From 3dc28a9251f18a2066bcbe91fbe19863dc783a16 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Sat, 17 Dec 2011 18:54:13 +0000
Subject: [PATCH] - Implemented LaTeX output for GroupEval
---
html/relnotes.html | 3 +-
.../inrialpes/exmo/align/cli/GroupEval.java | 634 +++++++++++-------
2 files changed, 389 insertions(+), 248 deletions(-)
diff --git a/html/relnotes.html b/html/relnotes.html
index c138c22c..daf714c9 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -73,7 +73,8 @@ with a warning:
<li>Implemented <tt>extractss</tt> for ** alignments in <tt>DistanceAlignment</tt> (impl)</li>
<li>Changed default type of <tt>StringDistAlignment</tt> to "?*" for
preserving the previous behaviour (impl)</li>
-<li>Added level lines in the triangle display of <tt>GroupEval</tt> (util)</li>
+<li>Added level lines in the triangle display of <tt>GroupEval</tt> (cli)</li>
+<li>Implemented LaTeX output in <tt>GroupEval</tt> (cli)</li>
<li>Added <tt>BasicAlignment.deleteAllCells()</tt> (impl)</li>
<li>Added a guard in <tt>loadOntology</tt> for OWLAPI 3.0, in case the
ontology has no URI (ontowrap)</li>
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
index fdc7b9a9..458446d4 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -38,6 +38,7 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
import java.io.File;
import java.io.PrintStream;
import java.io.FileOutputStream;
+import java.io.FileNotFoundException;
import java.lang.Integer;
import java.util.Hashtable;
import java.util.Vector;
@@ -280,9 +281,21 @@ public class GroupEval {
* This does not only print the results but compute the average as well
*/
public void print( Vector<Vector> result ) {
- if ( type.equals("html") ) printHTML( result );
- else if ( type.equals("tex") ) printLATEX( result );
- else if ( type.equals("triangle") ) printTRIANGLE( result );
+ PrintStream writer = null;
+ try {
+ if ( filename == null ) {
+ writer = System.out;
+ } else {
+ writer = new PrintStream(new FileOutputStream( filename ));
+ }
+ if ( type.equals("html") ) printHTML( result, writer );
+ else if ( type.equals("tex") ) printLATEX( result, writer );
+ else if ( type.equals("triangle") ) printTRIANGLE( result, writer );
+ } catch ( FileNotFoundException fnfex) {
+ fnfex.printStackTrace();
+ } finally {
+ writer.close();
+ }
}
/**
@@ -290,7 +303,7 @@ public class GroupEval {
* Added level lines provides by Christian Meilicke (U. Mannheim)
* See his program in comment below
*/
- public void printTRIANGLE( Vector<Vector> result ) {
+ public void printTRIANGLE( Vector<Vector> result, PrintStream writer ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -323,62 +336,62 @@ public class GroupEval {
}
}
}
- System.out.println("\\documentclass[11pt]{book}");
- System.out.println();
- System.out.println("\\usepackage{pgf}");
- System.out.println("\\usepackage{tikz}");
- System.out.println();
- System.out.println("\\begin{document}");
- System.out.println("\\date{today}");
- System.out.println("");
- System.out.println("\n%% Plot generated by GenPlot of alignapi");
- System.out.println("\\begin{tikzpicture}[cap=round]");
- System.out.println("% Draw grid");
- //System.out.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
- System.out.println("\\draw[|-|] (-0,0) -- (10,0);");
- System.out.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
- System.out.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
- System.out.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
-
- System.out.println("%% Level lines for recall");
- System.out.println("\\draw[dashed] (10,0) arc (0:60:10cm) node[anchor=south east] {{\\tiny R=1.}};");
- System.out.println("\\draw[dotted,very thin] (9,0) arc (0:63:9cm) node[anchor=south east] {{\\tiny R=.9}};");
- System.out.println("\\draw[dotted,very thin] (8,0) arc (0:66:8cm) node[anchor=south east] {{\\tiny R=.8}};");
- System.out.println("\\draw[dotted,very thin] (7,0) arc (0:70:7cm) node[anchor=south east] {{\\tiny R=.7}};");
- System.out.println("\\draw[dotted,very thin] (6,0) arc (0:73:6cm) node[anchor=south east] {{\\tiny R=.6}};");
- System.out.println("\\draw[dotted,very thin] (5,0) arc (0:76:5cm) node[anchor=south east] {{\\tiny R=.5}};");
- System.out.println("\\draw[dotted,very thin] (4,0) arc (0:78:4cm) node[anchor=south east] {{\\tiny R=.4}};");
- System.out.println("\\draw[dotted,very thin] (3,0) arc (0:80:3cm) node[anchor=south east] {{\\tiny R=.3}};");
- System.out.println("\\draw[dotted,very thin] (2,0) arc (0:82:2cm) node[anchor=south east] {{\\tiny R=.2}};");
- System.out.println("\\draw[dotted,very thin] (1,0) arc (0:84:1cm) node[anchor=south east] {{\\tiny R=.1}};");
- System.out.println("%% Level lines for precision");
- System.out.println("\\draw[dashed] (0,0) arc (180:120:10cm) node[anchor=south west] {{\\tiny P=1.}};");
- System.out.println("\\draw[dotted,very thin] (1,0) arc (180:117:9cm) node[anchor=south west] {{\\tiny P=.9}};");
- System.out.println("\\draw[dotted,very thin] (2,0) arc (180:114:8cm) node[anchor=south west] {{\\tiny P=.8}};");
- System.out.println("\\draw[dotted,very thin] (3,0) arc (180:110:7cm) node[anchor=south west] {{\\tiny P=.7}};");
- System.out.println("\\draw[dotted,very thin] (4,0) arc (180:107:6cm) node[anchor=south west] {{\\tiny P=.6}};");
- System.out.println("\\draw[dotted,very thin] (5,0) arc (180:105:5cm) node[anchor=south west] {{\\tiny P=.5}};");
- System.out.println("\\draw[dotted,very thin] (6,0) arc (180:103:4cm) node[anchor=south west] {{\\tiny P=.4}};");
- System.out.println("\\draw[dotted,very thin] (7,0) arc (180:100:3cm) node[anchor=south west] {{\\tiny P=.3}};");
- System.out.println("\\draw[dotted,very thin] (8,0) arc (180:96:2cm) node[anchor=south west] {{\\tiny P=.2}};");
- System.out.println("\\draw[dotted,very thin] (9,0) arc (180:90:1cm) node[anchor=south west] {{\\tiny P=.1}};");
- System.out.println("%% Level lines for F-measure");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.56,3.29) (1.55,3.10) (2.46,2.68) (3.31,2.05) (4.12,1.19) (5.00,0.00) (6.42,1.79) (9.44,3.29)};");
- System.out.println("\\draw (0.56,3.29) node[anchor=south west] {\\tiny{F=0.5}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.92,4.19) (1.96,4.05) (2.95,3.78) (3.93,3.48) (5.00,3.32) (6.56,3.63) (9.08,4.19)};");
- System.out.println("\\draw (0.92,4.19) node[anchor=south west] {\\tiny{F=0.6}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (1.45,5.19) (2.59,5.11) (3.74,4.98) (5.00,4.90) (6.73,5.03) (8.55,5.19)};");
- System.out.println("\\draw (1.45,5.19) node[anchor=south west] {\\tiny{F=0.7}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (2.22,6.29) (3.54,6.27) (5.00,6.24) (6.91,6.28) (7.78,6.29)};");
- System.out.println("\\draw (2.22,6.29) node[anchor=south west] {\\tiny{F=0.8}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (3.35,7.47) (5.00,7.48) (6.65,7.47)};");
- System.out.println("\\draw (3.35,7.47) node[anchor=south west] {\\tiny{F=0.9}};");
-
- System.out.println("\\draw (0,-0.3) node {$recall$};");
- System.out.println("\\draw (10,-0.3) node {$precision$};");
- //System.out.println("\\draw (0,-0.3) node {0.}; ");
- //System.out.println("\\draw (10,-0.3) node {1.}; ");
- System.out.println("% Plots");
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\usepackage{pgf}");
+ writer.println("\\usepackage{tikz}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GroupEval of alignapi");
+ writer.println("\\begin{tikzpicture}[cap=round]");
+ writer.println("% Draw grid");
+ //writer.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
+ writer.println("\\draw[|-|] (-0,0) -- (10,0);");
+ writer.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
+ writer.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
+ writer.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
+
+ writer.println("%% Level lines for recall");
+ writer.println("\\draw[dashed] (10,0) arc (0:60:10cm) node[anchor=south east] {{\\tiny R=1.}};");
+ writer.println("\\draw[dotted,very thin] (9,0) arc (0:63:9cm) node[anchor=south east] {{\\tiny R=.9}};");
+ writer.println("\\draw[dotted,very thin] (8,0) arc (0:66:8cm) node[anchor=south east] {{\\tiny R=.8}};");
+ writer.println("\\draw[dotted,very thin] (7,0) arc (0:70:7cm) node[anchor=south east] {{\\tiny R=.7}};");
+ writer.println("\\draw[dotted,very thin] (6,0) arc (0:73:6cm) node[anchor=south east] {{\\tiny R=.6}};");
+ writer.println("\\draw[dotted,very thin] (5,0) arc (0:76:5cm) node[anchor=south east] {{\\tiny R=.5}};");
+ writer.println("\\draw[dotted,very thin] (4,0) arc (0:78:4cm) node[anchor=south east] {{\\tiny R=.4}};");
+ writer.println("\\draw[dotted,very thin] (3,0) arc (0:80:3cm) node[anchor=south east] {{\\tiny R=.3}};");
+ writer.println("\\draw[dotted,very thin] (2,0) arc (0:82:2cm) node[anchor=south east] {{\\tiny R=.2}};");
+ writer.println("\\draw[dotted,very thin] (1,0) arc (0:84:1cm) node[anchor=south east] {{\\tiny R=.1}};");
+ writer.println("%% Level lines for precision");
+ writer.println("\\draw[dashed] (0,0) arc (180:120:10cm) node[anchor=south west] {{\\tiny P=1.}};");
+ writer.println("\\draw[dotted,very thin] (1,0) arc (180:117:9cm) node[anchor=south west] {{\\tiny P=.9}};");
+ writer.println("\\draw[dotted,very thin] (2,0) arc (180:114:8cm) node[anchor=south west] {{\\tiny P=.8}};");
+ writer.println("\\draw[dotted,very thin] (3,0) arc (180:110:7cm) node[anchor=south west] {{\\tiny P=.7}};");
+ writer.println("\\draw[dotted,very thin] (4,0) arc (180:107:6cm) node[anchor=south west] {{\\tiny P=.6}};");
+ writer.println("\\draw[dotted,very thin] (5,0) arc (180:105:5cm) node[anchor=south west] {{\\tiny P=.5}};");
+ writer.println("\\draw[dotted,very thin] (6,0) arc (180:103:4cm) node[anchor=south west] {{\\tiny P=.4}};");
+ writer.println("\\draw[dotted,very thin] (7,0) arc (180:100:3cm) node[anchor=south west] {{\\tiny P=.3}};");
+ writer.println("\\draw[dotted,very thin] (8,0) arc (180:96:2cm) node[anchor=south west] {{\\tiny P=.2}};");
+ writer.println("\\draw[dotted,very thin] (9,0) arc (180:90:1cm) node[anchor=south west] {{\\tiny P=.1}};");
+ writer.println("%% Level lines for F-measure");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.56,3.29) (1.55,3.10) (2.46,2.68) (3.31,2.05) (4.12,1.19) (5.00,0.00) (6.42,1.79) (9.44,3.29)};");
+ writer.println("\\draw (0.56,3.29) node[anchor=south west] {\\tiny{F=0.5}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.92,4.19) (1.96,4.05) (2.95,3.78) (3.93,3.48) (5.00,3.32) (6.56,3.63) (9.08,4.19)};");
+ writer.println("\\draw (0.92,4.19) node[anchor=south west] {\\tiny{F=0.6}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (1.45,5.19) (2.59,5.11) (3.74,4.98) (5.00,4.90) (6.73,5.03) (8.55,5.19)};");
+ writer.println("\\draw (1.45,5.19) node[anchor=south west] {\\tiny{F=0.7}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (2.22,6.29) (3.54,6.27) (5.00,6.24) (6.91,6.28) (7.78,6.29)};");
+ writer.println("\\draw (2.22,6.29) node[anchor=south west] {\\tiny{F=0.8}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (3.35,7.47) (5.00,7.48) (6.65,7.47)};");
+ writer.println("\\draw (3.35,7.47) node[anchor=south west] {\\tiny{F=0.9}};");
+
+ writer.println("\\draw (0,-0.3) node {$recall$};");
+ writer.println("\\draw (10,-0.3) node {$precision$};");
+ //writer.println("\\draw (0,-0.3) node {0.}; ");
+ //writer.println("\\draw (10,-0.3) node {1.}; ");
+ writer.println("% Plots");
int k = 0;
for ( String m: listAlgo ) {
double precision = (double)correctVect[k]/foundVect[k];
@@ -387,16 +400,321 @@ public class GroupEval {
double a = ((prec2-(recall*recall)+1)/2);
double b = java.lang.Math.sqrt( prec2 - (a*a) );
a = a*10; b = b*10; //for printing scale 10.
- System.out.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
- System.out.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ writer.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
+ writer.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ k++;
+ }
+ writer.println("\\end{tikzpicture}");
+ writer.println();
+ writer.println("\\end{document}");
+ }
+
+ public void printHTML( Vector<Vector> result, PrintStream writer ) {
+ // variables for computing iterative harmonic means
+ int expected = 0; // expected so far
+ int foundVect[]; // found so far
+ int correctVect[]; // correct so far
+ long timeVect[]; // time so far
+ Formatter formatter = new Formatter(writer);
+
+ fsize = format.length();
+ // JE: the h-means computation should be put out as well
+ // Print the header
+ 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>
+ for ( String m : listAlgo ) {
+ writer.println("<colgroup align='center' span='"+fsize+"' />");
+ }
+ // For each file do a
+ writer.println("<thead valign='top'><tr><th>algo</th>");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
+ }
+ writer.println("</tr></thead><tbody><tr><td>test</td>");
+ // for each algo <td>Prec.</td><td>Rec.</td>
+ for ( String m : listAlgo ) {
+ for ( int i = 0; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ writer.print("Prec.");
+ } else if ( format.charAt(i) == 'f' ) {
+ writer.print("FMeas.");
+ } else if ( format.charAt(i) == 'o' ) {
+ writer.print("Over.");
+ } else if ( format.charAt(i) == 't' ) {
+ writer.print("Time");
+ } else if ( format.charAt(i) == 'r' ) {
+ writer.print("Rec.");
+ }
+ writer.println("</td>");
+ }
+ //writer.println("<td>Prec.</td><td>Rec.</td>");
+ }
+ writer.println("</tr></tbody><tbody>");
+ foundVect = new int[ listAlgo.size() ];
+ correctVect = new int[ listAlgo.size() ];
+ timeVect = new long[ listAlgo.size() ];
+ for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctVect[k] = 0;
+ timeVect[k] = 0;
+ }
+ // </tr>
+ // For each directory <tr>
+ boolean colored = false;
+ for ( Vector test : result ) {
+ int nexpected = -1;
+ if ( colored == true && color != null ){
+ colored = false;
+ writer.println("<tr bgcolor=\""+color+"\">");
+ } else {
+ colored = true;
+ writer.println("<tr>");
+ };
+ // Print the directory <td>bla</td>
+ writer.println("<td>"+(String)test.get(0)+"</td>");
+ // For each record print the values <td>bla</td>
+ Enumeration f = test.elements();
+ f.nextElement();
+ for( int k = 0 ; f.hasMoreElements() ; k++) {
+ PRecEvaluator eval = (PRecEvaluator)f.nextElement();
+ if ( eval != null ){
+ // iterative H-means computation
+ if ( nexpected == -1 ){
+ expected += eval.getExpected();
+ nexpected = 0;
+ }
+ foundVect[k] += eval.getFound();
+ correctVect[k] += eval.getCorrect();
+ timeVect[k] += eval.getTime();
+
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", eval.getPrecision());
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", eval.getFmeasure());
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", eval.getOverall());
+ } else if ( format.charAt(i) == 't' ) {
+ if ( eval.getTime() == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", eval.getTime());
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", eval.getRecall());
+ }
+ writer.println("</td>");
+ }
+ } else {
+ writer.println("<td>n/a</td><td>n/a</td>");
+ }
+ }
+ writer.println("</tr>");
+ }
+ writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
+ // Here we are computing a sheer average.
+ // While in the column results we print NaN when the returned
+ // alignment is empty,
+ // here we use the real values, i.e., add 0 to both correctVect and
+ // foundVect, so this is OK for computing the average.
+ int k = 0;
+ // ???
+ for ( String m : listAlgo ) {
+ double precision = (double)correctVect[k]/foundVect[k];
+ double recall = (double)correctVect[k]/expected;
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", precision);
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", recall * (2 - (1 / precision)));
+ } else if ( format.charAt(i) == 't' ) {
+ if ( timeVect[k] == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", timeVect[k]);
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", recall);
+ }
+ writer.println("</td>");
+ };
+ k++;
+ }
+ writer.println("</tr>");
+ writer.println("</tbody></table>");
+ writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
+ writer.println("NaN: division per zero, likely due to empty alignment.</small></p>");
+ if ( embedded != true ) writer.println("</body></html>");
+ }
+
+ public void printLATEX( Vector<Vector> result, PrintStream writer ) {
+ // variables for computing iterative harmonic means
+ int expected = 0; // expected so far
+ int foundVect[]; // found so far
+ int correctVect[]; // correct so far
+ long timeVect[]; // time so far
+ Formatter formatter = new Formatter(writer);
+
+ fsize = format.length();
+ // JE: the h-means computation should be put out as well
+ // Print the header
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GroupEval of alignapi");
+ writer.println("\\setlength{\\tabcolsep}{3pt} % May be changed");
+ writer.println("\\begin{table}");
+ writer.print("\\begin{tabular}{|l||");
+ for ( int i = listAlgo.size(); i > 0; i-- ) {
+ for ( int j = fsize; j > 0; j-- ) writer.print("c");
+ writer.print("|");
+ }
+ writer.println("}");
+ writer.println("\\hline");
+ // For each file do a
+ writer.print("algo");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.print(" & \\multicolumn{"+fsize+"}{c|}{"+m+"}");
+ }
+ writer.println(" \\\\ \\hline");
+ writer.print("test");
+ // for each algo <td>Prec.</td><td>Rec.</td>
+ for ( String m : listAlgo ) {
+ for ( int i = 0; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ writer.print("Prec.");
+ } else if ( format.charAt(i) == 'f' ) {
+ writer.print("FMeas.");
+ } else if ( format.charAt(i) == 'o' ) {
+ writer.print("Over.");
+ } else if ( format.charAt(i) == 't' ) {
+ writer.print("Time");
+ } else if ( format.charAt(i) == 'r' ) {
+ writer.print("Rec.");
+ }
+ }
+ }
+ writer.println(" \\\\ \\hline");
+ foundVect = new int[ listAlgo.size() ];
+ correctVect = new int[ listAlgo.size() ];
+ timeVect = new long[ listAlgo.size() ];
+ for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctVect[k] = 0;
+ timeVect[k] = 0;
+ }
+ for ( Vector test : result ) {
+ int nexpected = -1;
+ // Print the directory
+ writer.print((String)test.get(0));
+ // For each record print the values
+ Enumeration f = test.elements();
+ f.nextElement();
+ for( int k = 0 ; f.hasMoreElements() ; k++) {
+ PRecEvaluator eval = (PRecEvaluator)f.nextElement();
+ if ( eval != null ){
+ // iterative H-means computation
+ if ( nexpected == -1 ){
+ expected += eval.getExpected();
+ nexpected = 0;
+ }
+ foundVect[k] += eval.getFound();
+ correctVect[k] += eval.getCorrect();
+ timeVect[k] += eval.getTime();
+
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", eval.getPrecision());
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", eval.getFmeasure());
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", eval.getOverall());
+ } else if ( format.charAt(i) == 't' ) {
+ if ( eval.getTime() == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", eval.getTime());
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", eval.getRecall());
+ }
+ }
+ } else {
+ writer.print(" & \\multicolumn{"+fsize+"}{c|}{n/a}");
+ }
+ }
+ writer.println(" \\\\");
+ }
+ writer.print("H-mean");
+ // Here we are computing a sheer average.
+ // While in the column results we print NaN when the returned
+ // alignment is empty,
+ // here we use the real values, i.e., add 0 to both correctVect and
+ // foundVect, so this is OK for computing the average.
+ int k = 0;
+ // ???
+ for ( String m : listAlgo ) {
+ double precision = (double)correctVect[k]/foundVect[k];
+ double recall = (double)correctVect[k]/expected;
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", precision);
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", recall * (2 - (1 / precision)));
+ } else if ( format.charAt(i) == 't' ) {
+ if ( timeVect[k] == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", timeVect[k]);
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", recall);
+ }
+ };
k++;
}
- System.out.println("\\end{tikzpicture}");
- System.out.println();
- System.out.println("\\end{document}");
+ writer.println(" \\\\ \\hline");
+ writer.println("\\end{tabular}");
+ writer.println("\\caption{Plot generated by GroupEval of alignapi \\protect\\footnote{n/a: result alignment not provided or not readable -- NaN: division per zero, likely due to empty alignment.}}");
+ writer.println("\\end{table}");
+ writer.println("\\end{document}");
}
- /*
+ public void usage() {
+ System.out.println("usage: GroupEval [options]");
+ System.out.println("options are:");
+ System.out.println("\t--format=prfot -r prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
+ // Apparently not implemented
+ //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
+ System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
+ System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
+
+ System.out.println("\t--type=html|xml|tex|ascii|triangle -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");
+ 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");
+ System.err.print("\n"+GroupEval.class.getPackage().getImplementationTitle()+" "+GroupEval.class.getPackage().getImplementationVersion());
+ System.err.println(" ($Id$)\n");
+ }
+
+/*
// Here is the code provided by Christian Meilicke and modified by JE
// For computing the F-measure level line in the Triangle representation
// The class can be put in FMeasureLines.java and compiled.
@@ -493,13 +811,9 @@ public class FMeasureLines {
return new double[]{pp, pr};
}
}
- */
-
- public void printLATEX( Vector result ) {
- }
+*/
- /* A few comments on how and why computing "weighted harmonic means"
- (J�r�me Euzenat)
+/* A few comments on how and why computing "weighted harmonic means" (J�r�me Euzenat)
Let Ai be the found alignment for test i, let Ri be the reference alignment for test i.
Let |A| be the size of A, i.e., the number of correspondences.
@@ -543,182 +857,8 @@ and
correctVect[k] / expected
which the program does...
- */
- public void printHTML( Vector<Vector> result ) {
- // variables for computing iterative harmonic means
- int expected = 0; // expected so far
- int foundVect[]; // found so far
- int correctVect[]; // correct so far
- long timeVect[]; // time so far
- PrintStream writer = null;
- fsize = format.length();
- // JE: the writer should be put out
- // JE: the h-means computation should be put out as well
- try {
- // Print result
- if ( filename == null ) {
- writer = System.out;
- } else {
- writer = new PrintStream(new FileOutputStream( filename ));
- }
- Formatter formatter = new Formatter(writer);
-
- // Print the header
- 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>
- for ( String m : listAlgo ) {
- writer.println("<colgroup align='center' span='"+fsize+"' />");
- }
- // For each file do a
- writer.println("<thead valign='top'><tr><th>algo</th>");
- // for each algo <td spancol='2'>name</td>
- for ( String m : listAlgo ) {
- writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
- }
- writer.println("</tr></thead><tbody><tr><td>test</td>");
- // for each algo <td>Prec.</td><td>Rec.</td>
- for ( String m : listAlgo ) {
- for ( int i = 0; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- writer.print("Prec.");
- } else if ( format.charAt(i) == 'f' ) {
- writer.print("FMeas.");
- } else if ( format.charAt(i) == 'o' ) {
- writer.print("Over.");
- } else if ( format.charAt(i) == 't' ) {
- writer.print("Time");
- } else if ( format.charAt(i) == 'r' ) {
- writer.print("Rec.");
- }
- writer.println("</td>");
- }
- //writer.println("<td>Prec.</td><td>Rec.</td>");
- }
- writer.println("</tr></tbody><tbody>");
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
- foundVect[k] = 0;
- correctVect[k] = 0;
- timeVect[k] = 0;
- }
- // </tr>
- // For each directory <tr>
- boolean colored = false;
- for ( Vector test : result ) {
- int nexpected = -1;
- if ( colored == true && color != null ){
- colored = false;
- writer.println("<tr bgcolor=\""+color+"\">");
- } else {
- colored = true;
- writer.println("<tr>");
- };
- // Print the directory <td>bla</td>
- writer.println("<td>"+(String)test.get(0)+"</td>");
- // For each record print the values <td>bla</td>
- Enumeration f = test.elements();
- f.nextElement();
- for( int k = 0 ; f.hasMoreElements() ; k++) {
- PRecEvaluator eval = (PRecEvaluator)f.nextElement();
- if ( eval != null ){
- // iterative H-means computation
- if ( nexpected == -1 ){
- expected += eval.getExpected();
- nexpected = 0;
- }
- foundVect[k] += eval.getFound();
- correctVect[k] += eval.getCorrect();
- timeVect[k] += eval.getTime();
-
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", eval.getPrecision());
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", eval.getFmeasure());
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", eval.getOverall());
- } else if ( format.charAt(i) == 't' ) {
- if ( eval.getTime() == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", eval.getTime());
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", eval.getRecall());
- }
- writer.println("</td>");
- }
- } else {
- writer.println("<td>n/a</td><td>n/a</td>");
- }
- }
- writer.println("</tr>");
- }
- writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
- // Here we are computing a sheer average.
- // While in the column results we print NaN when the returned
- // alignment is empty,
- // here we use the real values, i.e., add 0 to both correctVect and
- // foundVect, so this is OK for computing the average.
- int k = 0;
- // ???
- for ( String m : listAlgo ) {
- double precision = (double)correctVect[k]/foundVect[k];
- double recall = (double)correctVect[k]/expected;
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", precision);
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", recall * (2 - (1 / precision)));
- } else if ( format.charAt(i) == 't' ) {
- if ( timeVect[k] == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", timeVect[k]);
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", recall);
- }
- writer.println("</td>");
- };
- k++;
- }
- writer.println("</tr>");
- writer.println("</tbody></table>");
- writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
- writer.println("NaN: division per zero, likely due to empty alignment.</small></p>");
- if ( embedded != true ) writer.println("</body></html>");
- writer.close();
- } catch (Exception ex) {
- ex.printStackTrace();
- }
- }
+*/
- public void usage() {
- System.out.println("usage: GroupEval [options]");
- System.out.println("options are:");
- System.out.println("\t--format=prfot -r prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
- // Apparently not implemented
- //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
- System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
- System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
- System.out.println("\t--type=html|xml|tex|ascii|triangle -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");
- 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");
- System.err.print("\n"+GroupEval.class.getPackage().getImplementationTitle()+" "+GroupEval.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
- }
}
--
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