- new revision of the string distance alignments

src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java

 /*
  * $Id$
  *
- * Copyright (C) INRIA Rhne-Alpes, 2003-2005
+ * Copyright (C) INRIA Rhne-Alpes, 2003-2006
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published by
@@ -100,11 +100,25 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
       // This is a 1:1 alignment in fact
       else setType("11");
 
-      getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
-      getSimilarity().compute( params );
+      sim.initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
+      sim.compute( params );
+      if ( params.getParameter("printMatrix") != null ) printDistanceMatrix(params);
       extract( getType(), params );
     }
 
+    public void printDistanceMatrix( Parameters params ){
+	System.out.println("\\documentclass{article}\n");
+	System.out.println("\\usepackage{graphics}\n");
+	System.out.println("\\begin{document}\n");
+	System.out.println("\\begin{figure}");
+	sim.printClassSimilarityMatrix("tex");
+	System.out.println();
+	sim.printPropertySimilarityMatrix("tex");
+	System.out.println("\\caption{Class distance with measure "+(String)params.getParameter("stringFunction")+"}");
+	System.out.println("\\end{figure}");
+	System.out.println("\n\\end{document}");
+    }
+
     /**
      * Extract the alignment form the Similarity
      * There are theoretically 16 types of extractors composing the
@@ -192,7 +206,6 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
 			  found = true; max = val; ind2 = current;
 		      }
 		  }
-		  System.err.println(ind1+" -- "+ind2+" = "+max);
 		  if ( found ) addAlignCell(ind1,ind2, "=", max);
 	      }
 	  }

src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java

 /*
  * $Id$
  *
- * Copyright (C) INRIA Rhne-Alpes, 2003-2005
+ * Copyright (C) INRIA Rhne-Alpes, 2003-2006
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published by
@@ -23,6 +23,7 @@ package fr.inrialpes.exmo.align.impl;
 import java.util.Iterator;
 import java.util.HashMap;
 import java.net.URI;
+import java.text.NumberFormat;
 
 import org.semanticweb.owl.model.OWLOntology;
 import org.semanticweb.owl.model.OWLClass;
@@ -57,15 +58,22 @@ public abstract class MatrixMeasure implements Similarity {
     public int nbclass2 = 0; // number of classes in onto2
     public int nbprop1 = 0; // number of classes in onto1
     public int nbprop2 = 0; // number of classes in onto2
+    public int nbind1 = 0; // number of individuals in onto1
+    public int nbind2 = 0; // number of individuals in onto2
     public int i, j = 0;     // index for onto1 and onto2 classes
     public int l1, l2 = 0;   // length of strings (for normalizing)
     public HashMap classlist2 = null; // onto2 classes
     public HashMap classlist1 = null; // onto1 classes
     public HashMap proplist2 = null; // onto2 properties
     public HashMap proplist1 = null; // onto1 properties
+    public HashMap indlist2 = null; // onto2 individuals
+    public HashMap indlist1 = null; // onto1 individuals
+
+    private NumberFormat numFormat = null; // printing
 
     public double clmatrix[][];   // distance matrix
     public double prmatrix[][];   // distance matrix
+    public double indmatrix[][];   // distance matrix
 	
     public void initialize( OWLOntology onto1, OWLOntology onto2, Alignment align ){
 	initialize( onto1, onto2 );
@@ -79,6 +87,8 @@ public abstract class MatrixMeasure implements Similarity {
 	classlist1 = new HashMap(); // onto1 classes
 	proplist2 = new HashMap(); // onto2 properties
 	proplist1 = new HashMap(); // onto1 properties
+	indlist2 = new HashMap(); // onto2 instances
+	indlist1 = new HashMap(); // onto1 instances
 
 	try {
 	    // Create class lists
@@ -104,6 +114,15 @@ public abstract class MatrixMeasure implements Similarity {
 		proplist1.put( it.next(), new Integer(nbprop1) );
 	    }
 	    prmatrix = new double[nbprop1+1][nbprop2+1];
+	    // Create individual lists
+	    for ( Iterator it = onto2.getIndividuals().iterator(); it.hasNext(); nbind2++ ){
+		indlist2.put( it.next(), new Integer(nbind2) );
+	    }
+	    for ( Iterator it = onto1.getIndividuals().iterator(); it.hasNext(); nbind1++ ){
+		indlist1.put( it.next(), new Integer(nbind1)  );
+	    }
+	    indmatrix = new double[nbind1+1][nbind2+1];
+
 	} catch (OWLException e) { e.printStackTrace(); };
     }
 
@@ -117,6 +136,15 @@ public abstract class MatrixMeasure implements Similarity {
 		    clmatrix[((Integer)classlist1.get(cl1)).intValue()][((Integer)classlist2.get(cl2)).intValue()] = measure( cl1, cl2 );
 		}
 	    }
+	    // Compute distances on individuals
+	    // (this comes first because otherwise, it2 is defined)
+	    for ( Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ){
+		OWLIndividual ind2 = (OWLIndividual)it2.next();
+		for ( Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext(); ){
+		    OWLIndividual ind1 = (OWLIndividual)it1.next();
+		    indmatrix[((Integer)indlist1.get(ind1)).intValue()][((Integer)indlist2.get(ind2)).intValue()] = measure( ind1, ind2 );
+		}
+	    }
 	    // Compute distances on properties
 	    ConcatenatedIterator it2 = new
 		ConcatenatedIterator(onto2.getObjectProperties().iterator(),
@@ -131,13 +159,11 @@ public abstract class MatrixMeasure implements Similarity {
 		    prmatrix[((Integer)proplist1.get(pr1)).intValue()][((Integer)proplist2.get(pr2)).intValue()] = measure( pr1, pr2 );
 		}
 	    }
-	} catch (OWLException e) { e.printStackTrace(); }
+	} catch (Exception e) { e.printStackTrace(); }
     }
 
     public double getIndividualSimilarity( OWLIndividual i1, OWLIndividual i2 ){
-	// JE: non finished...
-        int i,j = 0;
-	return 0.;
+	return indmatrix[((Integer)indlist1.get(i1)).intValue()][((Integer)indlist2.get(i2)).intValue()];
     }
     public double getClassSimilarity( OWLClass c1, OWLClass c2 ){
 	return clmatrix[((Integer)classlist1.get(c1)).intValue()][((Integer)classlist2.get(c2)).intValue()];
@@ -145,4 +171,37 @@ public abstract class MatrixMeasure implements Similarity {
     public double getPropertySimilarity( OWLProperty p1, OWLProperty p2 ){
 	return prmatrix[((Integer)proplist1.get(p1)).intValue()][((Integer)proplist2.get(p2)).intValue()];
     }
+
+    // Not an efficient access...
+    public void printClassSimilarityMatrix( String type ){
+	// Number format class to format the values
+	numFormat = NumberFormat.getInstance();
+	numFormat.setMinimumFractionDigits( 2 );
+	numFormat.setMaximumFractionDigits( 2 );
+	System.out.print("\\begin{tabular}{r|");
+	for ( int i = 0; i < nbclass1 ; i++ ) System.out.print("c");
+	System.out.println("}");
+	try {
+	    for ( Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ){
+		OWLClass cl1 = (OWLClass)it1.next();
+		System.out.print(" & \\rotatebox{90}{"+cl1.getURI().getFragment()+"}");
+	    }
+	    System.out.println(" \\\\ \\hline");
+	    for ( Iterator it2 = onto2.getClasses().iterator(); it2.hasNext(); ){
+		OWLClass cl2 = (OWLClass)it2.next();
+		System.out.print(cl2.getURI().getFragment());
+		for ( Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ){
+		    OWLClass cl1 = (OWLClass)it1.next();
+		    System.out.print(" & "+numFormat.format(clmatrix[((Integer)classlist1.get(cl1)).intValue()][((Integer)classlist2.get(cl2)).intValue()]));
+		}
+		System.out.println("\\\\");
+	    }
+	} catch (OWLException e) { e.printStackTrace(); };
+	System.out.println("\n\\end{tabular}");
+    }
+
+    // Considered not useful so far
+    public void printPropertySimilarityMatrix( String type ){};
+    public void printIndividualSimilarityMatrix( String type ){};
+
 }

src/fr/inrialpes/exmo/align/impl/Similarity.java

 /*
  * $Id$
  *
- * Copyright (C) INRIA Rhne-Alpes, 2004
+ * Copyright (C) INRIA Rhne-Alpes, 2004, 2006
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published by
@@ -54,9 +54,19 @@ public interface Similarity
     public double getClassSimilarity( OWLClass c1, OWLClass c2 );
     public double getPropertySimilarity( OWLProperty p1, OWLProperty p2);
     public double getIndividualSimilarity( OWLIndividual i1, OWLIndividual i2 );
+
+    public void printClassSimilarityMatrix( String type );
+    public void printPropertySimilarityMatrix( String type );
+    public void printIndividualSimilarityMatrix( String type );
+
     // New implementation
-    public double measure( OWLClass c1, OWLClass c2 ) throws OWLException;
-    public double measure( OWLProperty p1, OWLProperty p2) throws OWLException;
-    public double measure( OWLIndividual i1, OWLIndividual i2 ) throws OWLException;
+    // JE: this is better as a new implementation.
+    // however, currently the implementation does not follow it:
+    // the abstract matrix class provides the get- accessors and the 
+    // concrete classes implement measure as their computation function.
+    // This is not clean. What should be done is:
+    public double measure( OWLClass c1, OWLClass c2 ) throws Exception;
+    public double measure( OWLProperty p1, OWLProperty p2) throws Exception;
+    public double measure( OWLIndividual i1, OWLIndividual i2 ) throws Exception;
 }
 

src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java

+/*
+ * $Id: StringDistAlignment.java 149 2005-06-17 08:25:34Z euzenat $
+ *
+ * Copyright (C) INRIA Rhne-Alpes, 2003-2006
+ *
+ * This program 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 2 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program 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, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
+ */
+
+package fr.inrialpes.exmo.align.impl.method; 
+
+import java.util.Iterator;
+import java.util.Hashtable;
+import java.lang.reflect.Method;
+
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLProperty;
+import org.semanticweb.owl.model.OWLIndividual;
+import org.semanticweb.owl.model.OWLException;
+
+import fr.inrialpes.exmo.align.impl.DistanceAlignment;
+import fr.inrialpes.exmo.align.impl.MatrixMeasure;
+import fr.inrialpes.exmo.align.impl.Similarity;
+
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentProcess;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Parameters;
+
+/**
+ * Represents an OWL ontology alignment. An ontology comprises a number of
+ * collections. Each ontology has a number of classes, properties and
+ * individuals, along with a number of axioms asserting information
+ * about those objects.
+ *
+ * An improvement of that class is that, since it is based on names only,
+ * it can match freely property names with class names...
+ *
+ * @author Jrme Euzenat
+ * @version $Id: NameEqAlignment.java 149 2005-06-17 08:25:34Z euzenat $ 
+ */
+
+public class StringDistAlignment extends DistanceAlignment implements AlignmentProcess {
+    
+    Method dissimilarity = null;
+
+    /** Creation **/
+    public StringDistAlignment( OWLOntology onto1, OWLOntology onto2 ){
+	super( onto1, onto2 );
+	setSimilarity( new MatrixMeasure() {
+		public double measure( OWLClass cl1, OWLClass cl2 ) throws Exception{
+		    String[] params = { cl1.getURI().getFragment(), cl2.getURI().getFragment() };
+		    //if ( debug > 4 ) 
+		    return ((Double)dissimilarity.invoke( null, params )).doubleValue();
+		}
+		public double measure( OWLProperty pr1, OWLProperty pr2 ) throws Exception{
+		    String[] params = { pr1.getURI().getFragment(), pr2.getURI().getFragment() };
+		    return ((Double)dissimilarity.invoke( null, params )).doubleValue();
+		}
+		public double measure( OWLIndividual id1, OWLIndividual id2 ) throws Exception{
+		    String[] params = { id1.getURI().getFragment(), id2.getURI().getFragment() };
+		    return ((Double)dissimilarity.invoke( null, params )).doubleValue();
+		}
+	    } );
+	setType("**");
+    };
+
+    /* Processing */
+    public void align( Alignment alignment, Parameters params ) throws AlignmentException, OWLException {
+	//ignore alignment;
+	double threshold = 1.; // threshold above which distances are to high
+
+	// Get function from params
+	String f = (String)params.getParameter("stringFunction");
+	try {
+	    String fname = "equalDistance";
+	    if ( f != null ) fname = f.trim();
+	    Class sClass = Class.forName("java.lang.String");
+	    Class[] mParams = { sClass, sClass };
+	    dissimilarity = Class.forName("fr.inrialpes.exmo.align.impl.method.StringDistances").getMethod( fname, mParams );
+	} catch (Exception e) { throw new AlignmentException("Missing Class or method");};
+	//NoSuchMethodException, ClassNotFoundException
+
+	// Initialize matrix
+	getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
+
+	// Compute similarity/dissimilarity
+	getSimilarity().compute( params );
+
+	// Print matrix if asked
+	if ( params.getParameter("printMatrix") != null ) printDistanceMatrix( params );
+
+	// Extract alignment
+	extract( type, params );
+    }
+}