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[DL-Learner SVN] SF.net SVN: dl-learner:[3952] trunk
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From: <lor...@us...> - 2013-05-06 10:34:57
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Revision: 3952
http://sourceforge.net/p/dl-learner/code/3952
Author: lorenz_b
Date: 2013-05-06 10:34:52 +0000 (Mon, 06 May 2013)
Log Message:
-----------
Improved Latex output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java 2013-05-05 14:56:53 UTC (rev 3951)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java 2013-05-06 10:34:52 UTC (rev 3952)
@@ -26,6 +26,8 @@
private String apiKey = "8fadfa2c-47de-4487-a1f5-b7af7378d693";
private String serviceURL = "http://rest.bioontology.org/bioportal/ontologies";
+ private boolean initialized = false;
+
private List<OntologyRepositoryEntry> entries = new ArrayList<OntologyRepositoryEntry>();
@Override
@@ -41,6 +43,7 @@
@Override
public void initialize() {
refresh();
+ initialized = true;
}
@Override
@@ -90,6 +93,9 @@
@Override
public Collection<OntologyRepositoryEntry> getEntries() {
+ if(!initialized){
+ initialize();
+ }
return entries;
}
@@ -121,8 +127,6 @@
for(OntologyRepositoryEntry entry : entries){
System.out.println("Loading " + entry.getOntologyShortName());
System.out.println("From " + entry.getPhysicalURI());
- OWLOntology ont = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(entry.getPhysicalURI()));
- System.out.println(ont.getAxiomCount());
}
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-05 14:56:53 UTC (rev 3951)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 10:34:52 UTC (rev 3952)
@@ -4,6 +4,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.io.StringWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
@@ -21,6 +22,8 @@
import org.aksw.commons.util.Pair;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
+import org.coode.owlapi.latex.LatexObjectVisitor;
+import org.coode.owlapi.latex.LatexWriter;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.SparqlEndpointKS;
@@ -62,6 +65,8 @@
private Connection conn;
private boolean fancyLatex = false;
+ private boolean dlSyntax = false;
+ private boolean formatNumbers = true;
public OWLAxiomPatternDetectionEvaluation() {
initDBConnection();
@@ -239,22 +244,41 @@
ps.setString(1, repository.getName());
avgNumberOfAboxAxioms = count(ps);
- latexTable +=
- repository.getName() + "&" +
- numberOfOntologies + "&" +
- numberOfErrorOntologies + "&" +
- minNumberOfLogicalAxioms + "&" +
- avgNumberOfLogicalAxioms + "&" +
- maxNumberOfLogicalAxioms + "&" +
- minNumberOfTboxAxioms + "&" +
- avgNumberOfTboxAxioms + "&" +
- maxNumberOfTboxAxioms + "&" +
- minNumberOfRboxAxioms + "&" +
- avgNumberOfRboxAxioms + "&" +
- maxNumberOfRboxAxioms + "&" +
- minNumberOfAboxAxioms + "&" +
- avgNumberOfAboxAxioms + "&" +
- maxNumberOfAboxAxioms + "\\\\\n";
+ if(formatNumbers){
+ latexTable +=
+ repository.getName() + "} & " +
+ "\\num{" + numberOfOntologies + "} & " +
+ "\\num{" + numberOfErrorOntologies + "} & " +
+ "\\num{" + minNumberOfLogicalAxioms + "} & " +
+ "\\num{" + avgNumberOfLogicalAxioms + "} & " +
+ "\\num{" + maxNumberOfLogicalAxioms + "} & " +
+ "\\num{" + minNumberOfTboxAxioms + "} & " +
+ "\\num{" + avgNumberOfTboxAxioms + "} & " +
+ "\\num{" + maxNumberOfTboxAxioms + "} & " +
+ "\\num{" + minNumberOfRboxAxioms + "} & " +
+ "\\num{" + avgNumberOfRboxAxioms + "} & " +
+ "\\num{" + maxNumberOfRboxAxioms + "} & " +
+ "\\num{" + minNumberOfAboxAxioms + "} & " +
+ "\\num{" + avgNumberOfAboxAxioms + "} & " +
+ "\\num{" + maxNumberOfAboxAxioms + "}\\\\\n";
+ } else {
+ latexTable +=
+ repository.getName() + " & " +
+ numberOfOntologies + " & " +
+ numberOfErrorOntologies + " & " +
+ minNumberOfLogicalAxioms + " & " +
+ avgNumberOfLogicalAxioms + " & " +
+ maxNumberOfLogicalAxioms + " & " +
+ minNumberOfTboxAxioms + " & " +
+ avgNumberOfTboxAxioms + " & " +
+ maxNumberOfTboxAxioms + " & " +
+ minNumberOfRboxAxioms + " & " +
+ avgNumberOfRboxAxioms + " & " +
+ maxNumberOfRboxAxioms + " & " +
+ minNumberOfAboxAxioms + " & " +
+ avgNumberOfAboxAxioms + " & " +
+ maxNumberOfAboxAxioms + "\\\\\n";
+ }
} catch (SQLException e) {
e.printStackTrace();
@@ -271,22 +295,34 @@
}
private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
+ StringWriter sw = new StringWriter();
+ LatexWriter w = new LatexWriter(sw);
+ LatexObjectVisitor renderer = new LatexObjectVisitor(w, df);
String latexTable = "\\begin{table}\n";
- latexTable += "\\begin{tabular}{lrr}\n";
+ latexTable += "\\begin{tabular}{lrrr}\n";
latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies & tf-idf \\\\\\midrule\n";
for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
OWLAxiom axiom = entry.getKey();
Integer frequency = entry.getValue().getKey();
- Integer idf = entry.getValue().getValue();
+ Integer df = entry.getValue().getValue();
if(axiom != null){
String axiomColumn = axiomRenderer.render(axiom);
if(fancyLatex){
axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
}
- latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
+ if(dlSyntax){
+ axiom.accept(renderer);
+ axiomColumn = sw.toString();sw.getBuffer().setLength(0);
+
+ }
+ if(formatNumbers){
+ latexTable += axiomColumn + " & " + "\\num{" + frequency + "} & " + df + "\\\\\n";
+ } else {
+ latexTable += axiomColumn + " & " + frequency + " & " + df + "\\\\\n";
+ }
}
}
latexTable += "\\bottomrule\n\\end{tabular}\n";
@@ -394,6 +430,16 @@
return rs.getInt(1);
}
+ private double tf_idf(int nrOfOccurrences, int nrOfOntologies, int nrOfOntologiesWithAxiom){
+ double tf = nrOfOccurrences;
+ double idf = Math.log10(nrOfOntologies / nrOfOntologiesWithAxiom);
+ return tf * idf;
+ }
+
+ private double popularity(int totalNrOfOntologies, int patternFrequency, int nrOfOntologiesWithPattern){
+ return (double)Math.log10(patternFrequency) * (nrOfOntologiesWithPattern / (double)totalNrOfOntologies);
+ }
+
public static void main(String[] args) throws Exception {
// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
boolean analyzeRepositories = true;
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