private static void saveExperimentPresets(List<ExperimentPreset> presets) {
final String rootDir = Core.getInstance().getRoot();
File outputDir = new File(rootDir + File.separator + Core.SETTINGS_DIR);
if (!outputDir.exists() && !outputDir.mkdirs()) {
LOG.error("Expriment Presets will not be stored. Could not create directory: " + outputDir);
return;
}
// serialize the object
try {
final String outputFile = outputDir.getAbsolutePath() + File.separator + EXPERIMENTS_FILE;
FileOutputStream fileOut = new FileOutputStream(outputFile);
BZip2CompressorOutputStream bzOut =
new BZip2CompressorOutputStream(fileOut); // bzip the serialized object to save space
ObjectOutputStream out = new ObjectOutputStream(bzOut);
out.writeObject(presets);
out.close();
bzOut.close();
fileOut.close();
LOG.debug("Serialized experiment presets to: " + outputFile);
} catch (IOException e) {
LOG.error(e);
}
}
@SuppressWarnings("unchecked")
private static List<ExperimentPreset> loadExperimentPresets() {
final String rootDir = Core.getInstance().getRoot();
File inputFile =
new File(rootDir + File.separator + Core.SETTINGS_DIR + File.separator + EXPERIMENTS_FILE);
if (!inputFile.exists()) {
LOG.error("Experiment Presets will not be read. File not found: " + inputFile);
return null;
}
List<ExperimentPreset> presetList = null;
try {
FileInputStream fileIn = new FileInputStream(inputFile);
BZip2CompressorInputStream bzIn = new BZip2CompressorInputStream(fileIn);
ObjectInputStream in = new ObjectInputStream(bzIn);
presetList = (List<ExperimentPreset>) in.readObject();
in.close();
bzIn.close();
fileIn.close();
LOG.info("Deserialized experiment presets from: " + inputFile);
} catch (IOException | ClassNotFoundException e) {
LOG.error(e);
return null;
}
return presetList;
}
public static List<Pair<MatchingTaskPreset, ExperimentPreset>> loadBatchModeRunsFromXML(
String filePath) {
if (!filePath.startsWith(File.separator)) {
filePath = Core.getInstance().getRoot() + filePath;
}
File inputFile = new File(filePath);
if (!inputFile.exists())
throw new AssertionError(
"UFL Batch Mode runs file not found.", new FileNotFoundException(filePath));
XStream xs = getXStream();
@SuppressWarnings("unchecked")
List<Pair<MatchingTaskPreset, ExperimentPreset>> presetList =
(List<Pair<MatchingTaskPreset, ExperimentPreset>>) xs.fromXML(inputFile);
LOG.info("Deserialized experiment runs from: " + inputFile);
return presetList;
}
/**
* @param runs The list of runs we are saving.
* @param fileName If this filename is relative (doesn't start with /) it will be made relative to
* the AM_ROOT.
*/
public static String saveBatchModeRunsToXML(
List<Pair<MatchingTaskPreset, ExperimentPreset>> runs, String fileName) {
if (!fileName.startsWith(File.separator)) {
fileName = Core.getInstance().getRoot() + fileName;
}
List<Pair<MatchingTaskPreset, ExperimentPreset>> runsCopy = new LinkedList<>();
runsCopy.addAll(runs);
Comparator<Pair<MatchingTaskPreset, ExperimentPreset>> c =
new Comparator<Pair<MatchingTaskPreset, ExperimentPreset>>() {
@Override
public int compare(
Pair<MatchingTaskPreset, ExperimentPreset> o1,
Pair<MatchingTaskPreset, ExperimentPreset> o2) {
int mt = o1.getLeft().getName().compareTo(o2.getRight().getName());
if (mt == 0) {
return o1.getRight().getName().compareTo(o2.getRight().getName());
}
return mt;
}
};
// serialize in order
Collections.sort(runsCopy, c);
XStream xs = getXStream();
try {
FileOutputStream fos = new FileOutputStream(fileName);
xs.toXML(runs, fos);
fos.close();
LOG.info("Saved UFL batch mode experiments: " + fileName);
return fileName;
} catch (IOException ioex) {
LOG.error(ioex);
}
return null;
}
/** 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;
}
}
