From b0d7974c18ea8625b8b5d0599f87165a49351340 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Mon, 27 Nov 2006 23:32:07 +0000
Subject: [PATCH] - Displays diagrams of performances of algorithms depending
on the problem
---
.../exmo/align/util/GroupOutput.java | 363 ++++++++++++++++++
1 file changed, 363 insertions(+)
create mode 100644 src/fr/inrialpes/exmo/align/util/GroupOutput.java
diff --git a/src/fr/inrialpes/exmo/align/util/GroupOutput.java b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
new file mode 100644
index 00000000..78cfe4ec
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
@@ -0,0 +1,363 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) 2003 The University of Manchester
+ * Copyright (C) 2003 The University of Karlsruhe
+ * Copyright (C) 2003-2006, INRIA Rhône-Alpes
+ * Copyright (C) 2004, Université de Montréal
+ *
+ * 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
+ * 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser 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.
+ */
+
+/* This program evaluates the results of several ontology aligners
+ and generates a LaTeX diagram for each of these
+*/
+package fr.inrialpes.exmo.align.util;
+
+import org.semanticweb.owl.model.OWLOntology;
+
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentProcess;
+import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Parameters;
+import org.semanticweb.owl.align.Evaluator;
+
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.io.FileOutputStream;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.BufferedWriter;
+import java.io.OutputStreamWriter;
+import java.net.URI;
+import java.lang.Double;
+import java.lang.Integer;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+
+import org.xml.sax.SAXException;
+
+import gnu.getopt.LongOpt;
+import gnu.getopt.Getopt;
+
+import fr.inrialpes.exmo.align.parser.AlignmentParser;
+
+/** A basic class for synthesizing the alignment results of an algorithm by a
+ * precision recall graph.
+ *
+ * These graphs are however computed on averaging the precision recall/graphs
+ * on test directories instead of recording the actual precision recall graphs
+ * which would amount at recoding all the valid and invalid alignment cells and
+ * their level.
+ *
+ * <pre>
+ * java -cp procalign.jar fr.inrialpes.exmo.align.util.GenPlot [options]
+ * </pre>
+ *
+ * where the options are:
+ * <pre>
+ * -o filename --output=filename
+ * -c --color
+ * -d debug --debug=level
+ * -l list of compared algorithms
+ * -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) each directory contains a the alignment files (one per algorithm) for that test and the
+ * reference alignment file.
+ *
+ * If output is
+ * requested (<CODE>-o</CODE> flags), then output will be written to
+ * <CODE>output</CODE> if present, stdout by default. In case of the Latex output, there are numerous files generated (regardless the <CODE>-o</CODE> flag).
+ *
+ * <pre>
+ * $Id$
+ * </pre>
+ *
+ * @author Jérôme Euzenat
+ */
+
+public class GroupOutput {
+
+ static int SIZE = 16;// Nb of cells = 2^ = 16
+ static int cellSpec[][] = { {101}, //liph=0
+ {201, 202, 203, 204, 205, 206, 207, 208, 209, 210}, //phi=1
+ {221},//lip=2
+ {224},//lph=3
+ {225,228,230,231},//hil=4
+ {232,237,238},//lp=5
+ {233,239,240},//li=6
+ {236},//lh=7
+ {249},//ph=8
+ {248,251,252},//ip=9
+ {250},//hi=10
+ {241,246,247},//l=11
+ {253,258,259},//p=12
+ {257},//h=13
+ {254,260,261},//i=14
+ {262,265,266} };//emptyset=15
+ Parameters params = null;
+ Vector listAlgo;
+ String fileNames = "";
+ String outFile = null;
+ String type = "tex";
+ String color = null;
+ int debug = 0;
+ Hashtable loaded = null;
+ PrintWriter output = null;
+
+ public static void main(String[] args) {
+ try { new GroupOutput().run( args ); }
+ catch (Exception ex) { ex.printStackTrace(); };
+ }
+
+ public void run(String[] args) throws Exception {
+ LongOpt[] longopts = new LongOpt[8];
+ loaded = new Hashtable();
+
+ longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
+ longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
+ longopts[2] = new LongOpt("color", LongOpt.OPTIONAL_ARGUMENT, null, 'c');
+ longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
+ longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
+ longopts[6] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
+
+ Getopt g = new Getopt("", args, "ho:c::d::l:t:", longopts);
+ int c;
+ String arg;
+
+ while ((c = g.getopt()) != -1) {
+ switch (c) {
+ case 'h' :
+ usage();
+ return;
+ case 'o' :
+ /* Write output here */
+ outFile = g.getOptarg();
+ break;
+ case 'c' :
+ /* Cell color */
+ arg = g.getOptarg();
+ if ( arg != null ) {
+ color = arg.trim();
+ } else color = "blue";
+ break;
+ case 't' :
+ /* Type of output (tex/tsv(/html/xml/ascii)) */
+ type = g.getOptarg();
+ break;
+ case 'l' :
+ /* List of filename */
+ fileNames = g.getOptarg();
+ break;
+ case 'd' :
+ /* Debug level */
+ arg = g.getOptarg();
+ if ( arg != null ) debug = Integer.parseInt(arg.trim());
+ else debug = 4;
+ break;
+ }
+ }
+
+ // JE: StringTokenizer is obsoleted in Java 1.4 in favor of split: to change
+ listAlgo = new Vector();
+ StringTokenizer st = new StringTokenizer(fileNames,",");
+ while (st.hasMoreTokens()) {
+ listAlgo.add(st.nextToken());
+ }
+
+ params = new BasicParameters();
+ if (debug > 0) params.setParameter("debug", new Integer(debug-1));
+
+ params.setParameter("step", new Integer(SIZE));
+
+ // Set output file
+ OutputStream stream;
+ if (outFile == null) {
+ stream = System.out;
+ } else {
+ stream = new FileOutputStream(outFile);
+ }
+ output = new PrintWriter (
+ new BufferedWriter(
+ new OutputStreamWriter( stream, "UTF-8" )), true);
+
+ // Header
+ if ( type.equals("tex") ) {
+ output.println("\\documentclass[11pt]{book}");
+ output.println();
+ output.println("\\usepackage{pgf}");
+ output.println("\\usepackage{tikz}");
+ output.println("\\usepackage{pgflibraryshapes}");
+ output.println();
+ output.println("\\begin{document}");
+ output.println("\\date{today}");
+ output.println("");
+ }
+ // Process
+ iterateAlgorithm( );
+ // Trailer
+ if ( type.equals("tex") ) {
+ output.println("\\end{document}");
+ output.println();
+ }
+
+ }
+
+ public void iterateAlgorithm(){
+ // for all alignments there,
+ for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; ) {
+ String algo = (String)e.nextElement();
+ if ( debug > 0 ) System.err.println("Algorithm: "+algo);
+ // type
+ if ( type.equals("tex") ) {
+ printPGFTeX( algo, iterateCells( algo ) );
+ } else System.err.println("Flag -t "+type+" : not implemented yet");
+ }
+ }
+
+ public double[] iterateCells( String algo ){
+ double[] cells = new double[SIZE];
+ for ( int i = 0; i < SIZE; i++ ){
+ cells[i] = iterateTests( algo, cellSpec[i] );
+ }
+ return cells;
+ }
+
+ public double iterateTests( String algo, int[] tests ){
+ File dir = (new File(System.getProperty("user.dir")));
+ double result = 0.0;
+ for ( int i=0; i<tests.length; i++ ){//size() or length
+ if ( debug > 1 ) System.err.println(" tests: "+tests[i]);
+ String prefix = dir.toURI().toString()+"/"+tests[i]+"/";
+ PRecEvaluator evaluator = (PRecEvaluator)eval( prefix+"refalign.rdf", prefix+algo+".rdf");
+ result = result + evaluator.getFmeasure();
+ }
+ // Unload the ontologies.
+ try {
+ for ( Enumeration e = loaded.elements() ; e.hasMoreElements(); ){
+ OWLOntology o = (OWLOntology)e.nextElement();
+ o.getOWLConnection().notifyOntologyDeleted( o );
+ }
+ } catch (Exception ex) { System.err.println(ex); };
+ return (double)result/(double)tests.length;
+ }
+
+ public Evaluator eval( String alignName1, String alignName2 ) {
+ Evaluator eval = null;
+ try {
+ int nextdebug;
+ if ( debug < 3 ) nextdebug = 0;
+ else nextdebug = debug - 3;
+ // Load alignments
+ AlignmentParser aparser1 = new AlignmentParser( nextdebug );
+ Alignment align1 = aparser1.parse( alignName1, loaded );
+ if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
+ AlignmentParser aparser2 = new AlignmentParser( nextdebug );
+ Alignment align2 = aparser2.parse( alignName2, loaded );
+ if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
+ // Create evaluator object
+ eval = new PRecEvaluator( align1, align2 );
+ // Compare
+ params.setParameter( "debug", new Integer( nextdebug ) );
+ eval.eval( params ) ;
+ } catch (Exception ex) {
+ // The returned value must be 0
+ eval = new PRecEvaluator( (Alignment)null, (Alignment)null );
+ ((PRecEvaluator)eval).init();
+ System.err.println(ex);
+ }
+ return eval;
+ }
+
+ public void printPGFTeX( String algo, double[] cells ){
+ output.println("\n%% Plot generated by GroupOutput of alignapi");
+ output.println("\\begin{figure}[!h]");
+ output.println("\\begin{center}");
+ output.println("\\begin{tikzpicture}");
+
+ output.println("\\draw (-.5,2.) node[anchor=east] {labels};");
+ output.println("\\draw (0,2.) node[diamond,minimum size=.5cm"+colorFormat(cells[11])+"] {"+stringFormat(cells[11])+"}; % l");
+ output.println("\\draw (0,1.) node[diamond,minimum size=.5cm"+colorFormat(cells[5])+"] {"+stringFormat(cells[5])+"}; % lp");
+ output.println("\\draw (0.5,1.5) node[diamond,minimum size=.5cm"+colorFormat(cells[2])+"] {"+stringFormat(cells[2])+"}; % lip");
+ output.println("\\draw (1.,2.) node[diamond,minimum size=.5cm"+colorFormat(cells[6])+"] {"+stringFormat(cells[6])+"}; %li");
+ output.println("");
+ output.println("\\draw (-.5,0.) node[anchor=east] {properties};");
+ output.println("\\draw (-0.5,-0.5) node[diamond,minimum size=.5cm"+colorFormat(cells[9])+"] {"+stringFormat(cells[9])+"}; % ip");
+ output.println("\\draw (0,0) node[diamond,minimum size=.5cm"+colorFormat(cells[12])+"] {"+stringFormat(cells[12])+"}; %p");
+ output.println("\\draw (.5,.5) node[diamond,minimum size=.5cm"+colorFormat(cells[3])+"] {"+stringFormat(cells[3])+"}; % lph");
+ output.println("\\draw (1.,1.) node[diamond,minimum size=.5cm"+colorFormat(cells[0])+"] {"+stringFormat(cells[0])+"}; % liph");
+ output.println("\\draw (1.5,1.5) node[diamond,minimum size=.5cm"+colorFormat(cells[4])+"] {"+stringFormat(cells[4])+"}; %hil");
+ output.println("\\draw (2.,2.) node[diamond,minimum size=.5cm"+colorFormat(cells[14])+"] {"+stringFormat(cells[14])+"}; %i");
+ output.println("\\draw (2.5,2.0) node[anchor=west] {instances};");
+ output.println("");
+ output.println("\\draw (2.,1.) node[diamond,minimum size=.5cm"+colorFormat(cells[10])+"] {"+stringFormat(cells[10])+"}; % hi");
+ output.println("\\draw (1.5,0.5) node[diamond,minimum size=.5cm"+colorFormat(cells[1])+"] {"+stringFormat(cells[1])+"}; % phi");
+ output.println("\\draw (1.,0) node[diamond,minimum size=.5cm"+colorFormat(cells[8])+"] {"+stringFormat(cells[8])+"}; % ph");
+ output.println("\\draw (2.,0) node[diamond,minimum size=.5cm"+colorFormat(cells[13])+"] {"+stringFormat(cells[13])+"}; % h");
+ output.println("\\draw (2.5,0.) node[anchor=west] {hierarchy};");
+ output.println("\\draw (2.5,-0.5) node[diamond,minimum size=.5cm"+colorFormat(cells[7])+"] {"+stringFormat(cells[7])+"}; % hl");
+
+
+ output.println("\\end{tikzpicture} ");
+ output.println("\\caption{"+algo+" evaluation on F-measure (the darkest the best).}\\label{fig:diag"+algo+"}");
+ output.println("\\end{center}");
+ output.println("\\end{figure}");
+ }
+
+ public void printTSV( double[][] result ) {
+ }
+
+ public String stringFormat(double f){
+ String result;
+ // JE: Must add the test is the value is Not a number, print NaN.
+ if ( f != f ) result = "N";
+ else {
+ int tmp = (int)(f*100);
+ int dec = tmp%100;
+ if( (int)(f*1000)%10 >= 5 ) dec++;
+ if ( tmp >= 100 || dec >= 100 ) result = "1.0";
+ else {
+ result = ".";
+ if (dec < 10) result = result+"0";
+ result = result+dec;
+ }
+ }
+ return result;
+ }
+
+ public String colorFormat(double f){
+ if ( color == null ) return "";
+ else return ",fill="+color+"!"+(int)(f*100);
+ }
+
+ public void usage() {
+ System.out.println("usage: GenPlot [options]");
+ System.out.println("options are:");
+ System.out.println("\t--type=tsv|tex|(html|xml) -t tsv|tex|(html|xml)\tSpecifies the output format");
+ System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
+ System.out.println("\t--color=color -c color\tSpecifies if the output must color even lines of the output");
+ System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
+ System.out.println("\t--help -h\t\t\tPrint this message");
+ }
+}
--
GitLab