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[DL-Learner SVN] SF.net SVN: dl-learner:[1284] trunk/src/dl-learner/org/dllearner
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From: <ku...@us...> - 2008-09-27 14:11:01
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Revision: 1284
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1284&view=rev
Author: kurzum
Date: 2008-09-27 14:10:57 +0000 (Sat, 27 Sep 2008)
Log Message:
-----------
prepared experiments
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
Property Changed:
----------------
trunk/src/dl-learner/org/dllearner/test/
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-27 07:48:14 UTC (rev 1283)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-27 14:10:57 UTC (rev 1284)
@@ -24,6 +24,7 @@
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
@@ -45,9 +46,11 @@
import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.configurators.ComponentFactory;
import org.dllearner.core.configurators.ExampleBasedROLComponentConfigurator;
+import org.dllearner.core.configurators.SparqlKnowledgeSourceConfigurator;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.gui.Config;
@@ -56,6 +59,7 @@
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.JamonMonitorLogger;
@@ -122,10 +126,16 @@
NORMAL_10s,
SPARQL_100s,
NORMAL_100s,
- SPARQL_1000_CONCEPT_TESTS,
- NORMAL_1000_CONCEPT_TESTS,
- SPARQL_10000_CONCEPT_TESTS,
- NORMAL_10000_CONCEPT_TESTS};
+ SPARQL_1000_CTESTS,
+ NORMAL_1000_CTESTS,
+ SPARQL_10000_CTESTS,
+ NORMAL_10000_CTESTS,
+ NORMAL_10000_CTESTS_FASTINST,
+
+ SPARQL_10000_CTESTS_SPECIAL_REC2_NOPROP,
+ SPARQL_10000_CTESTS_SPECIAL_REC2_NOCLOSEAFTERRECURSION,
+ SPARQL_10000_CTESTS_SPECIAL_REC1,
+ SPARQL_10000_CTESTS_SPECIAL_REC3};
//private static Class usedReasoner = FastInstanceChecker.class;
@@ -149,8 +159,8 @@
if(onJensMachine){
conductExperiment(Experiments.NORMAL_10s);
conductExperiment(Experiments.NORMAL_100s);
- conductExperiment(Experiments.NORMAL_1000_CONCEPT_TESTS);
- conductExperiment(Experiments.NORMAL_10000_CONCEPT_TESTS);
+ conductExperiment(Experiments.NORMAL_1000_CTESTS);
+ conductExperiment(Experiments.NORMAL_10000_CTESTS);
@@ -159,34 +169,34 @@
/*finished experiments:
* SPARQL_10s
* SPARQL_1000_CONCEPT_TESTS
- * running:
* NORMAL_1000_CONCEPT_TESTS
* SPARQL_10000_CONCEPT_TESTS
* NORMAL_10000_CONCEPT_TESTS
+ * missing:
+ * NORMAL_10s
+ * SPARQL_100s
+ * NORMAL_100s
*
+ * extra:
* */
- for (Experiments exp : Experiments.values()) {
- //if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
- //if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
- //if(exp.equals(Experiments.SPARQL_100s))continue;
- //if(exp.toString().contains("SPARQL"))continue;
- if(exp.equals(Experiments.NORMAL_10s))conductExperiment(exp);
- if(exp.equals(Experiments.SPARQL_100s))conductExperiment(exp);
- if(exp.equals(Experiments.NORMAL_100s))conductExperiment(exp);
- //~ if(exp.equals(Experiments.NORMAL_1000_CONCEPT_TESTS))conductExperiment(exp);
- //~ if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))conductExperiment(exp);
- //~ if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))conductExperiment(exp);
-
- }
+ conductExperiment(Experiments.NORMAL_10s);
+ conductExperiment(Experiments.SPARQL_100s);
+ conductExperiment(Experiments.NORMAL_100s);
+
+ //EXTRA
+ //conductExperiment(Experiments.NORMAL_10000_CTESTS_FASTINST);
+ //conductExperiment(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC2_NOPROP);
+ //conductExperiment(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC2_NOCLOSEAFTERRECURSION);
+ //conductExperiment(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC1);
+ //conductExperiment(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC3);
+
}
// write JaMON report in HTML file
- File jamonlog = new File(dir+"jamon.html");
- Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+
//total.printAndSet("Finished");
logger.warn(total.getAndSet("Finished"));
if(flawInExperiment){
@@ -198,9 +208,15 @@
}
+ public static void writeJamonLog(String filename){
+ File jamonlog = new File(filename);
+ Files.createFile(jamonlog, MonitorFactory.getReport());
+ Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ }
+
public static void conductExperiment(Experiments exp){
- try{
+
//prepare everything
List<String> confs = getFiles();
ComponentManager cm =ComponentManager.getInstance();
@@ -208,6 +224,9 @@
int count = 0;
for (String filename : confs) {
SimpleClock oneExperiment = new SimpleClock();
+ try{
+ //if(count!=64) continue;
+
if (count == nrOfFilesInExperiment){break;}
logger.warn("****"+exp+" "+(count+1) +" from file "+filename);
@@ -274,17 +293,24 @@
nrOfExtractedAxioms.addNumber(0.0);
}
- cm.freeAllComponents();
- fillTable(exp, (count+1));
+ }catch (Exception e) {
+ e.printStackTrace();
+ flawInExperiment = true;
+ logger.warn(t.getLatexString());
+ logger.warn(e);
+
+ }finally{
+ cm.freeAllComponents();
+
+ fillTable(exp, (count+1));
+
+ logger.warn(exp+" "+(count+1)+ " " +oneExperiment.getAndSet("")+"****" );
+ count++;
+ }
- logger.warn(exp+" "+(count+1)+ " " +oneExperiment.getAndSet("")+"****" );
- count++;
}//end for
- }catch (Exception e) {
- e.printStackTrace();
- flawInExperiment = true;
- }
+ writeJamonLog(dir+"jamon"+exp+".html");
reinitStat();
}//endconduct
@@ -296,6 +322,7 @@
try{fileContent = Files.readFile(new File(exampleDir+file));
}catch (Exception e) {
e.printStackTrace();
+ logger.warn(e);
}
ExampleContainer ec = new ExampleContainer(
SetManipulation.stringToInd(getIndividuals(fileContent, true)),
@@ -316,9 +343,13 @@
public static ExampleBasedROLComponent experimentalSetup(Experiments exp,SortedSet<Individual> posExamples, SortedSet<Individual> negExamples ){
ExampleBasedROLComponent la = null;
if(exp.toString().contains("SPARQL"))
- la = prepareSparqlExperiment(posExamples, negExamples);
+ la = prepareSparqlExperiment(exp, posExamples, negExamples);
else if(exp.toString().contains("NORMAL")){
- la = prepareNormalExperiment(posExamples, negExamples);
+ if(exp.equals(Experiments.NORMAL_10000_CTESTS_FASTINST)){
+ la = prepareNormalExperiment(true, posExamples, negExamples);
+ }else{
+ la = prepareNormalExperiment(false, posExamples, negExamples);
+ }
}else {
logger.error("undefined EXPERIMENT" + exp);
System.exit(0);
@@ -334,10 +365,11 @@
c.setMaxExecutionTimeInSeconds(100);
c.setMinExecutionTimeInSeconds(100);
- }else if(exp.toString().contains("1000_CONCEPT_TESTS")){
+ }else if(exp.toString().contains("1000_CTESTS")){
c.setMaxClassDescriptionTests(1000);
- }else if(exp.toString().contains("10000_CONCEPT_TESTS")){
+ }else if(exp.toString().contains("10000_CTESTS")){
c.setMaxClassDescriptionTests(10000);
+
}
//la.getConfigurator();
//appendtoFile
@@ -346,7 +378,7 @@
}
- public static ExampleBasedROLComponent prepareSparqlExperiment(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
+ public static ExampleBasedROLComponent prepareSparqlExperiment(Experiments exp, SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
ExampleBasedROLComponent la = null;
@@ -360,14 +392,26 @@
"http://localhost:2020/bible").toURL(), SetManipulation
.indToString(instances));
- ks.getConfigurator().setCloseAfterRecursion(true);
- ks.getConfigurator().setRecursionDepth(2);
- ks.getConfigurator().setPredefinedEndpoint("LOCALJOSEKIBIBLE");
- ks.getConfigurator().setUseLits(true);
- ks.getConfigurator().setGetAllSuperClasses(true);
- ks.getConfigurator().setGetPropertyInformation(true);
- ks.getConfigurator().setVerbosity("warning");
+ SparqlKnowledgeSourceConfigurator c = ks.getConfigurator();
+ c.setCloseAfterRecursion(true);
+ c.setRecursionDepth(2);
+ c.setPredefinedEndpoint("LOCALJOSEKIBIBLE");
+ c.setUseLits(true);
+ c.setGetAllSuperClasses(true);
+ c.setGetPropertyInformation(true);
+ c.setVerbosity("warning");
+
+ if(exp.equals(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC2_NOPROP)){
+ c.setGetPropertyInformation(false);
+ }else if(exp.equals(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC2_NOCLOSEAFTERRECURSION)){
+ c.setCloseAfterRecursion(false);
+ }else if(exp.equals(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC1)){
+ c.setRecursionDepth(1);
+ }else if(exp.equals(Experiments.SPARQL_10000_CTESTS_SPECIAL_REC3)){
+ c.setRecursionDepth(3);
+ }
+
Set<KnowledgeSource> tmp = new HashSet<KnowledgeSource>();
tmp.add(ks);
// reasoner
@@ -384,17 +428,19 @@
// learning algorithm
la = ComponentFactory.getExampleBasedROLComponent(lp, rs);
la.getConfigurator().setGuaranteeXgoodDescriptions(1);
- Config c = new Config(ComponentManager.getInstance(), ks, f, rs, lp, la);
- new ConfigSave(c).saveFile(new File(tmpFilename));
+ Config conf = new Config(ComponentManager.getInstance(), ks, f, rs, lp, la);
+ new ConfigSave(conf).saveFile(new File(tmpFilename));
}catch (Exception e) {
e.printStackTrace();
+ logger.warn(e);
+ logger.warn("error in sparqlprepare");
flawInExperiment = true;
}
return la;
}
- public static ExampleBasedROLComponent prepareNormalExperiment(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
+ public static ExampleBasedROLComponent prepareNormalExperiment(boolean fic, SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
ExampleBasedROLComponent la = null;
try{
SortedSet<Individual> instances = new TreeSet<Individual>();
@@ -412,11 +458,16 @@
Set<KnowledgeSource> tmp = new HashSet<KnowledgeSource>();
tmp.add(ks);
+
+ ReasonerComponent f = null;
+
// reasoner
- OWLAPIReasoner f = ComponentFactory
- .getOWLAPIReasoner(tmp);
- ReasoningService rs = ComponentManager.getInstance()
- .reasoningService(f);
+ if(fic){
+ f = ComponentFactory.getFastInstanceChecker(tmp);
+ }else{
+ f = ComponentFactory.getOWLAPIReasoner(tmp);
+ }
+ ReasoningService rs = ComponentManager.getInstance().reasoningService(f);
// learning problem
PosNegDefinitionLP lp = ComponentFactory.getPosNegDefinitionLP(rs,
@@ -431,6 +482,8 @@
}catch (Exception e) {
e.printStackTrace();
+ logger.warn(e);
+ logger.warn("error in normalprepare");
flawInExperiment = true;
}
return la;
@@ -439,27 +492,33 @@
public static void initAllComponents(){
ComponentManager cm = ComponentManager.getInstance();
- for(Component c : cm.getLiveComponents()){
+ List<Component> l = new ArrayList<Component>();
+ l.addAll(cm.getLiveComponents());
+
+ for(Component c : l){
+
try{
SimpleClock time = new SimpleClock();
- c.init();
- if (c instanceof SparqlKnowledgeSource) {
+ c.init();
+ if (c instanceof SparqlKnowledgeSource) {
ksinitializationTime.addNumber((double) time.getTime()/1000);
-
}else if (c instanceof OWLFile) {
ksinitializationTime.addNumber((double) time.getTime()/1000);
-
+ }else if (c instanceof FastInstanceChecker) {
+ reasonerInitializationTime.addNumber((double) time.getTime()/1000);
}else if (c instanceof OWLAPIReasoner) {
reasonerInitializationTime.addNumber((double) time.getTime()/1000);
-
}
}catch (Exception e) {
e.printStackTrace();
+ logger.warn(e);
+ logger.warn("error in initAllComponents");
flawInExperiment = true;
}
- }
+ }// end for
+
}
public static void prepareTable(){
Property changes on: trunk/src/dl-learner/org/dllearner/test
___________________________________________________________________
Modified: svn:ignore
- JamonTest.java
JenaAmpBug.java
TestHeapSize.java
+ JamonTest.java
JenaAmpBug.java
TestHeapSize.java
JavaTest.java
Modified: trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java 2008-09-27 07:48:14 UTC (rev 1283)
+++ trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java 2008-09-27 14:10:57 UTC (rev 1284)
@@ -24,6 +24,30 @@
}
+
+ /**
+ * used for regex difficult chars like _ or %
+ * @param s
+ * @param search
+ * @param replacement
+ * @return
+ */
+ public static String myReplaceAll(String s, char search, String replacement ){
+ String ret ="";
+ char[] arr = s.toCharArray();
+ for (int i = 0; i < arr.length; i++) {
+ if(arr[i]==search){
+ ret+=replacement;
+ }else{
+ ret+=arr[i];
+ }
+ }
+ return ret;
+
+ }
+
+
+
public static String doubleToPercent(double d, int decimals, boolean addPercentSign){
String format = (decimals==0)?"00":".";
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-27 07:48:14 UTC (rev 1283)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-27 14:10:57 UTC (rev 1284)
@@ -53,25 +53,35 @@
}
public static void main(String[] args) {
- Table t = new Table("myTable");
- String tableFile = "results/table/myTable";
- TableColumn c1 = new TableColumn("col1", new String[]{"a","b"});
- TableColumn c2 = new TableColumn("col2", new String[]{"c","d"});
- t.addColumn(c1);
- System.out.println(t.getLatexString());
+ boolean production = true;
+ if(production){
+ String tablename = "myTable";
+ String tableFile = "sembib100/sofar/table";
+
+ Table t = createTableFromSerializedColums(tablename, tableFile);
+ Files.createFile(new File(tableFile+".tex"), t.getLatexString());
+
+ }else{
+
+ Table t = new Table("myTable");
+ String tableFile = "results/table/myTable";
+ TableColumn c1 = new TableColumn("col1", new String[]{"a","b"});
+ TableColumn c2 = new TableColumn("col2", new String[]{"c","d"});
+ t.addColumn(c1);
+ System.out.println(t.getLatexString());
+
+ serializeColumns(t, "results/table",tableFile );
+
+ t = createTableFromSerializedColums("myTable", tableFile);
+ System.out.println(t.getLatexString());
+
+ t.addColumn(c2);
+ serializeColumns(t, "results/table",tableFile );
+ t = createTableFromSerializedColums("myTable", tableFile);
+ System.out.println(t.getLatexString());
+ }
- serializeColumns(t, "results/table",tableFile );
- t = createTableFromSerializedColums("myTable", tableFile);
- System.out.println(t.getLatexString());
-
- t.addColumn(c2);
- serializeColumns(t, "results/table",tableFile );
- t = createTableFromSerializedColums("myTable", tableFile);
- System.out.println(t.getLatexString());
-
-
-
}
public String getLatexString(){
@@ -81,23 +91,31 @@
}
String headers = latexRow(getColumnHeaders());
-
+ headers = StringFormatter.myReplaceAll(headers, '_', "\\_");
+ headers = StringFormatter.myReplaceAll(headers, '%', "\\%");
+
String table="";
-
- table += "\\begin{table*}\n";
+ table += "\\documentclass{article}\n";
+ table += "\\usepackage{rotating}\n";
+ table += "\\begin{document}\n";
+ table += "\\begin{sidewaystable*}\n";
table += "\t\\centering\n";
table += "\t\t\\begin{tabular}{"+tabular+"}\n";
table += "\\hline\n";
- table += headers;
+ table += headers.replaceAll("\\_", "\\_");
table += "\\hline\n";
// add here
for (int i = 0; i < getNumberOfRows(); i++) {
- table +=getRowInLatex(i);
+ String tmp = getRowInLatex(i);
+ tmp = StringFormatter.myReplaceAll(tmp, '_', "\\_");
+ tmp = StringFormatter.myReplaceAll(tmp, '%', "\\%");
+ table += tmp;
}
table += "\\end{tabular}\n";
table += "\t\\caption{"+caption+"}\n";
table += "\t\\label{"+label+"}\n";
- table += "\\end{table*}\n\n";
+ table += "\\end{sidewaystable*}\n\n";
+ table += "\\end{document} \n\n";
//List<String> myList = new ArrayList<String>({""});
@@ -166,6 +184,7 @@
String[] columnFiles = Files.readFileAsArray(new File(tableFile));
for (String filename : columnFiles) {
+ if(filename.replaceAll(" ", "").length()==0)continue;
TableColumn col = TableColumn.deSerialize(new File(filename));
//TableColumn col = (TableColumn) Files.readObjectfromFile(new File(filename));
ret.addColumn(col);
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