diff --git a/html/tutorial/tutorial3/MyApp.java b/html/tutorial/tutorial3/MyApp.java
index 176960a7703425721d4544e100dc3fc7b652a97b..995099e619973fc11938ef14d42b7d2cb748e0b7 100644
--- a/html/tutorial/tutorial3/MyApp.java
+++ b/html/tutorial/tutorial3/MyApp.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2009, 2010
+ * Copyright (C) INRIA, 2006-2010
*
* Modifications to the initial code base are copyright of their
* respective authors, or their employers as appropriate. Authorship
@@ -48,11 +48,16 @@ import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
import java.io.File;
import java.net.URI;
+import java.util.Properties;
/**
* MyApp
*
* Takes two files as arguments and align them.
+ * Match them with different matching methods
+ * Merge the results
+ * Selects the threshold that provide the best F-measure
+ * Return the alignment trimmed at that threshold as OWL Axioms
*/
public class MyApp {
@@ -61,6 +66,7 @@ public class MyApp {
URI onto1 = null;
URI onto2 = null;
Properties params = new BasicParameters();
+ int question = 1;
try {
// Loading ontologies
@@ -72,6 +78,7 @@ public class MyApp {
return ;
}
+
// Run two different alignment methods (e.g., ngram distance and smoa)
AlignmentProcess a1 = new StringDistAlignment();
params.setProperty("stringFunction","smoaDistance");
@@ -83,41 +90,59 @@ public class MyApp {
params.setProperty("stringFunction","ngramDistance");
a2.align( (Alignment)null, params );
- // Merge the two results.
- ((BasicAlignment)a1).ingest(a2);
-
- // Threshold at various thresholds
- // Evaluate them against the references
- // and choose the one with the best F-Measure
- AlignmentParser aparser = new AlignmentParser(0);
- // Changed by Angel for Windows
- //Alignment reference = aparser.parse( "file://"+(new File ( "refalign.rdf" ) . getAbsolutePath()) );
- Alignment reference = aparser.parse( (new File ( "refalign.rdf" ) ) . toURL() . toString());
- Evaluator evaluator = new PRecEvaluator( reference, a1 );
+ if ( question == 2 ) {
+ // Clone a1
+ System.err.println( a1.nbCells() );
+ BasicAlignment a3 = (BasicAlignment)(a1.clone());
+ System.err.println( a3.nbCells() );
+
+ // Merge the two results.
+ a3.ingest( a2 );
+ System.err.println( a3.nbCells() );
- double best = 0.;
- Alignment result = null;
- Properties p = new BasicParameters();
- for ( int i = 0; i <= 10 ; i += 2 ){
- a1.cut( ((double)i)/10 );
- // JE: I do not understand why I must create a new one!
- evaluator = new PRecEvaluator( reference, a1 );
- evaluator.eval( p );
- System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure()+" over "+a1.nbCells()+" cells");
- if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
- result = (BasicAlignment)((BasicAlignment)a1).clone();
- best = ((PRecEvaluator)evaluator).getFmeasure();
+ // Invert the alignement
+ Alignment a4 = a3.inverse();
+ System.err.println( a4.nbCells() );
+
+ // Trim above .5
+ a4.cut( .5 );
+ System.err.println( a4.nbCells() );
+ } else {
+ // Merge the two results.
+ ((BasicAlignment)a1).ingest(a2);
+
+ // Trim at various thresholds
+ // Evaluate them against the references
+ // and choose the one with the best F-Measure
+ AlignmentParser aparser = new AlignmentParser(0);
+ // Changed by Angel for Windows
+ //Alignment reference = aparser.parse( "file://"+(new File ( "../refalign.rdf" ) . getAbsolutePath()) );
+ Alignment reference = aparser.parse( new File( "../refalign.rdf" ).toURI() );
+
+ double best = 0.;
+ Alignment result = null;
+ Properties p = new BasicParameters();
+ for ( int i = 0; i <= 10 ; i += 2 ){
+ a1.cut( ((double)i)/10 );
+ // This operation must be repeated because the modifications in a1
+ // are not taken into account otherwise
+ Evaluator evaluator = new PRecEvaluator( reference, a1 );
+ evaluator.eval( p );
+ System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure()+" over "+a1.nbCells()+" cells");
+ if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
+ result = (BasicAlignment)((BasicAlignment)a1).clone();
+ best = ((PRecEvaluator)evaluator).getFmeasure();
+ }
}
+ // Displays it as OWL Rules
+ PrintWriter writer = new PrintWriter (
+ new BufferedWriter(
+ new OutputStreamWriter( System.out, "UTF-8" )), true);
+ AlignmentVisitor renderer = new OWLAxiomsRendererVisitor(writer);
+ result.render(renderer);
+ writer.flush();
+ writer.close();
}
- // Displays it as OWL Rules
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( System.out, "UTF-8" )), true);
- AlignmentVisitor renderer = new OWLAxiomsRendererVisitor(writer);
- a1.render(renderer);
- writer.flush();
- writer.close();
-
} catch (Exception e) { e.printStackTrace(); };
}
}
diff --git a/html/tutorial/tutorial3/Skeleton.java b/html/tutorial/tutorial3/Skeleton.java
index cc47774b1c8556efcaed36add0531ff0a1a5ce12..5744cb6e6923ce36cb12aaf6c1c2118d752e5280 100644
--- a/html/tutorial/tutorial3/Skeleton.java
+++ b/html/tutorial/tutorial3/Skeleton.java
@@ -44,6 +44,7 @@ import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
import java.io.File;
import java.net.URI;
+import java.util.Properties;
/**
* The Skeleton of code for embeding the alignment API
diff --git a/html/tutorial/tutorial3/embed.html b/html/tutorial/tutorial3/embed.html
index 3cc5b146abd521f95068ecbb1b8224124188727a..163eb65ad74d4642f95ef5fc622d39caf2cd324d 100644
--- a/html/tutorial/tutorial3/embed.html
+++ b/html/tutorial/tutorial3/embed.html
@@ -56,11 +56,11 @@ div.logic {
<p>A skeleton of program using the Alignment <abbr>API</abbr> is <a href="Skeleton.java">Skeleton.java</a>. It can be compiled by invoking:</p>
<div class="fragment">
-$ javac -classpath ../../lib/align.jar:../../lib/procalign.jar -d results Skeleton.java
+$ javac -classpath ../../../lib/align.jar:../../../lib/procalign.jar -d results Skeleton.java
</div>
<p>and run by:</p>
<div class="fragment">
-$ java -cp ../../lib/Procalign.jar:results Skeleton file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl
+$ java -cp ../../../lib/Procalign.jar:results Skeleton file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl
</div>
<p>Now considering the <abbr>API</abbr> (that can be consulted through its
@@ -116,6 +116,7 @@ parameters corresponding to "smoaDistance" and "ngramDistance".
a1.align( (Alignment)null, params );
AlignmentProcess a2 = new StringDistAlignment();
a2.init ( onto1, onto2 );
+ params = new BasicParameters();
params.setProperty("stringFunction","ngramDistance");
a2.align( (Alignment)null, params );
</pre>
@@ -159,15 +160,15 @@ corresondences in the resulting alignment.
System.err.println( a1.nbCells() );
BasicAlignment a3 = (BasicAlignment)(a1.clone());
System.err.println( a3.nbCells() );
-
+
// Merge the two results.
a3.ingest( a2 );
System.err.println( a3.nbCells() );
// Invert the alignement
- BasicAlignment a4 = a3.inverse();
+ Alignment a4 = a3.inverse();
System.err.println( a4.nbCells() );
-
+
// Trim above .5
a4.cut( .5 );
System.err.println( a4.nbCells() );
@@ -197,10 +198,12 @@ reference alignment, then creates an instance
of <tt>PRecEvaluator</tt> for computing precision and recall between
the alignment <tt>a1</tt> above with respects to the reference alignment.
<div class="fragment">
+ // Load the reference alignment
AlignmentParser aparser = new AlignmentParser(0);
- Alignment reference = aparser.parse( (new File ( "refalign.rdf" ) ).toURL().toString() );
+ Alignment reference = aparser.parse( new File( "../refalign.rdf" ).toURI() );
+
Evaluator evaluator = new PRecEvaluator( reference, a1 );
- evaluator.eval( new BasicParameters() );
+ evaluator.eval();
</div>
As previously, results are stored within the <tt>Evaluator</tt> object
and are accessed through specific accessors.
@@ -218,17 +221,22 @@ F-measure.
</div>
<div class="explain" id="qu5">
<pre>
+ // Trim at various thresholds
+ // Evaluate them against the references
+ // and choose the one with the best F-Measure
double best = 0.;
Alignment result = null;
Properties p = new BasicParameters();
for ( int i = 0; i <= 10 ; i += 2 ){
a1.cut( ((double)i)/10 );
- evaluator = new PRecEvaluator( reference, a1 );
+ // This operation must be repeated because the modifications in a1
+ // are not taken into account otherwise
+ Evaluator evaluator = new PRecEvaluator( reference, a1 );
evaluator.eval( p );
System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure()+" over "+a1.nbCells()+" cells");
if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
- result = (BasicAlignment)((BasicAlignment)a1).clone();
- best = ((PRecEvaluator)evaluator).getFmeasure();
+ result = (BasicAlignment)((BasicAlignment)a1).clone();
+ best = ((PRecEvaluator)evaluator).getFmeasure();
}
}
</pre>
@@ -260,8 +268,8 @@ alignment selected at the previous exercise as a set of OWL axioms.
<pre>
// Displays it as OWL Rules
PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( System.out, "UTF-8" )), true);
+ new BufferedWriter(
+ new OutputStreamWriter( System.out, "UTF-8" )), true);
AlignmentVisitor renderer = new OWLAxiomsRendererVisitor(writer);
result.render(renderer);
writer.flush();
@@ -292,32 +300,37 @@ alignment selected at the previous exercise as a set of OWL axioms.
// Merge the two results.
((BasicAlignment)a1).ingest(a2);
- // Threshold at various thresholds
- // Evaluate them against the references
- // and choose the one with the best F-Measure
+ // Load the reference alignment
AlignmentParser aparser = new AlignmentParser(0);
- Alignment reference = aparser.parse( (new File ( "refalign.rdf" ) ) . toURL() . toString());
- Evaluator evaluator = new PRecEvaluator( reference, a1 );
+ // Changed by Angel for Windows
+ //Alignment reference = aparser.parse( "file://"+(new File ( "../refalign.rdf" ) . getAbsolutePath()) );
+ Alignment reference = aparser.parse( new File( "../refalign.rdf" ).toURI() );
+ // Trim at various thresholds
+ // Evaluate them against the references
+ // and choose the one with the best F-Measure
double best = 0.;
Alignment result = null;
Properties p = new BasicParameters();
for ( int i = 0; i <= 10 ; i += 2 ){
a1.cut( ((double)i)/10 );
- evaluator = new PRecEvaluator( reference, a1 );
+ // This operation must be repeated because the modifications in a1
+ // are not taken into account otherwise
+ Evaluator evaluator = new PRecEvaluator( reference, a1 );
evaluator.eval( p );
System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure()+" over "+a1.nbCells()+" cells");
if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
- result = (BasicAlignment)((BasicAlignment)a1).clone();
- best = ((PRecEvaluator)evaluator).getFmeasure();
+ result = (BasicAlignment)((BasicAlignment)a1).clone();
+ best = ((PRecEvaluator)evaluator).getFmeasure();
}
}
+
// Displays it as OWL Rules
PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( System.out, "UTF-8" )), true);
+ new BufferedWriter(
+ new OutputStreamWriter( System.out, "UTF-8" )), true);
AlignmentVisitor renderer = new OWLAxiomsRendererVisitor(writer);
- a1.render(renderer);
+ result.render(renderer);
writer.flush();
writer.close();
</pre></div>
@@ -326,22 +339,24 @@ alignment selected at the previous exercise as a set of OWL axioms.
This can be compiled and used through:
</p>
<div class="fragment">
-$ javac -classpath ../../lib/align.jar:../../lib/procalign.jar -d results MyApp.java
-$ java -cp ../../lib/Procalign.jar:results MyApp file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl > results/MyApp.owl
+$ javac -classpath ../../../lib/align.jar:../../../lib/procalign.jar -d results MyApp.java
+$ java -cp ../../../lib/Procalign.jar:results MyApp file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl > results/MyApp.owl
</div>
<p>The execution provides an insight about the best threshold:
<pre>
-Threshold 0.0 : 0.4693877551020408 over 148 cells
-Threshold 0.2 : 0.5227272727272727 over 128 cells
-Threshold 0.4 : 0.5476190476190476 over 120 cells
-Threshold 0.6 : 0.6478873239436619 over 94 cells
-Threshold 0.8 : 0.75 over 72 cells
-Threshold 1.0 : 0.5151515151515151 over 18 cells
+Threshold 0.0 : 0.4999999999999999 over 140 cells
+Threshold 0.2 : 0.5529411764705882 over 122 cells
+Threshold 0.4 : 0.5802469135802468 over 114 cells
+Threshold 0.6 : 0.6861313868613137 over 89 cells
+Threshold 0.8 : 0.7692307692307693 over 69 cells
+Threshold 1.0 : 0.5230769230769231 over 17 cells
</pre>
<p>
<p>A full working solution is <a href="MyApp.java">MyApp.java</a>.</p>
+<div class="logic"><p><b>Advanced question:</b> Can you tell why the stored alignment does not seem to contain 69 cells? (Hint: try to render the alignments in RDF and see what happens)</p></div>
+
<div class="logic"><p><b>More work:</b> You can add a switch like the <tt>-i</tt> switch of <tt>Procalign</tt> so that the main class of the application can be passed at commant-line.</p></div>
<div class="logic"><p><b>Advanced:</b> What about writing an editor for the alignment <abbr>API</abbr>?</p></div>