- improved LaTeX rendering of PRGRaphs (not perfect yet but close)

- cleaned up some copyright notices
- investigated the PRGraph evaluator algorithm (and make it start at 1/0)

html/relnotes.html

@@ -35,10 +35,12 @@
 <h2>Current SVN trunk version</h2>
 
 <p><ul compact="1">
-<li>Adding HTML Alignement server profile (under development)</li>
-<li>Adding SQL storage support (under development)</li>
 <li>Adding Alignement server (under development)</li>
+<li>Adding SQL storage support (under development)</li>
+<li>Adding HTML Alignement server profile (under development)</li>
+<li>Suppressed outdated "tutorial" from repository (see html/tutorial)</li>
 <li>Corrected Cell id rendering/parse in RDF/XML (rdf:about)</li>
+<li>Improved Precision/recall graph rendering in LaTeX</li>
 </ul></p>
 
 <h2>July 10th, 2006</h2>

src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java

@@ -152,6 +152,7 @@ public class PRGraphEvaluator extends BasicEvaluator {
       // Collect the points that change recall
       // (the other provide lower precision from the same recall
       //  and are not considered)
+      points.add( new Pair( 0., 1. ) );
       for( Iterator it = cellSet.iterator(); it.hasNext(); ){
 	  nbfound++;
 	  Cell c2 = (Cell)it.next();
@@ -175,6 +176,12 @@ public class PRGraphEvaluator extends BasicEvaluator {
 	      }
 	  }
       }
+      // Now if we want to have a regular curve we must penalize those system
+      // that do not reach 100% recall.
+      // for that purpose, and for each other bound we add a point with the worse
+      // precision which is the required recall level divided with the maximum
+      // cardinality possible (i.e., the multiplication of the ontology sizes).
+      points.add( new Pair( 1.0, 0. ) ); // useless because 
 
       // Interpolate curve points at each n-recall level
       // This is inspired form Ray Mooney's program
@@ -194,7 +201,7 @@ public class PRGraphEvaluator extends BasicEvaluator {
 	  if ( precrec.getY() > best ) best = precrec.getY();
 	  j--;
       }
-      precisions[0] = best;
+      precisions[0] = best; // It should be 1. that's why it is now added in points.
 
       return 0.0; // useless
       }

src/fr/inrialpes/exmo/align/util/ExtGroupEval.java

@@ -6,11 +6,6 @@
  * Copyright (C) 2003-2005, INRIA Rhne-Alpes
  * Copyright (C) 2004, Universit de Montral
  *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.  Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
  * 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 the Free Software Foundation; either version 2.1 of
@@ -28,6 +23,8 @@
  */
 
 /* This program evaluates the results of several ontology aligners in a row.
+   It uses the generalisations of precision and recall described in
+   [Ehrig & Euzenat 2005].
 */
 package fr.inrialpes.exmo.align.util;
 
@@ -61,12 +58,13 @@ import gnu.getopt.Getopt;
 
 import fr.inrialpes.exmo.align.parser.AlignmentParser;
 
-/** A basic class for synthesizing the results of a set of alignments provided by
-    different algorithms. The output is a table showing various classical measures
-    for each test and for each algorithm. Average is also computed as Harmonic means.
+/** A basic class for synthesizing the results of a set of alignments provided
+    by different algorithms. The output is a table showing various generalisations
+    of precision and recall for each test and for each algorithm.
+    Average is also computed as Harmonic means.
     
     <pre>
-    java -cp procalign.jar fr.inrialpes.exmo.align.util.GroupEval [options]
+    java -cp procalign.jar fr.inrialpes.exmo.align.util.ExtGroupEval [options]
     </pre>
 
     where the options are:
@@ -79,12 +77,13 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
     -t output --type=output: xml/tex/html/ascii
    </pre>
 
-   The input is taken in the current directory in a set of subdirectories (one per
-   test which will be rendered by a line) each directory contains a number of
-   alignment files (one per algorithms which will be renderer as a column).
+   The input is taken in the current directory in a set of subdirectories
+   (one per test which will be rendered by a line) each directory contains
+   a number of alignment files (one per algorithms which will be renderer
+   as a column).
 
-    If output is requested (<CODE>-o</CODE> flags), then output will be written to
-    <CODE>output</CODE> if present, stdout by default.
+    If output is requested (<CODE>-o</CODE> flags), then output will be
+    written to <CODE>output</CODE> if present, stdout by default.
 
 <pre>
 $Id$
@@ -430,7 +429,7 @@ public class ExtGroupEval {
     public static void usage() {
 	System.out.println("usage: ExtGroupEval [options]");
 	System.out.println("options are:");
-	System.out.println("\t--format=prfmo -r prfmo\tSpecifies the output order (symetric/effort-based/oriented)");
+	System.out.println("\t--format=seo -r seo\tSpecifies the extended measure used (symetric/effort-based/oriented)");
 	System.out.println("\t--dominant=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
 	System.out.println("\t--type=html|xml|tex|ascii -t html|xml|tex|ascii\tSpecifies the output format");
 	System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");

src/fr/inrialpes/exmo/align/util/GenPlot.java

@@ -3,14 +3,9 @@
  *
  * Copyright (C) 2003 The University of Manchester
  * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, INRIA Rhne-Alpes
+ * Copyright (C) 2003-2006, INRIA Rhne-Alpes
  * Copyright (C) 2004, Universit de Montral
  *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.  Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
  * 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 the Free Software Foundation; either version 2.1 of
@@ -295,12 +290,12 @@ public class GenPlot {
     public static void printPGFTex( double[][] result ){
 	int i = 0;
 	String marktable[] = { "+", "*", "x", "-", "|", "o", "asterisk", "star", "oplus", "oplus*", "otimes", "otimes*", "square", "square*", "triangle", "triangle*", "diamond", "diamond*", "pentagon", "pentagon*"};
-	String colortable[] = { "black", "white", "red", "green", "blue", "cyan", "magenta", "yellow" }	;
+	String colortable[] = { "black", "red", "green", "blue", "cyan", "magenta", "yellow" }	;
 	output.println("\\documentclass[11pt]{book}");
 	output.println();
-	output.println("\\usepackage{pgflibraryplotmarks}");
 	output.println("\\usepackage{pgf}");
 	output.println("\\usepackage{tikz}");
+	output.println("\\usepackage{pgflibraryplotmarks}");
 	output.println();
 	output.println("\\begin{document}");
 	output.println("\\date{today}");
@@ -327,19 +322,25 @@ public class GenPlot {
 	output.println("\\begin{tikzpicture}[cap=round]");
 	output.println("% Draw grid");
 	output.println("\\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
-	output.println("\\draw[->] (-0.2,0) -- (10.2,0) node[below] {$recall$}; ");
+	output.println("\\draw[->] (-0.2,0) -- (10.2,0);");
+	output.println("\\draw (5,-0.3) node {$recall$}; ");
 	output.println("\\draw (0,-0.3) node {0.}; ");
 	output.println("\\draw (10,-0.3) node {1.}; ");
-	output.println("\\draw[->] (0,-0.2) -- (0,10.2) node[above] {$precision$}; ");
+	output.println("\\draw[->] (0,-0.2) -- (0,10.2);");
 	output.println("\\draw (-0.3,0) node {0.}; ");
+	output.println("\\draw (-0.3,5) node[rotate=90] {$precision$}; ");
 	output.println("\\draw (-0.3,10) node {1.}; ");
 	output.println("% Plots");
 	for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
-	    output.println("\\draw["+colortable[i%8]+"] plot[mark="+marktable[i%20]+",smooth] file {"+(String)e.nextElement()+".table};");
-	    //output.println("\\draw plot[mark=+,smooth] file {"+(String)e.nextElement()+".table};");
+	    output.println("\\draw["+colortable[i%7]+"] plot[mark="+marktable[i%19]+",smooth] file {"+(String)e.nextElement()+".table};");
 	}
 	// And a legend
 	output.println("% Legend");
+	i = 0;
+	for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
+	    output.println("\\draw["+colortable[i%7]+"] plot[mark="+marktable[i%19]+",smooth] coordinates {("+((i%3)*3+1)+","+(-(i/3)*.8-1)+") ("+((i%3)*3+3)+","+(-(i/3)*.8-1)+")};");
+	    output.println("\\draw["+colortable[i%7]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-.8)+") node {"+(String)e.nextElement()+"};");
+	}
 	output.println("\\end{tikzpicture}");
 	output.println();
 	output.println("\\end{document}");
@@ -361,8 +362,8 @@ public class GenPlot {
 		writer.println("%% Include in PGF tex by:\n");
 		writer.println("%% \\begin{tikzpicture}[cap=round]");
 		writer.println("%% \\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
-		writer.println("%% \\draw[->] (-0.2,0) -- (10.2,0) node[right] {$precision$}; ");
-		writer.println("%% \\draw[->] (0,-0.2) -- (0,10.2) node[above] {$recall$}; ");
+		writer.println("%% \\draw[->] (-0.2,0) -- (10.2,0) node[right] {$recall$}; ");
+		writer.println("%% \\draw[->] (0,-0.2) -- (0,10.2) node[above] {$precision$}; ");
 		writer.println("%% \\draw plot[mark=+,smooth] file {"+algo+".table};");
 		writer.println("%% \\end{tikzpicture}");
 		writer.println();

src/fr/inrialpes/exmo/align/util/GroupEval.java

@@ -3,14 +3,9 @@
  *
  * Copyright (C) 2003 The University of Manchester
  * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, INRIA Rhne-Alpes
+ * Copyright (C) 2003-2006, INRIA Rhne-Alpes
  * Copyright (C) 2004, Universit de Montral
  *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.  Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
  * 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 the Free Software Foundation; either version 2.1 of
@@ -103,6 +98,7 @@ public class GroupEval {
     static String format = "pr";
     static int fsize = 2;
     static String type = "html";
+    static boolean embedded = false;
     static String dominant = "s";
     static Vector listAlgo = null;
     static int debug = 0;
@@ -284,6 +280,14 @@ public class GroupEval {
      * This does not only print the results but compute the average as well
      */
     public static void print( Vector result ) {
+	if ( type.equals("html") ) printHTML( result );
+	else if ( type.equals("tex") ) printLATEX( result );
+    }
+
+    public static void printLATEX( Vector result ) {
+    }
+
+    public static void printHTML( Vector result ) {
 	// variables for computing iterative harmonic means
 	int expected = 0; // expected so far
 	int foundVect[]; // found so far
@@ -301,7 +305,7 @@ public class GroupEval {
 		writer = new PrintStream(new FileOutputStream( filename ));
 	    }
 	    // Print the header
-	    writer.println("<html><head></head><body>");
+	    if ( embedded != true ) writer.println("<html><head></head><body>");
 	    writer.println("<table border='2' frame='sides' rules='groups'>");
 	    writer.println("<colgroup align='center' />");
 	    // for each algo <td spancol='2'>name</td>
@@ -442,7 +446,7 @@ public class GroupEval {
 	    }
 	    writer.println("</tr>");
 	    writer.println("</tbody></table>");
-	    writer.println("</body></html>");
+	    if ( embedded != true ) writer.println("</body></html>");
 	    writer.close();
 	} catch (Exception ex) {
 	    ex.printStackTrace();

src/fr/inrialpes/exmo/align/util/Procalign.java

@@ -6,11 +6,6 @@
  * Copyright (C) 2003-2006, INRIA Rhne-Alpes
  * Copyright (C) 2004, Universit de Montral
  *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.  Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
  * 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 the Free Software Foundation; either version 2.1 of