Menu
▾
▴
[DL-Learner SVN] SF.net SVN: dl-learner:[1834] trunk/src/dl-learner/org/dllearner
|
From: <lor...@us...> - 2009-09-02 10:19:52
|
Revision: 1834
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1834&view=rev
Author: lorenz_b
Date: 2009-09-02 10:19:41 +0000 (Wed, 02 Sep 2009)
Log Message:
-----------
added explanation intended view
added update method to pellet reasoner, updating the CWA data
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/OREApplication.java
trunk/src/dl-learner/org/dllearner/tools/ore/OntologyModifier.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomRanker.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RootFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/GraphicalCoveragePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/IndividualsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ManchesterSyntaxRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ManchesterSyntaxTableCellRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatusBar.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/Wizard.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ClassChoosePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/KnowledgeSourcePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/RepairPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/UnsatisfiableExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/LearningPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/RepairPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/tools/ore/TaskManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/RelevanceBasedGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SimpleSelectionFunction.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTablePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairPlanPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatsPanel.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ChangePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ChangesPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/DescriptionPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ExplanationTablePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/RepairPlanPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/StatsPanel.java
Modified: trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -59,7 +59,6 @@
import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.tools.ore.explanation.PelletExplanationGenerator;
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.ConceptTransformation;
@@ -72,10 +71,12 @@
import org.mindswap.pellet.utils.SetUtils;
import org.mindswap.pellet.utils.progress.ProgressMonitor;
import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.inference.OWLReasonerException;
import org.semanticweb.owl.model.AddAxiom;
import org.semanticweb.owl.model.OWLAnnotation;
import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLClassAssertionAxiom;
import org.semanticweb.owl.model.OWLConstant;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDataProperty;
@@ -87,7 +88,9 @@
import org.semanticweb.owl.model.OWLLabelAnnotation;
import org.semanticweb.owl.model.OWLNamedObject;
import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owl.model.OWLObjectPropertyAssertionAxiom;
import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyChange;
import org.semanticweb.owl.model.OWLOntologyChangeException;
import org.semanticweb.owl.model.OWLOntologyCreationException;
import org.semanticweb.owl.model.OWLOntologyFormat;
@@ -286,6 +289,46 @@
dematerialise();
}
+ /*
+ * Updates the CWA ontology dematerialised before
+ */
+ public void updateCWAOntology(List<OWLOntologyChange> changes){
+ for(OWLOntologyChange change : changes){
+ OWLAxiom axiom = change.getAxiom();
+ if(axiom instanceof OWLClassAssertionAxiom){
+ Individual ind = OWLAPIConverter.convertIndividual(((OWLClassAssertionAxiom)axiom).getIndividual());
+ Description desc = OWLAPIConverter.convertClass(((OWLClassAssertionAxiom)axiom).getDescription().asOWLClass());
+ if(change instanceof RemoveAxiom){
+ classInstancesPos.get(desc).remove(ind);
+ } else if(change instanceof AddAxiom){
+ classInstancesPos.get(desc).add(ind);
+ }
+ } else if(axiom instanceof OWLObjectPropertyAssertionAxiom){System.out.println(axiom);
+ Individual obj = OWLAPIConverter.convertIndividual(((OWLObjectPropertyAssertionAxiom)axiom).getObject());
+ Individual sub = OWLAPIConverter.convertIndividual(((OWLObjectPropertyAssertionAxiom)axiom).getSubject());
+ ObjectProperty prop = OWLAPIConverter.convertObjectProperty(((OWLObjectPropertyAssertionAxiom)axiom).getProperty().asOWLObjectProperty());
+ if(change instanceof RemoveAxiom){
+ SortedSet<Individual> fillers = opPos.get(prop).get(sub);
+ if(fillers != null){
+ fillers.remove(obj);
+ }
+ } else if(change instanceof AddAxiom){
+ SortedSet<Individual> fillers = opPos.get(prop).get(sub);
+ if(fillers == null){
+ fillers = new TreeSet<Individual>();
+ fillers.add(obj);
+ opPos.get(prop).put(sub, fillers);
+ } else {
+ fillers.add(obj);
+ }
+ }
+
+
+ }
+ }
+
+ }
+
private void dematerialise(){
long dematStartTime = System.currentTimeMillis();
@@ -409,6 +452,15 @@
reasoner.classify();
}
+ public void realise(){
+ try {
+ reasoner.realise();
+ } catch (OWLReasonerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
public void refresh(){
reasoner.refresh();
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -1,14 +1,14 @@
package org.dllearner.tools.ore;
import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.dllearner.tools.ore.explanation.CachedExplanationGenerator;
import org.dllearner.tools.ore.explanation.Explanation;
import org.dllearner.tools.ore.explanation.RootFinder;
-import org.mindswap.pellet.owlapi.PelletReasonerFactory;
import org.mindswap.pellet.owlapi.Reasoner;
import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLClass;
@@ -36,11 +36,14 @@
private RootFinder rootFinder;
private boolean ontologyChanged = true;
- private boolean isLaconicMode = false;
+
private boolean isComputeAllExplanations = false;
private int maxExplantionCount = 1;
private boolean allExplanationWarningChecked = false;
+ private Map<Explanation, List<Map<OWLAxiom, Integer>>> orderingMap;
+ private DefaultExplanationOrderer explanationOrderer;
+
private List<ExplanationManagerListener> listeners;
@@ -55,10 +58,11 @@
this.ontology = reasoner.getLoadedOntologies().iterator().next();
manager.addOntologyChangeListener(this);
-// manager.addOntologyChangeListener(reasoner);
dataFactory = manager.getOWLDataFactory();
RepairManager.getRepairManager(oreMan).addListener(this);
-
+
+ explanationOrderer = new DefaultExplanationOrderer();
+ orderingMap = new HashMap<Explanation, List<Map<OWLAxiom, Integer>>>();
rootFinder = new RootFinder();
@@ -95,7 +99,7 @@
return rootFinder.getRootClasses();
}
- public Set<List<OWLAxiom>> getUnsatisfiableExplanations(OWLClass unsat) {
+ public Set<Explanation> getUnsatisfiableExplanations(OWLClass unsat) {
OWLSubClassAxiom entailment = dataFactory.getOWLSubClassAxiom(unsat,
dataFactory.getOWLNothing());
@@ -107,10 +111,10 @@
explanations = gen.getExplanations(entailment, maxExplantionCount);
}
- return getOrderedExplanations(explanations);
+ return explanations;
}
- public Set<List<OWLAxiom>> getInconsistencyExplanations(){
+ public Set<Explanation> getInconsistencyExplanations(){
OWLSubClassAxiom entailment = dataFactory.getOWLSubClassAxiom(dataFactory.getOWLThing(),
dataFactory.getOWLNothing());
@@ -121,43 +125,44 @@
explanations = gen.getExplanations(entailment, maxExplantionCount);
}
- return getOrderedExplanations(explanations);
+ return explanations;
}
+ public List<Map<OWLAxiom, Integer>> getOrdering(Explanation exp){
+ List<Map<OWLAxiom, Integer>> orderedAxioms = orderingMap.get(exp);
+ if(orderedAxioms == null){
+ orderedAxioms = new ArrayList<Map<OWLAxiom, Integer>>(exp.getAxioms().size());
+ orderedAxioms.addAll(orderExplanation(exp));
+ orderingMap.put(exp, orderedAxioms);
+ }
+ return orderedAxioms;
+ }
-
- private ArrayList<OWLAxiom> getTree2List(Tree<OWLAxiom> tree){
- ArrayList<OWLAxiom> ordering = new ArrayList<OWLAxiom>();
- ordering.add((OWLAxiom)tree.getUserObject());
+ private List<Map<OWLAxiom, Integer>> orderExplanation(Explanation exp){
+ explanationOrderer = new DefaultExplanationOrderer();
+ List<Map<OWLAxiom, Integer>> ordering = new ArrayList<Map<OWLAxiom, Integer>>(exp.getAxioms().size());
+ ExplanationTree tree = explanationOrderer.getOrderedExplanation(exp.getEntailment(), exp.getAxioms());
for(Tree<OWLAxiom> child : tree.getChildren()){
ordering.addAll(getTree2List(child));
}
return ordering;
}
- private Set<List<OWLAxiom>> getOrderedExplanations(Set<Explanation> explanations){
- DefaultExplanationOrderer orderer = new DefaultExplanationOrderer();
- Set<List<OWLAxiom>> orderedExplanations = new HashSet<List<OWLAxiom>>();
- ArrayList<OWLAxiom> ordering;
- for(Explanation explanation : explanations){
- ordering = new ArrayList<OWLAxiom>();
- ExplanationTree tree = orderer.getOrderedExplanation(explanation.getEntailment(), explanation.getAxioms());
-
-// ordering.add(tree.getUserObject());
- for(Tree<OWLAxiom> child : tree.getChildren()){
- ordering.addAll(getTree2List(child));
- }
- orderedExplanations.add(ordering);
+
+
+ private ArrayList<Map<OWLAxiom, Integer>> getTree2List(Tree<OWLAxiom> tree){
+ ArrayList<Map<OWLAxiom, Integer>> ordering = new ArrayList<Map<OWLAxiom, Integer>>();
+ Map<OWLAxiom, Integer> axiom2Depth = new HashMap<OWLAxiom, Integer>();
+ axiom2Depth.put((OWLAxiom)tree.getUserObject(), Integer.valueOf(tree.getUserObjectPathToRoot().size()));
+ ordering.add(axiom2Depth);
+ for(Tree<OWLAxiom> child : tree.getChildren()){
+ ordering.addAll(getTree2List(child));
}
- return orderedExplanations;
+ return ordering;
}
- @Override
- public void ontologiesChanged(List<? extends OWLOntologyChange> changes)
- throws OWLException {
- ontologyChanged = true;
- }
+
public int getArity(OWLClass cl, OWLAxiom ax) {
int arity = 0;
@@ -249,6 +254,12 @@
public Set<OWLAxiom> getRemainingAxioms(OWLAxiom source, OWLAxiom part){
return gen.getRemainingAxioms(source, part);
}
+
+ @Override
+ public void ontologiesChanged(List<? extends OWLOntologyChange> changes)
+ throws OWLException {
+ ontologyChanged = true;
+ }
@Override
public void activeOntologyChanged() {
@@ -257,5 +268,4 @@
gen = new CachedExplanationGenerator(ontology, reasoner);
}
-
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/OREApplication.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/OREApplication.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/OREApplication.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -31,11 +31,13 @@
import org.dllearner.tools.ore.ui.wizard.Wizard;
import org.dllearner.tools.ore.ui.wizard.WizardPanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.ClassChoosePanelDescriptor;
+import org.dllearner.tools.ore.ui.wizard.descriptors.InconsistencyExplanationPanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.IntroductionPanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.KnowledgeSourcePanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.LearningPanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.RepairPanelDescriptor;
import org.dllearner.tools.ore.ui.wizard.descriptors.SavePanelDescriptor;
+import org.dllearner.tools.ore.ui.wizard.descriptors.UnsatisfiableExplanationPanelDescriptor;
/**
@@ -77,18 +79,24 @@
WizardPanelDescriptor descriptor2 = new KnowledgeSourcePanelDescriptor();
wizard.registerWizardPanel(KnowledgeSourcePanelDescriptor.IDENTIFIER, descriptor2);
+
+// WizardPanelDescriptor descriptor3 = new InconsistencyExplanationPanelDescriptor();
+// wizard.registerWizardPanel(InconsistencyExplanationPanelDescriptor.IDENTIFIER, descriptor3);
+//
+// WizardPanelDescriptor descriptor4 = new UnsatisfiableExplanationPanelDescriptor();
+// wizard.registerWizardPanel(UnsatisfiableExplanationPanelDescriptor.IDENTIFIER, descriptor4);
- WizardPanelDescriptor descriptor3 = new ClassChoosePanelDescriptor();
- wizard.registerWizardPanel(ClassChoosePanelDescriptor.IDENTIFIER, descriptor3);
+ WizardPanelDescriptor descriptor5 = new ClassChoosePanelDescriptor();
+ wizard.registerWizardPanel(ClassChoosePanelDescriptor.IDENTIFIER, descriptor5);
- WizardPanelDescriptor descriptor4 = new LearningPanelDescriptor();
- wizard.registerWizardPanel(LearningPanelDescriptor.IDENTIFIER, descriptor4);
+ WizardPanelDescriptor descriptor6 = new LearningPanelDescriptor();
+ wizard.registerWizardPanel(LearningPanelDescriptor.IDENTIFIER, descriptor6);
- WizardPanelDescriptor descriptor5 = new RepairPanelDescriptor();
- wizard.registerWizardPanel(RepairPanelDescriptor.IDENTIFIER, descriptor5);
+ WizardPanelDescriptor descriptor7 = new RepairPanelDescriptor();
+ wizard.registerWizardPanel(RepairPanelDescriptor.IDENTIFIER, descriptor7);
- WizardPanelDescriptor descriptor6 = new SavePanelDescriptor();
- wizard.registerWizardPanel(SavePanelDescriptor.IDENTIFIER, descriptor6);
+ WizardPanelDescriptor descriptor8 = new SavePanelDescriptor();
+ wizard.registerWizardPanel(SavePanelDescriptor.IDENTIFIER, descriptor8);
if (!(args.length == 1)){
wizard.setCurrentPanel(IntroductionPanelDescriptor.IDENTIFIER);
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/OntologyModifier.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/OntologyModifier.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/OntologyModifier.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -21,6 +21,7 @@
package org.dllearner.tools.ore;
import java.net.URI;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
@@ -35,15 +36,8 @@
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectPropertyAssertion;
import org.dllearner.core.owl.ObjectQuantorRestriction;
-import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.reasoning.PelletReasoner;
import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
-import org.mindswap.pellet.owlapi.Reasoner;
-import org.semanticweb.owl.apibinding.OWLManager;
-import org.semanticweb.owl.debugging.BlackBoxOWLDebugger;
-import org.semanticweb.owl.debugging.OWLDebugger;
-import org.semanticweb.owl.inference.OWLReasonerException;
-import org.semanticweb.owl.inference.OWLSatisfiabilityChecker;
import org.semanticweb.owl.io.RDFXMLOntologyFormat;
import org.semanticweb.owl.model.AddAxiom;
import org.semanticweb.owl.model.OWLAxiom;
@@ -52,7 +46,6 @@
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDescription;
import org.semanticweb.owl.model.OWLEquivalentClassesAxiom;
-import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLInverseObjectPropertiesAxiom;
import org.semanticweb.owl.model.OWLObjectProperty;
@@ -226,6 +219,7 @@
RemoveAxiom rm = new RemoveAxiom(ontology, owlCl);
changes.add(rm);
try {
+ reasoner.updateCWAOntology(changes);
manager.applyChange(rm);
return changes;
} catch (OWLOntologyChangeException e) {
@@ -254,10 +248,9 @@
OWLClassAssertionAxiom owlCl = factory.getOWLClassAssertionAxiom(individualOWLAPI, owlDesc);
AddAxiom am = new AddAxiom(ontology, owlCl);
-
-
changes.add(am);
try {
+ reasoner.updateCWAOntology(changes);
manager.applyChange(am);
return changes;
} catch (OWLOntologyChangeException e) {
@@ -299,9 +292,8 @@
try {
+ reasoner.updateCWAOntology(changes);
manager.applyChanges(changes);
- saveOntology();
-
return changes;
} catch (OWLOntologyChangeException e) {
// TODO Auto-generated catch block
@@ -358,7 +350,8 @@
changes.addAll(removeList);
try {
- manager.applyChanges(removeList);
+ reasoner.updateCWAOntology(changes);
+ manager.applyChanges(changes);
return changes;
} catch (OWLOntologyChangeException e) {
// TODO Auto-generated catch block
@@ -400,6 +393,7 @@
try {
if(remove != null){
+ reasoner.updateCWAOntology(changes);
manager.applyChange(remove);
}
@@ -432,6 +426,7 @@
AddAxiom axiom = new AddAxiom(ontology, objAssertion);
changes.add(axiom);
try {
+ reasoner.updateCWAOntology(changes);
manager.applyChange(axiom);
return changes;
} catch (OWLOntologyChangeException e) {
@@ -450,25 +445,25 @@
*/
public void undoChanges(Collection<OWLOntologyChange> changes){
-
+ List<OWLOntologyChange> undoChanges = new ArrayList<OWLOntologyChange>(changes.size());
for(OWLOntologyChange change : changes){
if(change instanceof RemoveAxiom){
AddAxiom add = new AddAxiom(ontology, change.getAxiom());
- try {
- manager.applyChange(add);
- } catch (OWLOntologyChangeException e) {
- e.printStackTrace();
- }
+ undoChanges.add(add);
} else if(change instanceof AddAxiom){
RemoveAxiom remove = new RemoveAxiom(ontology, change.getAxiom());
- try {
- manager.applyChange(remove);
- } catch (OWLOntologyChangeException e) {
- e.printStackTrace();
- }
+ undoChanges.add(remove);
}
}
+ try {
+ reasoner.updateCWAOntology(undoChanges);
+ manager.applyChanges(undoChanges);
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
}
@@ -575,50 +570,5 @@
public OWLOntology getOntology() {
return ontology;
}
-
-/**
- * Prints reasons for inconsistent classes.
- */
- public void reason(){
-// reasoner.getInconsistencyReasons(ontology);
-
-
-
- /* Create a satisfiability checker */
- OWLSatisfiabilityChecker checker = new Reasoner(manager);
- try {
- checker.loadOntologies(Collections.singleton(ontology));
- } catch (OWLReasonerException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- OWLDebugger debugger = new BlackBoxOWLDebugger(manager, ontology, checker);
-
- for(OWLClass owlClass : reasoner.getInconsistentOWLClasses()){
- /* Find the sets of support and print them */
- Set<Set<OWLAxiom>> allsos = null;
- try {
- allsos = debugger.getAllSOSForIncosistentClass(owlClass);
- } catch (OWLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- for (Set<OWLAxiom> sos : allsos){
- System.out.println(sos);
- }
- }
-
-
-
- }
-
-
-
-
-
-
-
-
}
Added: trunk/src/dl-learner/org/dllearner/tools/ore/TaskManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/TaskManager.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/TaskManager.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,53 @@
+package org.dllearner.tools.ore;
+
+import javax.swing.JDialog;
+import javax.swing.SwingWorker;
+
+import org.dllearner.tools.ore.ui.StatusBar;
+
+public class TaskManager {
+
+ private static TaskManager instance;
+
+ private SwingWorker<?, ?> currentTask;
+
+ private Thread currentThread;
+
+ private StatusBar statusBar;
+
+ private JDialog dialog;
+
+ public static synchronized TaskManager getInstance(){
+ if(instance == null){
+ instance = new TaskManager();
+ }
+ return instance;
+ }
+
+ public void setStatusBar(StatusBar statusBar){
+ this.statusBar = statusBar;
+ }
+
+ public void setDialog(JDialog dialog){
+ this.dialog = dialog;
+ }
+
+ public void setCurrentTask(SwingWorker<?, ?> task){
+ this.currentTask = task;
+ }
+
+ public void setCurrentThread(Thread t){
+ this.currentThread = t;
+ }
+
+ public void cancelCurrentTask(){
+ if(currentTask != null && !currentTask.isCancelled() && !currentTask.isDone()){
+ currentTask.cancel(true);
+ }
+// statusBar.setProgressTitle("Canceled");
+// dialog.setCursor(null);
+ }
+
+ public synchronized void cancelCurrentThread(){currentThread.stop();
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomRanker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomRanker.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomRanker.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -51,6 +51,7 @@
this.factory = manager.getOWLDataFactory();
ModuleExtractor extractor = ModuleExtractorFactory.createModuleExtractor();
classifier = new IncrementalClassifier(manager, reasoner, extractor);
+
}
public Set<OWLAxiom> computeImpactOnRemoval(OWLAxiom ax){
@@ -58,8 +59,8 @@
try {
// IncrementalClassifier classifier = new IncrementalClassifier(manager);
-// classifier.loadOntology(ontology);
-// classifier.classify();
+ classifier.loadOntology(ontology);
+ classifier.classify();
Set<OWLClass> inc = classifier.getInconsistentClasses();
for(OWLDescription cl : ontology.getClassesInSignature()){
if(!inc.contains(cl)){
@@ -79,8 +80,9 @@
manager.applyChange(new RemoveAxiom(ontology, ax));
+
classifier.classify();
- inc = classifier.getInconsistentClasses();
+ inc = classifier.getInconsistentClasses();System.out.println(inc);
for(OWLDescription cl : ontology.getClassesInSignature()){
if(!inc.contains(cl)){
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -149,29 +149,35 @@
@Override
public void repairPlanExecuted(List<OWLOntologyChange> changes) {
- Map<OWLAxiom, Set<Explanation>> copy = new HashMap<OWLAxiom, Set<Explanation>>();
- for(OWLOntologyChange change : changes){
- if(change instanceof RemoveAxiom){
- for(Entry<OWLAxiom, Set<Explanation>> entry: regularExplanationCache.entrySet()){
- Set<Explanation> explanationsCopy = new HashSet<Explanation>();
- for(Explanation explanation : entry.getValue()){
- if(explanation.getAxioms().contains(change.getAxiom())){
- explanationsCopy.add(explanation);
- }
- }
- if(!explanationsCopy.isEmpty()){
- copy.put(entry.getKey(), explanationsCopy);
- }
-
-
- }
- }
- }
- for(Entry<OWLAxiom, Set<Explanation>> copyEntry : copy.entrySet()){
- regularExplanationCache.get(copyEntry.getKey()).removeAll(copyEntry.getValue());
-
- }
+// Map<OWLAxiom, Set<Explanation>> copy = new HashMap<OWLAxiom, Set<Explanation>>();
+// for(OWLOntologyChange change : changes){
+// if(change instanceof RemoveAxiom){
+// for(Entry<OWLAxiom, Set<Explanation>> entry: regularExplanationCache.entrySet()){
+// Set<Explanation> explanationsCopy = new HashSet<Explanation>();
+// for(Explanation explanation : entry.getValue()){
+// if(explanation.getAxioms().contains(change.getAxiom())){
+// explanationsCopy.add(explanation);
+// }
+// }
+// if(!explanationsCopy.isEmpty()){
+// copy.put(entry.getKey(), explanationsCopy);
+// }
+//
+//
+// }
+// }
+// }
+// for(Entry<OWLAxiom, Set<Explanation>> copyEntry : copy.entrySet()){
+// regularExplanationCache.get(copyEntry.getKey()).removeAll(copyEntry.getValue());
+//
+// }
+ regularExplanationCache.clear();
+ laconicExplanationCache.clear();
+ axiom2Module.clear();
+ lastRequestedRegularSize.clear();
+ lastRequestedLaconicSize.clear();
+
}
public Set<OWLAxiom> getSourceAxioms(OWLAxiom ax){
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RootFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RootFinder.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RootFinder.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -16,6 +16,7 @@
import org.semanticweb.owl.inference.OWLReasoner;
import org.semanticweb.owl.inference.OWLReasonerException;
import org.semanticweb.owl.inference.OWLReasonerFactory;
+import org.semanticweb.owl.model.AddAxiom;
import org.semanticweb.owl.model.AxiomType;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLDataAllRestriction;
@@ -122,6 +123,11 @@
public void computeRootDerivedClasses(){
rootClasses.clear();
derivedClasses.clear();
+ depend2Classes.clear();
+ depth2ExistsRestrictionPropertyMap.clear();
+ depth2UniversalRestrictionPropertyMap.clear();
+ child2Parents.clear();
+ parent2Children.clear();
computePossibleRoots();
pruneRoots();
derivedClasses.removeAll(rootClasses);
@@ -181,8 +187,10 @@
}
}
for (OWLClass cls : roots) {
- manager.addAxiom(ontology, manager.getOWLDataFactory()
+ OWLOntologyChange add = new AddAxiom(ontology, manager.getOWLDataFactory()
.getOWLDeclarationAxiom(cls));
+ manager.applyChange(add);
+ appliedChanges.add(add);
}
OWLReasoner checker = reasonerFactory.createReasoner(manager);
checker.loadOntologies(Collections.singleton(ontology));
@@ -191,6 +199,13 @@
rootClasses.remove(root);
}
}
+ for(OWLOntologyChange change: appliedChanges){
+ if(change instanceof RemoveAxiom){
+ manager.applyChange(new AddAxiom(ontology, change.getAxiom()));
+ } else if(change instanceof AddAxiom){
+ manager.applyChange(new RemoveAxiom(ontology, change.getAxiom()));
+ }
+ }
} catch (OWLOntologyChangeException e) {
e.printStackTrace();
} catch (OWLReasonerException e) {
Added: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/RelevanceBasedGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/RelevanceBasedGenerator.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/RelevanceBasedGenerator.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,400 @@
+package org.dllearner.tools.ore.explanation.relevance;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.mindswap.pellet.owlapi.PelletReasonerFactory;
+import org.mindswap.pellet.owlapi.Reasoner;
+import org.mindswap.pellet.utils.SetUtils;
+import org.mindswap.pellet.utils.Timer;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.inference.OWLReasonerException;
+import org.semanticweb.owl.model.OWLAxiom;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyChangeException;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+
+import com.clarkparsia.explanation.GlassBoxExplanation;
+import com.clarkparsia.explanation.PelletExplanation;
+import com.clarkparsia.explanation.TransactionAwareSingleExpGen;
+import com.clarkparsia.explanation.util.OntologyUtils;
+
+public class RelevanceBasedGenerator {
+ static{
+ setup();
+ }
+
+ public static void setup() {
+ GlassBoxExplanation.setup();
+ }
+
+ public static final Logger log = Logger.getLogger(RelevanceBasedGenerator.class);
+
+
+ private Reasoner globalReasoner;
+ private OWLOntology ontology;
+ private OWLOntologyManager manager;
+ private Reasoner localReasoner;
+
+ private TransactionAwareSingleExpGen singleExpGen;
+ private PelletReasonerFactory reasonerFactory;
+
+ private Set<Set<OWLAxiom>> allJusts;
+ private Set<HittingSet> hittingSets;
+
+ private SimpleSelectionFunction selector;
+
+ private PelletExplanation pellet;
+
+
+ Map<OWLAxiom, Integer> axiomMap;
+
+ public RelevanceBasedGenerator(OWLOntologyManager manager,
+ OWLOntology ontology, Reasoner reasoner) {
+ log.setLevel(Level.DEBUG);
+
+ this.globalReasoner = reasoner;
+ this.manager = manager;
+ this.ontology = ontology;//getExampleOntology();
+
+ reasonerFactory = new PelletReasonerFactory();
+
+ allJusts = new HashSet<Set<OWLAxiom>>();
+ hittingSets = new HashSet<HittingSet>();
+
+ selector = new SimpleSelectionFunction();
+ selector.init(ontology);
+ }
+
+ private OWLOntology getExampleOntology(){
+ try {
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ OWLClass u = factory.getOWLClass(URI.create("U"));
+ OWLClass a = factory.getOWLClass(URI.create("A"));
+ OWLClass b = factory.getOWLClass(URI.create("B"));
+ OWLClass c = factory.getOWLClass(URI.create("C"));
+ OWLClass d = factory.getOWLClass(URI.create("D"));
+ OWLClass e = factory.getOWLClass(URI.create("E"));
+ OWLClass f = factory.getOWLClass(URI.create("F"));
+ OWLClass g = factory.getOWLClass(URI.create("G"));
+ OWLClass h = factory.getOWLClass(URI.create("H"));
+ OWLClass k = factory.getOWLClass(URI.create("K"));
+ List<OWLAxiom> examples = new ArrayList<OWLAxiom>();
+ examples.add( factory.getOWLSubClassAxiom(u, a));
+ examples.add( factory.getOWLSubClassAxiom(u, factory.getOWLObjectComplementOf(a)));
+ examples.add( factory.getOWLSubClassAxiom(u, c));
+ examples.add( factory.getOWLSubClassAxiom(c, factory.getOWLObjectComplementOf(b)));
+ examples.add( factory.getOWLSubClassAxiom(a, b));
+ examples.add( factory.getOWLSubClassAxiom(u, g));
+ examples.add( factory.getOWLSubClassAxiom(g, e));
+ examples.add( factory.getOWLSubClassAxiom(u, f));
+ examples.add( factory.getOWLSubClassAxiom(f, factory.getOWLObjectComplementOf(e)));
+ examples.add( factory.getOWLSubClassAxiom(u, d));
+ examples.add( factory.getOWLSubClassAxiom(d, e));
+ examples.add( factory.getOWLSubClassAxiom(c, k));
+ examples.add( factory.getOWLSubClassAxiom(k, factory.getOWLObjectComplementOf(h)));
+ examples.add( factory.getOWLSubClassAxiom(b, h));
+ OWLOntology example = manager.createOntology(new HashSet<OWLAxiom>(examples));
+ axiomMap = new HashMap<OWLAxiom, Integer >();
+ for(int i = 1; i<=examples.size(); i++){
+ axiomMap.put(examples.get(i - 1), Integer.valueOf(i));
+ }
+ return example;
+ } catch (OWLOntologyCreationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private Set<Integer> axioms2Integer(Set<OWLAxiom> axioms){
+ Set<Integer> path = new HashSet<Integer>();
+ for(OWLAxiom ax: axioms){
+ path.add(axiomMap.get(ax));
+ }
+ return path;
+ }
+
+ public Set<Set<OWLAxiom>> getExplanations(OWLClass unsat){
+ computeAllJusts(unsat);
+ return allJusts;
+ }
+
+ private void computeAllJusts(OWLClass unsat){
+ try {
+ allJusts.clear();
+ hittingSets.clear();
+
+ Set<HittingSet> hittingSetsLocal = new HashSet<HittingSet>();
+
+ int step = 1;
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology temp = man.createOntology(Collections.<OWLAxiom>emptySet());
+
+ localReasoner = new PelletReasonerFactory().createReasoner(man);
+ localReasoner.loadOntology(temp);
+
+ singleExpGen = new GlassBoxExplanation(man);
+ singleExpGen.setOntology(temp);
+ singleExpGen.setReasoner(localReasoner);
+ singleExpGen.setReasonerFactory(reasonerFactory);
+ setup();
+
+ Set<OWLAxiom> selectedAxioms = selector.getRelatedAxioms(unsat);
+ Set<OWLAxiom> allAxioms = new HashSet<OWLAxiom>();
+ allAxioms.addAll(selectedAxioms);
+
+ while(!selectedAxioms.isEmpty()){log.debug("Step: " + step);
+ addAxioms(selectedAxioms);
+ localReasoner.refresh();
+
+ if(!hittingSetsLocal.isEmpty()){
+ for(HittingSet hit : hittingSetsLocal){
+ removeAxioms(hit, ontology, manager);globalReasoner.refresh();
+ if(globalReasoner.isSatisfiable(unsat)){
+ hittingSets.add(hit);
+ }
+ addAxioms(hit, ontology, manager);globalReasoner.refresh();
+ }
+
+ hittingSetsLocal.removeAll(hittingSets);
+
+ if(hittingSetsLocal.isEmpty()){
+ return;
+ }
+
+ Set<HittingSet> hittingSetsTemp = new HashSet<HittingSet>(hittingSetsLocal);
+ for(HittingSet hit : hittingSetsTemp){
+ removeAxioms(hit, temp, man);
+ Set<HittingSet> hittingSetsLocalTemp = expandHittingSetTree(unsat, temp, man, hit);
+ for(HittingSet hit2 : hittingSetsLocalTemp){
+ hit2.addAll(hit);
+ hittingSetsLocal.add(hit2);
+ }
+ addAxioms(hit, temp, man);
+ }
+
+
+ } else if(!singleExpGen.getReasoner().isSatisfiable(unsat)){
+
+ hittingSetsLocal.addAll(expandHittingSetTree(unsat, temp, man, new HittingSet()));
+
+ }
+ step++;
+ selectedAxioms = selector.getRelatedAxioms(selectedAxioms);
+ selectedAxioms.removeAll(allAxioms);
+ allAxioms.addAll(selectedAxioms);
+
+
+ }
+
+ } catch (OWLOntologyCreationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLReasonerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ private Set<HittingSet> expandHittingSetTree(OWLClass unsat, OWLOntology ont, OWLOntologyManager man, HittingSet currentPath){
+ Set<HittingSet> hittingSets = new HashSet<HittingSet>();
+ Set<HittingSet> hittingSets1 = new HashSet<HittingSet>();
+ Set<Set<OWLAxiom>> currentJusts = new HashSet<Set<OWLAxiom>>();
+// log.debug("CurrentPath: " + axioms2Integer(currentPath));
+ log.debug("CurrentPath: " + currentPath);
+ Set<OWLAxiom> justification = null;
+ if(!allJusts.isEmpty()){
+ for(Set<OWLAxiom> just : allJusts){
+ if(!SetUtils.intersects(just, currentPath)){
+ log.debug("using global ontology justification reuse:" + just);
+// log.debug("using global ontology justification reuse:" + axioms2Integer(just));
+ justification = just;
+ currentJusts.add(justification);
+ break;
+ }
+ }
+ }
+ if(justification == null){
+// pellet = new PelletExplanation(man, Collections.singleton(ont));
+ justification = singleExpGen.getExplanation(unsat);//pellet.getUnsatisfiableExplanation(unsat);
+ if(!justification.isEmpty()){
+// log.debug("Found new justification: " + axioms2Integer(justification));
+ log.debug("Found new justification: " + justification);
+ if(allJusts.isEmpty()){
+ singleExpGen.beginTransaction();
+ }
+ allJusts.add(justification);
+ currentJusts.add(justification);
+ }
+ }
+
+
+ for(OWLAxiom ax : justification){
+ hittingSets1.add(new HittingSet(ax));
+ }
+
+ while(true){
+ Set<HittingSet> hittingSets2 = new HashSet<HittingSet>();
+ for(HittingSet hit : hittingSets1){
+ boolean earlyPathTermination = false;
+ for(HittingSet h : SetUtils.union(hittingSets,this.hittingSets)){
+ if(hit.containsAll(h)){
+ earlyPathTermination = true;
+// log.debug("early path termination:" + axioms2Integer(hit) + " contains all " + axioms2Integer(h));
+ log.debug("early path termination:" + hit + " contains all " + h);
+ break;
+ }
+ }
+ if(!earlyPathTermination){
+ removeAxioms(hit);localReasoner.refresh();
+ if(localReasoner.isSatisfiable(unsat)){
+ hittingSets.add(hit);
+ } else {
+ hittingSets2.add(hit);
+ }
+ addAxioms(hit);localReasoner.refresh();
+ }
+ }
+
+ if(hittingSets1.isEmpty() || hittingSets2.isEmpty()){
+ return hittingSets;
+ }
+
+ hittingSets1.clear();
+ for(HittingSet hit : hittingSets2){
+// log.debug("CurrentPath: " + axioms2Integer(hit));
+ log.debug("CurrentPath: " + hit);
+
+ justification = null;
+ if(!currentJusts.isEmpty()){
+ for(Set<OWLAxiom> just : allJusts){
+ if(!SetUtils.intersects(just, hit)){
+ log.debug("using sub ontology justification reuse: " + just);
+// log.debug("using sub ontology justification reuse: " + axioms2Integer(just));
+ justification = just;
+ break;
+ }
+ }
+ }
+ if(justification == null){
+ removeAxioms(hit);System.out.println(singleExpGen.getExplanation(unsat));
+// pellet = new PelletExplanation(man, Collections.singleton(ont));
+ justification = singleExpGen.getExplanation(unsat);//pellet.getUnsatisfiableExplanation(unsat);
+ if(!justification.isEmpty()){
+// log.debug("found new justification: " + axioms2Integer(justification));
+ log.debug("found new justification: " + justification);
+ allJusts.add(justification);
+ currentJusts.add(justification);
+ }
+ }
+
+ for(OWLAxiom ax : justification){
+ HittingSet h = new HittingSet(hit);
+ h.add(ax);
+ hittingSets1.add(h);
+ }
+
+ addAxioms(hit);
+ }
+
+ }
+ }
+
+ private void removeAxioms(Set<OWLAxiom> axioms, OWLOntology ontology, OWLOntologyManager man){
+ try {
+ for(OWLAxiom ax : axioms){
+ OntologyUtils.removeAxiom(ax, Collections.singleton(ontology), man);
+ }
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ private void removeAxioms(Set<OWLAxiom> axioms){
+ try {
+ for(OWLAxiom ax : axioms){
+ OntologyUtils.removeAxiom(ax, singleExpGen.getReasoner().getLoadedOntologies(), singleExpGen.getOntologyManager());
+ }
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ private void addAxioms(Set<OWLAxiom> axioms, OWLOntology ontology, OWLOntologyManager man){
+ try {
+ for(OWLAxiom ax : axioms){
+ OntologyUtils.addAxiom(ax, Collections.singleton(ontology), man);
+ }
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ private void addAxioms(Set<OWLAxiom> axioms){
+ try {
+ for(OWLAxiom ax : axioms){
+ OntologyUtils.addAxiom(ax, singleExpGen.getReasoner().getLoadedOntologies(), singleExpGen.getOntologyManager());
+ }
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ public static void main(String[] args) throws OWLOntologyCreationException {
+// URI file = URI.create("file:examples/ore/koala.owl");
+// String base = "http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#";
+// URI classURI = URI.create(base + "KoalaWithPhD");
+
+ URI file = URI.create("file:examples/ore/tambis.owl");
+ String base = "http://krono.act.uji.es/Links/ontologies/tambis.owl#";
+ URI classURI = URI.create(base + "metal");
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ OWLClass cl = factory.getOWLClass(classURI);
+ OWLOntology ontology = manager.loadOntology(file);
+ Reasoner reasoner = new PelletReasonerFactory().createReasoner(manager);
+ reasoner.loadOntology(ontology);
+
+ PelletExplanation pellet = new PelletExplanation(manager, Collections.singleton(ontology));
+ Timer t1 = new Timer("pellet");
+ t1.start();
+ System.out.println(pellet.getUnsatisfiableExplanations(cl).size());
+ t1.stop();
+ System.out.println(t1.getTotal());
+
+ RelevanceBasedGenerator expGen = new RelevanceBasedGenerator(manager, ontology, reasoner);
+ Timer t2 = new Timer("relevance");
+ t2.start();
+ System.out.println(expGen.getExplanations(cl).size());
+ t2.stop();
+ System.out.println(t2.getTotal());
+
+ }
+}
Added: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SimpleSelectionFunction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SimpleSelectionFunction.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SimpleSelectionFunction.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,135 @@
+/* SimpleSelectionFunction - Decompiled by JODE
+ * Visit http://jode.sourceforge.net/
+ */
+package org.dllearner.tools.ore.explanation.relevance;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import org.semanticweb.owl.model.OWLAxiom;
+import org.semanticweb.owl.model.OWLEntity;
+import org.semanticweb.owl.model.OWLOntology;
+
+public class SimpleSelectionFunction {
+ private Set<OWLAxiom> allAxioms = new HashSet<OWLAxiom>();
+ public Map<OWLAxiom, Set<OWLEntity>> axiomEntities = new HashMap<OWLAxiom, Set<OWLEntity>>();
+
+
+ public void init(OWLOntology onto) {
+ allAxioms.clear();
+ allAxioms = onto.getAxioms();
+
+ initAxiomEntities(allAxioms);
+ }
+
+ public void init(HashSet<OWLAxiom> axioms) {
+ allAxioms.clear();
+ allAxioms.addAll(axioms);
+ initAxiomEntities(allAxioms);
+ }
+
+ public void initAxiomEntities(Set<OWLAxiom> axioms) {
+ axiomEntities.clear();
+ for (OWLAxiom ax : axioms) {
+ axiomEntities.put(ax, ax.getSignature());
+ }
+
+ }
+
+ public Set<OWLAxiom> getRelatedAxioms(OWLEntity concept) {
+ Set<OWLAxiom> relatedAxioms = new HashSet<OWLAxiom>();
+ for (OWLAxiom ax : allAxioms) {
+ if (connected(concept, ax)) {
+ relatedAxioms.add(ax);
+ }
+ }
+
+ return relatedAxioms;
+ }
+
+ public Vector<OWLAxiom> getAllRelatedAxioms(OWLEntity concept) {
+ Vector<OWLAxiom> allRelated = new Vector<OWLAxiom>();
+ Set<OWLAxiom> relatedAxioms = new HashSet<OWLAxiom>();
+ Set<OWLAxiom> relatedAxioms_all = new HashSet<OWLAxiom>();
+ for (relatedAxioms = getRelatedAxioms(concept); relatedAxioms.size() > 0; relatedAxioms = getRelatedAxioms(relatedAxioms_all)) {
+ allRelated
+ .addAll((HashSet<OWLAxiom>) ((HashSet<OWLAxiom>) relatedAxioms)
+ .clone());
+ relatedAxioms_all
+ .addAll((HashSet<OWLAxiom>) ((HashSet<OWLAxiom>) relatedAxioms)
+ .clone());
+ }
+ return allRelated;
+ }
+
+ public Set<OWLAxiom> getRelatedAxioms(Set<OWLAxiom> originalAxioms_in) {
+ Set<OWLAxiom> relatedAxioms = new HashSet<OWLAxiom>();
+ Set<OWLEntity> originalEntities = new HashSet<OWLEntity>();
+ Set<OWLAxiom> originalAxioms = new HashSet<OWLAxiom>(originalAxioms_in);
+ for (OWLAxiom ax : originalAxioms) {
+ if (axiomEntities.containsKey(ax)) {
+ originalEntities.addAll(axiomEntities.get(ax));
+ }
+ }
+ for (OWLEntity ent : originalEntities) {
+ for (OWLAxiom ax : allAxioms) {
+ if (!originalAxioms.contains(ax) && connected(ent, ax)) {
+ relatedAxioms.add(ax);
+ }
+ }
+ }
+ relatedAxioms.removeAll(originalAxioms_in);
+ return relatedAxioms;
+ }
+
+ public Vector<OWLAxiom> getAllRelatedAxioms(Set<OWLAxiom> originalAxioms_in) {
+ Vector<OWLAxiom> allRelated = new Vector<OWLAxiom>();
+ Set<OWLAxiom> relatedAxioms = new HashSet<OWLAxiom>();
+ Set<OWLAxiom> relatedAxioms_all = new HashSet<OWLAxiom>();
+ for (relatedAxioms = getRelatedAxioms(originalAxioms_in); relatedAxioms
+ .size() > 0; relatedAxioms = getRelatedAxioms(relatedAxioms_all)) {
+ allRelated
+ .addAll((HashSet<OWLAxiom>) ((HashSet<OWLAxiom>) relatedAxioms)
+ .clone());
+ relatedAxioms_all
+ .addAll((HashSet<OWLAxiom>) ((HashSet<OWLAxiom>) relatedAxioms)
+ .clone());
+ }
+ return allRelated;
+ }
+
+ public boolean connected(HashSet<OWLAxiom> axioms, OWLAxiom a) {
+ boolean flag = false;
+ for (OWLAxiom ax : axioms) {
+ if (connected(ax, a) > 0) {
+ flag = true;
+ break;
+ }
+ }
+
+ return flag;
+ }
+
+ public int connected(OWLAxiom a1, OWLAxiom a2) {
+ int num = 0;
+ Set<OWLEntity> ents1 = axiomEntities.get(a1);
+ Set<OWLEntity> ents2 = axiomEntities.get(a2);
+ for(OWLEntity ent : ents1){
+ if(ents2.contains(ent)){
+ num++;
+ }
+ }
+
+ return num;
+ }
+
+ public boolean connected(OWLEntity c, OWLAxiom a) {
+ Set<OWLEntity> entities = axiomEntities.get(a);
+ if (entities.contains(c))
+ return true;
+ return false;
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java 2009-09-01 13:44:00 UTC (rev 1833)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -76,7 +76,7 @@
e.printStackTrace();
}
logger.addAppender( fileAppender );
- logger.setLevel(Level.DEBUG);
+ logger.setLevel(Level.OFF);
}
@@ -509,7 +509,7 @@
public static void main(String[] args){
URI file = URI.create("http://krono.act.uji.es/Links/ontologies/tambis.owl/at_download/file");
String base = "http://krono.act.uji.es/Links/ontologies/tambis.owl#";
- URI classURI = URI.create(base + "protein");
+ URI classURI = URI.create(base + "metal");
try {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
@@ -590,22 +590,23 @@
Timer t1 = new Timer("pellet");
t1.start();
PelletExplanation exp1 = new PelletExplanation(manager, Collections.singleton(ontology));
- exp1.getUnsatisfiableExplanations(cl, 1);
+ exp1.getUnsatisfiableExplanations(cl);
t1.stop();
Timer t3 = new Timer("module-based");
t3.start();
OWLOntology module = OntologyUtils.getOntologyFromAxioms(ModularityUtils.extractModule(ontology, cl.getSignature(), ModuleType.TOP_OF_BOT));
System.out.println(module);
PelletExplanation exp2 = new PelletExplanation(manager, Collections.singleton(module));
- exp2.getUnsatisfiableExplanations(cl, 1);
+ System.out.println(exp2.getUnsatisfiableExplanations(cl).size());
t3.stop();
Timer t2 = new Timer("syntactic relevance");
t2.start();
Reasoner reasoner = new PelletReasonerFactory().createReasoner(manager);
reasoner.loadOntologies(Collections.singleton(ontology));
- SyntacticRelevanceBasedExplanationGenerator expGen =
+ SyntacticRelevanceBasedExplanationGenerator exp3 =
new SyntacticRelevanceBasedExplanationGenerator(reasoner, manager);
+ System.out.println(exp3.getUnsatisfiableExplanations(cl, Strategie.All_Just_Relevance).size());
System.out.print("J = {");
// for(Set<OWLAxiom> explanation : expGen.getUnsatisfiableExplanations(cl, Strategie.All_Just_Relevance)){
Added: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTable.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTable.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTable.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,138 @@
+package org.dllearner.tools.ore.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.List;
+
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.table.DefaultTableCellRenderer;
+
+import org.jdesktop.swingx.JXTable;
+import org.semanticweb.owl.model.OWLOntologyChange;
+
+public class ChangesTable extends JXTable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1137642531002327026L;
+
+ public ChangesTable(){
+ setBackground(Color.WHITE);
+ setModel(new ChangesTableModel());
+ setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ setEditable(false);
+ setTableHeader(null);
+ setGridColor(Color.LIGHT_GRAY);
+ setRowHeight(getRowHeight() + 5);
+ getColumn(0).setMaxWidth(20);
+ getColumn(2).setMaxWidth(40);
+ setShowGrid(false);
+ getColumn(1).setCellRenderer(new ManchesterSyntaxTableCellRenderer());
+ getColumn(2).setCellRenderer(new UndoCellRenderer());
+
+ addKeyListener(new KeyAdapter() {
+
+ public void keyPressed(KeyEvent e)
+ {
+ handleKeyPressed(e);
+ }
+
+
+ });
+
+ addMouseMotionListener(new MouseAdapter() {
+
+ final ChangesTable table;
+ {
+ table = ChangesTable.this;
+ }
+
+ public void mouseMoved(MouseEvent e) {
+ int row = rowAtPoint(e.getPoint());
+ int column = columnAtPoint(e.getPoint());
+
+ if(column == 2 && row <= table.getRowCount() && row >= 0){
+ setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+
+ } else {
+ setCursor(null);
+ }
+ }
+
+ });
+
+ addMouseListener(new MouseAdapter() {
+ final ChangesTable table;
+ {
+ table = ChangesTable.this;
+ }
+
+ public void mouseClicked(MouseEvent e) {
+ int row = rowAtPoint(e.getPoint());
+ int column = columnAtPoint(e.getPoint());
+
+ if(row >= 0 && row <= table.getRowCount() && column == 2){
+ ((ChangesTableModel)table.getModel()).removeChange(rowAtPoint(e.getPoint()));
+ setCursor(null);
+ }
+ }
+ });
+ }
+
+ private void handleKeyPressed(KeyEvent e)
+ {
+ int selRow = getSelectedRow();
+ if(e.getKeyCode() == KeyEvent.VK_DELETE){
+ ((ChangesTableModel)getModel()).removeChange(selRow);
+ }
+
+ getSelectionModel().clearSelection();
+ }
+
+ public void addChanges(List<OWLOntologyChange> changes){
+ ((ChangesTableModel)getModel()).addChanges(changes);
+ }
+
+ public void removeChanges(List<OWLOntologyChange> changes){
+ ((ChangesTableModel)getModel()).removeChanges(changes);
+ }
+
+ public void clear(){
+ ((ChangesTableModel)getModel()).clear();
+ }
+
+ public List<OWLOntologyChange> getChanges(){
+ return ((ChangesTableModel)getModel()).getChanges();
+ }
+
+
+ class UndoCellRenderer extends DefaultTableCellRenderer{
+
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 6941030561135280273L;
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column) {
+ if(value instanceof LinkLabel){
+ return (LinkLabel)value;
+ }
+
+ return this;
+ }
+
+ }
+}
+
+
Added: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTableModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTableModel.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTableModel.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,87 @@
+package org.dllearner.tools.ore.ui;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.table.AbstractTableModel;
+
+import org.dllearner.tools.ore.OREManager;
+import org.semanticweb.owl.model.OWLOntologyChange;
+import org.semanticweb.owl.model.RemoveAxiom;
+
+public class ChangesTableModel extends AbstractTableModel {
+
+ @Override
+ public boolean isCellEditable(int rowIndex, int columnIndex) {
+ if(columnIndex == 2){
+ return true;
+ }
+ return super.isCellEditable(rowIndex, columnIndex);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 7573340273483900311L;
+
+ private List<OWLOntologyChange> changes;
+
+ public ChangesTableModel(){
+ changes = new ArrayList<OWLOntologyChange>();
+ }
+
+ @Override
+ public int getColumnCount() {
+ return 3;
+ }
+
+ @Override
+ public int getRowCount() {
+ return changes.size();
+ }
+
+ @Override
+ public Object getValueAt(int rowIndex, int columnIndex) {
+ if(columnIndex == 0){
+ if(changes.get(rowIndex) instanceof RemoveAxiom){
+ return "–";
+ } else {
+ return "+";
+ }
+ } else if(columnIndex == 1){
+ return changes.get(rowIndex).getAxiom();
+ }
+ else {
+ return new LinkLabel("Undo");
+ }
+
+ }
+
+ public void addChanges(List<OWLOntologyChange> changes){
+ this.changes.addAll(changes);
+ fireTableDataChanged();
+ }
+
+ public void removeChanges(List<OWLOntologyChange> changes){
+ this.changes.removeAll(changes);
+ fireTableDataChanged();
+ }
+
+ public void removeChange(int rowIndex){
+ List<OWLOntologyChange> undoChanges = new ArrayList<OWLOntologyChange>(1);
+ undoChanges.add(changes.get(rowIndex));
+ this.changes.remove(rowIndex);
+ OREManager.getInstance().getModifier().undoChanges(undoChanges);
+ fireTableDataChanged();
+ }
+
+ public void clear(){
+ this.changes.clear();
+ fireTableDataChanged();
+ }
+
+ public List<OWLOntologyChange> getChanges(){
+ return changes;
+ }
+
+}
Copied: trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionPanel.java (from rev 1830, trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/DescriptionPanel.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionPanel.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionPanel.java 2009-09-02 10:19:41 UTC (rev 1834)
@@ -0,0 +1,136 @@
+/**
+ * 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.tools.ore.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.border.BevelBorder;
+
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.tools.ore.OREManager;
+
+/**
+ * Panel where learned class description is shown, and parts that might occur errors are red colored.
+ * @author Lorenz Buehmann
+ *
+ */
+public class DescriptionPanel extends JPanel{
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -3684937339236885595L;
+
+
+ private Individual ind;
+ private ActionListener aL;
+ private String mode;
+ private boolean correct = false;
+ private Description newClassDescription;
+
+ public DescriptionPanel(Individual ind, ActionListener aL, String mode){
+ super();
+ setBackground(Color.WHITE);
+ setBorder(BorderFactory.createBevelBorder(BevelBorder.LOWERED));
+ this.newClassDescription = OREManager.getInstance().getNewClassDescription().getDescription();
+ this.ind = ind;
+ this.aL = aL;
+ this.mode = mode;
+ if(mode.equals("neg")){
+ for(JLabel jL : OREManager.getInstance().descriptionToJLabelNeg(ind, newClassDescription)){
+ add(jL);
+ if(jL instanceof DescriptionLabel){
+
+ ((DescriptionLabel) jL).setIndOre(ind);
+ ((DescriptionLabel) jL).init();
+ ((DescriptionLabel) jL).addActionListeners(aL);
+
+ }
+
+ }
+ } else if(mode.equals("pos")){
+ for(JLabel jL : OREManager.getInstance().descriptionToJLabelPos(ind, newClassDescription)){
+ add(jL);
+ if(jL instanceof DescriptionLabel){
+
+ ((DescriptionLabel) jL).setIndOre(ind);
+ ((DescriptionLabel) jL).init();
+ ((DescriptionLabel) jL).addActionListeners(aL);
+
+ }
+
+ }
+ }
+ }
+
+ /**
+ * Updates the panel.
+ */
+ public void updatePanel(){
+ for(Component c : getComponents()){
+ if(c instanceof JLabel){
+ remove(c);
+ }
+ }
+// ore.updateReasoner();
+ correct = true;
+ if (mode.equals("neg")) {
+ for (JLabel jL : OREManager.getInstance().descriptionToJLabelNeg(ind, newClassDescription)) {
+ add(jL);
+ if (jL instanceof DescriptionLabel) {
+ ((DescriptionLabel) jL).setIndOre(ind);
+ ((DescriptionLabel) jL).init();
+ ((DescriptionLabel) jL).addActionListeners(aL);
+ correct = false;
+
+ }
+ }
+ } else if(mode.equals("pos")){
+ for (JLabel jL : OREManager.getInstance().descriptionToJLabelPos(ind, newClassDescription)) {
+ add(jL);
+ if (jL instanceof DescriptionLabel) {
+ ((DescriptionLabe...
[truncated message content] |
