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Jérôme Euzenat authoredJérôme Euzenat authored
GenPlot.java 12.61 KiB
/*
* $Id$
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
* 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
* 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 in a row.
*/
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.PRGraphEvaluator;
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
* -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 Jrme Euzenat
*/
public class GenPlot {
static int STEP = 10;
static Parameters params = null;
static Vector listAlgo;
static String fileNames = "";
static String outFile = null;
static String type = "tsv";
static int debug = 0;
static Hashtable loaded = null;
static PrintWriter output = null;
public static void main(String[] args) {
try { run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
}
public static 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[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: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 '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(STEP));
// 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);
// type
if ( type.equals("tsv") ){
printTSV( iterateDirectories() );
} else if ( type.equals("tex") ) {
printPGFTex( iterateDirectories() );
} else System.err.println("Flag -t "+type+" : not implemented yet");
}
/**
* Iterate on each subdirectory
* Returns a vector[ each algo ] of vector [ each point ]
* The points are computed by aggregating the values
* (and in the end computing the average)
*/
public static double[][] iterateDirectories (){
File [] subdir = null;
try {
subdir = (new File(System.getProperty("user.dir"))).listFiles();
} catch (Exception e) {
System.err.println("Cannot stat dir "+ e.getMessage());
usage();
}
// Initialize the vector of results
double[][] result = new double[listAlgo.size()][STEP+1];
for( int i=0; i < listAlgo.size(); i++){
for( int j=0; j <= STEP; j++){
result[i][j] = 0.0; }
}
int size = 0;
// Evaluate the results in each directory
for ( int k = subdir.length-1 ; k >= 0; k-- ) {
if( subdir[k].isDirectory() ) {
// eval the alignments in a subdirectory
iterateAlignments( subdir[k], result );
size++;
}
}
// Compute the average by dividing each value by the number of tests
// (not a very good method anyway)
for( int i=0; i < listAlgo.size(); i++){
for( int j=0; j <= STEP; j++){
result[i][j] = result[i][j] / size;
}
}
return result;
}
public static void iterateAlignments ( File dir, double[][] result ) {
String prefix = dir.toURI().toString()+"/";
int i = 0;
if( debug > 0 ) System.err.println("Directory : "+dir);
// for all alignments there,
for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
String algo = (String)e.nextElement();
// call eval
if ( debug > 0 ) System.err.println(" Considering result "+algo+" ("+i+")");
PRGraphEvaluator evaluator = eval( prefix+"refalign.rdf", prefix+algo+".rdf");
// store the result
if ( evaluator != null ){
for( int j = 0; j <= STEP ; j++ ){
result[i][j] = result[i][j] + evaluator.getPrecision(j);
}
}
}
// 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); };
}
public static PRGraphEvaluator eval( String alignName1, String alignName2 ) {
PRGraphEvaluator eval = null;
try {
int nextdebug;
if ( debug < 2 ) nextdebug = 0;
else nextdebug = debug - 2;
// Load alignments
AlignmentParser aparser1 = new AlignmentParser( nextdebug );
Alignment align1 = aparser1.parse( alignName1, loaded );
if ( debug > 1 ) System.err.println(" Alignment structure1 parsed");
AlignmentParser aparser2 = new AlignmentParser( nextdebug );
Alignment align2 = aparser2.parse( alignName2, loaded );
if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
// Create evaluator object
eval = new PRGraphEvaluator( align1, align2 );
// Compare
params.setParameter( "debug", new Integer( nextdebug ) );
eval.eval( params ) ;
// Unload the ontologies.
for ( Enumeration e = loaded.elements() ; e.hasMoreElements(); ){
OWLOntology o = (OWLOntology)e.nextElement();
o.getOWLConnection().notifyOntologyDeleted( o );
}
} catch (Exception ex) { ex.printStackTrace(); };
return eval;
}
/**
* This does average plus plot
*
*/
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*"};
output.println("\\documentclass[11pt]{book}");
output.println();
// This does not work genuinely
//output.println("\\usepackage{pgf,pgflibraryplotmarks}");
output.println("\\usepackage{pgf}");
output.println("\\usepackage{tikz}");
output.println();
output.println("\\begin{document}");
output.println("\\date{today}");
output.println("\n%% Plot generated by GenPlot of alignapi");
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] {$precision$}; ");
output.println("\\draw[->] (0,-0.2) -- (0,10.2) node[above] {$recall$}; ");
output.println("% Plots");
for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
//output.println("\\draw plot[mark="+marktable[i]+",smooth] file {"+(String)e.nextElement()+".table};");
output.println("\\draw plot[mark=+,smooth] file {"+(String)e.nextElement()+".table};");
}
// And a legend
output.println("% Legend");
output.println("\\end{tikzpicture}");
output.println();
output.println("\\end{document}");
i = 0;
for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; i++) {
String algo = (String)e.nextElement();
// Open one file
PrintWriter writer;
try {
writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter(
new FileOutputStream(algo+".table"), "UTF-8" )), true);
// Print header
writer.println("#Curve 0, "+(STEP+1)+" points");
writer.println("#x y type");
writer.println("%% Plot generated by GenPlot of alignapi");
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 plot[mark=+,smooth] file {"+algo+".table};");
writer.println("%% \\end{tikzpicture}");
writer.println();
for( int j = 0; j <= STEP; j++ ){
writer.print((double)j*10/STEP);
writer.println(" "+result[i][j]*10);
}
writer.close(); } catch (Exception ex) { ex.printStackTrace(); }
// UnsupportedEncodingException + FileNotFoundException
}
}
public static void printTSV( double[][] result ) {
// Print first line
for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; ) {
output.print("\t"+(String)e.nextElement() );
}
output.println();
// Print others
for( int j = 0; j <= STEP; j++ ){
output.print((double)j/STEP);
for( int i = 0; i < listAlgo.size(); i++ ){
output.print("\t"+result[i][j]);
}
output.println();
}
}
public static 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--debug[=n] -d [n]\t\tReport debug info at level n");
System.out.println("\t--help -h\t\t\tPrint this message");
}
}