private void runAnalysis(
String sourceOntologyFile,
String sourceOntologyName,
String targetOntologyFile,
String targetOntologyName,
String referenceAlignmentFile) {
LOG.info("Loading ontology " + sourceOntologyFile);
// load source ontology
Ontology sourceOntology = null;
try {
OntologyDefinition sourceOntDef =
new OntologyDefinition(
true, sourceOntologyFile, OntologyLanguage.OWL, OntologySyntax.RDFXML);
OntoTreeBuilder sourceBuilder = new OntoTreeBuilder(sourceOntDef);
sourceBuilder.build();
sourceOntology = sourceBuilder.getOntology();
} catch (Exception e) {
e.printStackTrace();
}
LOG.info("Loading ontology " + targetOntologyFile);
// load target ontology
Ontology targetOntology = null;
try {
OntologyDefinition targetOntDef =
new OntologyDefinition(
true, targetOntologyFile, OntologyLanguage.OWL, OntologySyntax.RDFXML);
OntoTreeBuilder targetBuilder = new OntoTreeBuilder(targetOntDef);
targetBuilder.build();
targetOntology = targetBuilder.getOntology();
} catch (Exception e) {
e.printStackTrace();
}
// set the settings for the matcher
matcherToAnalyze.setSourceOntology(sourceOntology);
matcherToAnalyze.setTargetOntology(targetOntology);
matcherToAnalyze.setPerformSelection(false);
if (matcherToAnalyze.needsParam()) matcherToAnalyze.setParam(prefParams);
matcherToAnalyze.setMaxSourceAlign(prefSourceCardinality);
matcherToAnalyze.setMaxTargetAlign(prefTargetCardinality);
try {
matcherToAnalyze.match();
} catch (Exception e) {
LOG.error("Analysis aborted.", e);
return;
}
// load the reference file
ReferenceAlignmentParameters refParam = new ReferenceAlignmentParameters();
refParam.onlyEquivalence = true;
refParam.fileName = referenceAlignmentFile;
refParam.format = ReferenceAlignmentMatcher.OAEI;
AbstractMatcher referenceAlignmentMatcher;
try {
referenceAlignmentMatcher =
MatcherFactory.getMatcherInstance(ReferenceAlignmentMatcher.class);
} catch (MatcherNotFoundException e1) {
LOG.error("Analysis aborted.", e1);
return;
}
referenceAlignmentMatcher.setParam(refParam);
referenceAlignmentMatcher.setSourceOntology(sourceOntology);
referenceAlignmentMatcher.setTargetOntology(targetOntology);
try {
referenceAlignmentMatcher.match();
} catch (Exception e) {
LOG.error("Analysis aborted.", e);
return;
}
// open the output files
File outputPrecision =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-precision.txt");
File outputRecall =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-recall.txt");
File outputFMeasure =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-fmeasure.txt");
File outputMaxFM =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-max-fmeasure.txt");
try {
BufferedWriter writerPrecision = new BufferedWriter(new FileWriter(outputPrecision));
BufferedWriter writerRecall = new BufferedWriter(new FileWriter(outputRecall));
BufferedWriter writerFMeasure = new BufferedWriter(new FileWriter(outputFMeasure));
BufferedWriter writerMaxFM = new BufferedWriter(new FileWriter(outputMaxFM));
// ok, we ran the matcher, now do the threshold analysis
double maxFMeasure = 0.0;
double maxFMTh = 0.0;
for (double currentThreshold = prefStartThreshold;
currentThreshold < prefEndThreshold;
currentThreshold += prefThresholdIncrement) {
currentThreshold = Utility.roundDouble(currentThreshold, 4);
LOG.info("Selecting with threshold = " + currentThreshold);
matcherToAnalyze.getParam().threshold = currentThreshold;
matcherToAnalyze.select();
ReferenceEvaluationData currentEvaluation =
ReferenceEvaluator.compare(
matcherToAnalyze.getAlignment(), referenceAlignmentMatcher.getAlignment());
writerPrecision.write(
currentThreshold
+ ","
+ Utility.roundDouble(currentEvaluation.getPrecision(), 2)
+ "\n");
writerRecall.write(
currentThreshold + "," + Utility.roundDouble(currentEvaluation.getRecall(), 2) + "\n");
writerFMeasure.write(
currentThreshold
+ ","
+ Utility.roundDouble(currentEvaluation.getFmeasure(), 2)
+ "\n");
LOG.info(
"Results: (precision, recall, f-measure) = ("
+ Utility.roundDouble(currentEvaluation.getPrecision() * 100.0d, 2)
+ ", "
+ Utility.roundDouble(currentEvaluation.getRecall() * 100.0d, 2)
+ ", "
+ Utility.roundDouble(currentEvaluation.getFmeasure() * 100.0d, 2)
+ ")");
LOG.info(
" : (found mappings, correct mappings, reference mappings) = ("
+ currentEvaluation.getFound()
+ ", "
+ currentEvaluation.getCorrect()
+ ", "
+ currentEvaluation.getExist()
+ ")");
if (maxFMeasure < currentEvaluation.getFmeasure()) {
maxFMeasure = currentEvaluation.getFmeasure();
maxFMTh = Utility.roundDouble(currentThreshold * 100f, 4);
}
}
writerMaxFM.write(
Utility.roundDouble(maxFMTh, 2) + ", " + Utility.roundDouble(maxFMeasure, 2));
writerPrecision.close();
writerRecall.close();
writerFMeasure.close();
writerMaxFM.close();
} catch (IOException e) {
// cannot create files
e.printStackTrace();
return;
}
// analysis done
}
/**
* TODO: Check to see if this method could be merged with the work done in the {@link
* ThresholdAnalysis#runAnalysis()} method.
*
* @param reference it can be either an Alignment<Mapping> or a List<MatchingPair>
*/
public static ThresholdAnalysisData thresholdAnalysis(
AbstractMatcher toBeEvaluated,
Object reference,
double[] thresholds,
boolean removeDuplicates) {
Alignment<Mapping> referenceSet = null;
List<MatchingPair> referencePairs = null;
if (reference instanceof Alignment) referenceSet = (Alignment<Mapping>) reference;
else if (reference instanceof List) referencePairs = (List<MatchingPair>) reference;
else return null;
double step = 0.05;
if (thresholds == null) thresholds = Utility.getDoubleArray(0.0d, 0.01d, 101);
ReferenceEvaluationData maxrd = null;
ReferenceEvaluationData rd;
Alignment<Mapping> evaluateSet;
double maxTh = step;
double sumPrecision = 0;
double sumRecall = 0;
double sumFmeasure = 0;
int sumFound = 0;
int sumCorrect = 0;
String matcherName = toBeEvaluated.getName();
ThresholdAnalysisData tad = new ThresholdAnalysisData(thresholds);
tad.setMatcherName(matcherName);
String report = matcherName + "\n\n";
double th;
report += "Threshold:\tFound\tCorrect\tReference\tPrecision\tRecall\tF-Measure\n";
// output the info to the console for easy copy/pasting
// System.out.println("Threshold, " +
// "Precision, " +
// "Recall, " +
// "F-Measure" );
for (int t = 0; t < thresholds.length; t++) {
th = thresholds[t];
toBeEvaluated.getParam().threshold = th;
toBeEvaluated.select();
evaluateSet = toBeEvaluated.getAlignment();
if (referenceSet != null) rd = ReferenceEvaluator.compare(evaluateSet, referenceSet);
else {
Alignment<Mapping> alignment = toBeEvaluated.getAlignment();
List<MatchingPair> pairs = AlignmentUtilities.alignmentToMatchingPairs(alignment);
AlignmentUtilities.removeDuplicates(referencePairs);
AlignmentUtilities.removeDuplicates(pairs);
rd = AlignmentUtilities.compare(pairs, referencePairs);
tad.addEvaluationData(rd);
}
report += Utility.getNoDecimalPercentFromDouble(th) + "\t" + rd.getMeasuresLine();
sumPrecision += rd.getPrecision();
sumRecall += rd.getRecall();
sumFmeasure += rd.getFmeasure();
sumFound += rd.getFound();
sumCorrect += rd.getCorrect();
// output this information to the console for easy copy/pasting // TODO: make a button to be
// able to copy/paste this info
// System.out.println(Double.toString(th) + ", " +
// Double.toString(rd.getPrecision()) + ", " +
// Double.toString(rd.getRecall()) + ", " +
// Double.toString(rd.getFmeasure()) );
if (maxrd == null || maxrd.getFmeasure() < rd.getFmeasure()) {
maxrd = rd;
maxTh = th;
}
}
toBeEvaluated.getParam().threshold = maxTh;
toBeEvaluated.select();
toBeEvaluated.setRefEvaluation(maxrd);
report += "Best Run:\n";
report += Utility.getNoDecimalPercentFromDouble(maxTh) + "\t" + maxrd.getMeasuresLine();
sumPrecision /= thresholds.length;
sumRecall /= thresholds.length;
sumFmeasure /= thresholds.length;
sumFound /= thresholds.length;
sumCorrect /= thresholds.length;
report +=
"Average:\t"
+ sumFound
+ "\t"
+ sumCorrect
+ "\t"
+ maxrd.getExist()
+ "\t"
+ Utility.getOneDecimalPercentFromDouble(sumPrecision)
+ "\t"
+ Utility.getOneDecimalPercentFromDouble(sumRecall)
+ "\t"
+ Utility.getOneDecimalPercentFromDouble(sumFmeasure)
+ "\n\n";
tad.setReport(report);
return tad;
}
/** This is a single matcher mode. The matcher should have been already executed. */
private void runSingleAnalysis() {
// load the reference file
ReferenceAlignmentParameters refParam = new ReferenceAlignmentParameters();
refParam.onlyEquivalence = true;
refParam.fileName = singleRunReferenceAlignment;
refParam.format = ReferenceAlignmentMatcher.OAEI;
AbstractMatcher referenceAlignmentMatcher;
try {
referenceAlignmentMatcher =
MatcherFactory.getMatcherInstance(ReferenceAlignmentMatcher.class);
} catch (MatcherNotFoundException e1) {
LOG.error("Analysis aborted.", e1);
return;
}
referenceAlignmentMatcher.setParam(refParam);
try {
referenceAlignmentMatcher.match();
} catch (Exception e) {
LOG.error("Analysis aborted.", e);
return;
}
String sourceOntologyName = Core.getInstance().getSourceOntology().getTitle();
String targetOntologyName = Core.getInstance().getTargetOntology().getTitle();
File outputPrecision, outputRecall, outputFMeasure, outputMaxFM;
// open the output files
if (prefFilenameOntologyNames) {
outputPrecision =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-precision.txt");
outputRecall =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-recall.txt");
outputFMeasure =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-fmeasure.txt");
outputMaxFM =
new File(
outputDirectory
+ "/"
+ outputPrefix
+ "-"
+ sourceOntologyName
+ "-"
+ targetOntologyName
+ "-max-fmeasure.txt");
} else {
outputPrecision = new File(outputDirectory + "/" + outputPrefix + "-" + "-precision.txt");
outputRecall = new File(outputDirectory + "/" + outputPrefix + "-" + "-recall.txt");
outputFMeasure = new File(outputDirectory + "/" + outputPrefix + "-" + "-fmeasure.txt");
outputMaxFM = new File(outputDirectory + "/" + outputPrefix + "-" + "-max-fmeasure.txt");
}
try {
BufferedWriter writerPrecision = new BufferedWriter(new FileWriter(outputPrecision));
BufferedWriter writerRecall = new BufferedWriter(new FileWriter(outputRecall));
BufferedWriter writerFMeasure = new BufferedWriter(new FileWriter(outputFMeasure));
BufferedWriter writerMaxFM = new BufferedWriter(new FileWriter(outputMaxFM));
// ok, we ran the matcher, now do the threshold analysis
double maxFMeasure = 0.0;
double maxFMTh = 0.0;
for (double currentThreshold = prefStartThreshold;
currentThreshold < prefEndThreshold;
currentThreshold += prefThresholdIncrement) {
currentThreshold = Utility.roundDouble(currentThreshold, 4);
LOG.info("Selecting with threshold = " + currentThreshold);
matcherToAnalyze.getParam().threshold = currentThreshold;
matcherToAnalyze.select();
ReferenceEvaluationData currentEvaluation =
ReferenceEvaluator.compare(
matcherToAnalyze.getAlignment(), referenceAlignmentMatcher.getAlignment());
double th = Utility.roundDouble(currentThreshold * 100f, 4);
writerPrecision.write(
th + "," + Utility.roundDouble(currentEvaluation.getPrecision() * 100.0d, 2) + "\n");
writerRecall.write(
th + "," + Utility.roundDouble(currentEvaluation.getRecall() * 100.0d, 2) + "\n");
writerFMeasure.write(
th + "," + Utility.roundDouble(currentEvaluation.getFmeasure() * 100.0d, 2) + "\n");
LOG.info(
"Results: (precision, recall, f-measure) = ("
+ Utility.roundDouble(currentEvaluation.getPrecision() * 100.0d, 2)
+ ", "
+ Utility.roundDouble(currentEvaluation.getRecall() * 100.0d, 2)
+ ", "
+ Utility.roundDouble(currentEvaluation.getFmeasure() * 100.0d, 2)
+ ")");
LOG.info(
" : (found mappings, correct mappings, reference mappings) = ("
+ currentEvaluation.getFound()
+ ", "
+ currentEvaluation.getCorrect()
+ ", "
+ currentEvaluation.getExist()
+ ")");
writerPrecision.flush();
writerRecall.flush();
writerFMeasure.flush();
if (maxFMeasure < currentEvaluation.getFmeasure()) {
maxFMeasure = currentEvaluation.getFmeasure();
maxFMTh = Utility.roundDouble(currentThreshold * 100f, 4);
}
}
writerMaxFM.write(maxFMTh + ", " + Utility.roundDouble(maxFMeasure * 100.0d, 2));
writerPrecision.close();
writerRecall.close();
writerFMeasure.close();
writerMaxFM.close();
} catch (IOException e) {
// cannot create files
e.printStackTrace();
return;
}
}