology();
- reasoner = new IncrementalClassifier(cohaerentOntology);
- manager.addOntologyChangeListener(reasoner);
+ reasoner = new IncrementalClassifier(coherentOntology);
+ reasoner.setMultiThreaded(false);
+// manager.addOntologyChangeListener(reasoner);
reasoner.classify();
- boolean isCohaerent = true;
- for(double j = 0; j < 1; j += STEP_SIZE){System.out.println(j);
- if(isCohaerent){
- for(i = 0; i < stepSize.length; i++){
- cnt[i] = cnt[i] + stepSize[i];
+ boolean isCoherent = true;
+ for(double j = 0; j < 1; j += stepSize){//increase by stepsize p until 100%
+ if(isCoherent){
+ for(i = 0; i < stepSizeArray.length; i++){//for each axiomtype
+ cnt[i] = cnt[i] + stepSizeArray[i];//sum up value which was computed by p * #axioms
int x = (int)cnt[i];
- System.out.println("Adding " + x + " " + type[i] + " axioms from " + axiomType2CountMap.get(type[i]));
-// System.out.println(axiomType2AxiomsMap.get(type[i]).size());
-// for(int k = 0; k < x; k++){
-// OWLAxiom ax = axiomType2AxiomsMap.get(type[i]).remove(0);
-// man.addAxiom(cohaerentOntology, ax);
-// isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().isEmpty();
-// if(!isCohaerent){
-// man.removeAxiom(cohaerentOntology, ax);
+ if(x > 0){
+ logger.info("Adding " + x + " " + type[i] + " axioms from " + axiomType2CountMap.get(type[i]));
+ Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
+ manager.addAxioms(coherentOntology, toAdd);
+ axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
+ isCoherent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
+ if(!isCoherent){
+ manager.removeAxioms(coherentOntology, toAdd);
+ logger.info("Incoherency detected. Undoing changes.");
+ isCoherent = true;
// break;
-// }
-// }
+ }
+ }
- /*Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
- manager.addAxioms(cohaerentOntology, toAdd);
- axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
- isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
- if(!isCohaerent){
- manager.removeAxioms(cohaerentOntology, toAdd);System.out.println("Incohaerency detected");
- break;
- }*/
-
- List<OWLAxiom> toAdd = axiomType2AxiomsMap.get(type[i]).subList(0, x);
+ //same procedure with divide and conquer optimization
+ /*List<OWLAxiom> toAdd = axiomType2AxiomsMap.get(type[i]).subList(0, x);
addAxioms(toAdd);
axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
+ */
cnt[i] = cnt[i] - x;
}
}
- System.out.println(cohaerentOntology.getLogicalAxiomCount());
+ logger.info("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
try {
- manager.saveOntology(cohaerentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File("coherent.owl"))));
+ manager.saveOntology(coherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File(target))));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- return cohaerentOntology;
+ return coherentOntology;
}
private Set<OWLAxiom> addAxioms(List<OWLAxiom> axioms){
Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
Set<OWLAxiom> axiomSet = new HashSet<OWLAxiom>(axioms);
- manager.addAxioms(cohaerentOntology, axiomSet);
+ manager.addAxioms(coherentOntology, axiomSet);
reasoner.classify();
boolean isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
if(!isCohaerent){
System.out.println("Incohaerency detected. Splitting...");
- manager.removeAxioms(cohaerentOntology, axiomSet);
+ manager.removeAxioms(coherentOntology, axiomSet);
if(axioms.size() == 1){
return addedAxioms;
}
@@ -145,8 +156,8 @@
return addedAxioms;
}
- public OWLOntology getCoharentOntology(OWLReasoner reasoner) throws OWLOntologyCreationException{
- return getCoharentOntology(reasoner.getRootOntology());
+ public OWLOntology getCoherentOntology(OWLReasoner reasoner, String target, double stepSize) throws OWLOntologyCreationException{
+ return getCoherentOntology(reasoner.getRootOntology(), target, stepSize);
}
private BidiMap<AxiomType<? extends OWLAxiom>, Integer> getAxiomTypeCount(OWLOntology ontology){
@@ -164,11 +175,30 @@
}
public static void main(String[] args) throws Exception{
+ Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getRootLogger().removeAllAppenders();
+ Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/greedy_out.log"));
+
+ if(args.length != 3){
+ System.out.println("USAGE: GreedyCoherencyExtractor <incoherent.owl> <target.owl> <stepsizeInPercent>");
+ System.exit(0);
+ }
+ String filename = args[0];
+ String target = args[1];
+ double stepSize = Double.parseDouble(args[2]);
+
+ System.out.println("Loading ontology...");
+ InputStream is = new BufferedInputStream(new FileInputStream(filename));
+ if(args[0].endsWith("bz2")){
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ }
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/papers/ESWC2012/dbpedia_0.75_no_datapropaxioms.owl"));
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
+ System.out.println("...done.");
GreedyCohaerencyExtractor ge = new GreedyCohaerencyExtractor();
- ge.getCoharentOntology(schema);
+ ge.getCoherentOntology(schema, target, stepSize);
}
}
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