List of usage examples for org.apache.commons.cli OptionBuilder isRequired
public static OptionBuilder isRequired(boolean newRequired)
required is true. From source file:apps.classification.LearnSVMPerf.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = LearnSVMPerf.class.getName() + " [OPTIONS] <path to svm_perf> <trainingIndexDirectory>"; Options options = new Options(); OptionBuilder.withArgName("c"); OptionBuilder.withDescription("The c value for svm_perf (default 0.01)"); OptionBuilder.withLongOpt("c"); OptionBuilder.isRequired(false); OptionBuilder.hasArg();/*w w w .j a v a 2 s. c om*/ options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("l"); OptionBuilder.withDescription("The loss function to optimize (default 2):\n" + " 0 Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n" + " 1 F1: 100 minus the F1-score in percent.\n" + " 2 Errorrate: Percentage of errors in prediction vector.\n" + " 3 Prec/Rec Breakeven: 100 minus PRBEP in percent.\n" + " 4 Prec@p: 100 minus precision at p in percent.\n" + " 5 Rec@p: 100 minus recall at p in percent.\n" + " 10 ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea)."); OptionBuilder.withLongOpt("l"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("w"); OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n" + " 0: n-slack algorithm described in [2]\n" + " 1: n-slack algorithm with shrinking heuristic\n" + " 2: 1-slack algorithm (primal) described in [5]\n" + " 3: 1-slack algorithm (dual) described in [5]\n" + " 4: 1-slack algorithm (dual) with constraint cache [5]\n" + " 9: custom algorithm in svm_struct_learn_custom.c"); OptionBuilder.withLongOpt("w"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("p"); OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)"); OptionBuilder.withLongOpt("p"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfLearnerCustomizer classificationLearnerCustomizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]); if (line.hasOption("c")) classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c"))); if (line.hasOption("w")) classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w"))); if (line.hasOption("p")) classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p"))); if (line.hasOption("l")) classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l"))); if (line.hasOption("v")) classificationLearnerCustomizer.printSvmPerfOutput(true); if (line.hasOption("s")) classificationLearnerCustomizer.setDeleteTrainingFiles(false); if (line.hasOption("t")) classificationLearnerCustomizer.setTempPath(line.getOptionValue("t")); } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } if (remainingArgs.length != 2) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[1]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); // LEARNING SvmPerfLearner classificationLearner = new SvmPerfLearner(); classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer); FileSystemStorageManager storageManager = new FileSystemStorageManager(indexPath, false); storageManager.open(); IIndex training = TroveReadWriteHelper.readIndex(storageManager, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); storageManager.close(); IClassifier classifier = classificationLearner.build(training); File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath()); SvmPerfDataManager dataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer( executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify")); String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-" + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL(); if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5) description += "_P-" + classificationLearnerCustomizer.getP(); if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0) description += "_" + classificationLearnerCustomizer.getAdditionalParameters(); storageManager = new FileSystemStorageManager(indexPath, false); storageManager.open(); dataManager.write(storageManager, indexName + description, classifier); storageManager.close(); }
From source file:apps.classification.ClassifySVMPerf.java
public static void main(String[] args) throws IOException { boolean dumpConfidences = false; String cmdLineSyntax = ClassifySVMPerf.class.getName() + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <modelDirectory>"; Options options = new Options(); OptionBuilder.withArgName("d"); OptionBuilder.withDescription("Dump confidences file"); OptionBuilder.withLongOpt("d"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false);//www. j a v a 2 s .co m options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfClassifierCustomizer customizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); customizer = new SvmPerfClassifierCustomizer(remainingArgs[0]); if (line.hasOption("d")) dumpConfidences = true; if (line.hasOption("v")) customizer.printSvmPerfOutput(true); if (line.hasOption("s")) { customizer.setDeleteTestFiles(false); customizer.setDeletePredictionsFiles(false); } if (line.hasOption("t")) customizer.setTempPath(line.getOptionValue("t")); } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } if (remainingArgs.length != 3) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String testFile = remainingArgs[1]; File file = new File(testFile); String testName = file.getName(); String testPath = file.getParent(); String classifierFile = remainingArgs[2]; file = new File(classifierFile); String classifierName = file.getName(); String classifierPath = file.getParent(); FileSystemStorageManager storageManager = new FileSystemStorageManager(testPath, false); storageManager.open(); IIndex test = TroveReadWriteHelper.readIndex(storageManager, testName, TroveContentDBType.Full, TroveClassificationDBType.Full); storageManager.close(); SvmPerfDataManager dataManager = new SvmPerfDataManager(customizer); storageManager = new FileSystemStorageManager(classifierPath, false); storageManager.open(); SvmPerfClassifier classifier = (SvmPerfClassifier) dataManager.read(storageManager, classifierName); storageManager.close(); classifier.setRuntimeCustomizer(customizer); // CLASSIFICATION String classificationName = testName + "_" + classifierName; Classifier classifierModule = new Classifier(test, classifier, dumpConfidences); classifierModule.setClassificationMode(ClassificationMode.PER_CATEGORY); classifierModule.exec(); IClassificationDB testClassification = classifierModule.getClassificationDB(); storageManager = new FileSystemStorageManager(testPath, false); storageManager.open(); TroveReadWriteHelper.writeClassification(storageManager, testClassification, classificationName + ".cla", true); storageManager.close(); if (dumpConfidences) { ClassificationScoreDB confidences = classifierModule.getConfidences(); ClassificationScoreDB.write(testPath + Os.pathSeparator() + classificationName + ".confidences", confidences); } }
From source file:edu.harvard.med.screensaver.io.libraries.LibraryContentsLoader.java
@SuppressWarnings("static-access") public static void main(String[] args) { CommandLineApplication application = new CommandLineApplication(args); application.addCommandLineOption(/*from ww w . java 2 s.c om*/ OptionBuilder.hasArg().withArgName(LIBRARY_SHORT_NAME_OPTION[SHORT_OPTION_INDEX]).isRequired() .withDescription(LIBRARY_SHORT_NAME_OPTION[DESCRIPTION_INDEX]) .withLongOpt(LIBRARY_SHORT_NAME_OPTION[LONG_OPTION_INDEX]) .create(LIBRARY_SHORT_NAME_OPTION[SHORT_OPTION_INDEX])); application.addCommandLineOption(OptionBuilder.hasArg().withArgName(INPUT_FILE_OPTION[SHORT_OPTION_INDEX]) .isRequired().withDescription(INPUT_FILE_OPTION[DESCRIPTION_INDEX]) .withLongOpt(INPUT_FILE_OPTION[LONG_OPTION_INDEX]).create(INPUT_FILE_OPTION[SHORT_OPTION_INDEX])); application.addCommandLineOption( OptionBuilder.isRequired(false).withDescription(RELEASE_IF_SUCCESS_OPTION[DESCRIPTION_INDEX]) .withLongOpt(RELEASE_IF_SUCCESS_OPTION[LONG_OPTION_INDEX]) .create(RELEASE_IF_SUCCESS_OPTION[SHORT_OPTION_INDEX])); application.processOptions(true, true); String libraryShortName = application .getCommandLineOptionValue(LIBRARY_SHORT_NAME_OPTION[SHORT_OPTION_INDEX]); File libraryContentsFile = application.getCommandLineOptionValue(INPUT_FILE_OPTION[SHORT_OPTION_INDEX], File.class); boolean releaseIfSuccess = application.isCommandLineFlagSet(RELEASE_IF_SUCCESS_OPTION[SHORT_OPTION_INDEX]); edu.harvard.med.screensaver.service.libraries.LibraryContentsLoader libraryContentsLoader = (edu.harvard.med.screensaver.service.libraries.LibraryContentsLoader) application .getSpringBean("libraryContentsLoader"); edu.harvard.med.screensaver.service.libraries.LibraryContentsVersionManager libraryContentsVersionManager = (edu.harvard.med.screensaver.service.libraries.LibraryContentsVersionManager) application .getSpringBean("libraryContentsVersionManager"); GenericEntityDAO dao = (GenericEntityDAO) application.getSpringBean("genericEntityDao"); try { AdministratorUser admin = application.findAdministratorUser(); Library library = dao.findEntityByProperty(Library.class, "shortName", libraryShortName); if (library == null) { throw new IllegalArgumentException("no library with short name: " + libraryShortName); } LibraryContentsVersion lcv = libraryContentsLoader.loadLibraryContents(library, admin, null /*TODO*/, new FileInputStream(libraryContentsFile)); if (releaseIfSuccess) { log.info("releasing..."); libraryContentsVersionManager.releaseLibraryContentsVersion(lcv, admin); } } catch (ParseErrorsException e) { for (ParseError error : e.getErrors()) { log.error(error.toString(), e); } System.exit(1); } catch (Exception e) { log.error("application exception", e); System.exit(1); } }
From source file:com.buddycloud.channeldirectory.cli.Main.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { JsonElement rootElement = new JsonParser().parse(new FileReader(QUERIES_FILE)); JsonArray rootArray = rootElement.getAsJsonArray(); Map<String, Query> queries = new HashMap<String, Query>(); for (int i = 0; i < rootArray.size(); i++) { JsonObject queryElement = rootArray.get(i).getAsJsonObject(); String queryName = queryElement.get("name").getAsString(); String type = queryElement.get("type").getAsString(); Query query = null;// w ww . j av a2 s. c om if (type.equals("solr")) { query = new QueryToSolr(queryElement.get("agg").getAsString(), queryElement.get("core").getAsString(), queryElement.get("q").getAsString()); } else if (type.equals("dbms")) { query = new QueryToDBMS(queryElement.get("q").getAsString()); } queries.put(queryName, query); } LinkedList<String> queriesNames = new LinkedList<String>(queries.keySet()); Collections.sort(queriesNames); Options options = new Options(); options.addOption(OptionBuilder.isRequired(true).withLongOpt("query").hasArg(true) .withDescription("The name of the query. Possible queries are: " + queriesNames).create('q')); options.addOption(OptionBuilder.isRequired(false).withLongOpt("args").hasArg(true) .withDescription("Arguments for the query").create('a')); options.addOption(new Option("?", "help", false, "Print this message")); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { printHelpAndExit(options); } if (cmd.hasOption("help")) { printHelpAndExit(options); } String queryName = cmd.getOptionValue("q"); String argsCmd = cmd.getOptionValue("a"); Properties configuration = ConfigurationUtils.loadConfiguration(); Query query = queries.get(queryName); if (query == null) { printHelpAndExit(options); } System.out.println(query.exec(argsCmd, configuration)); }
From source file:apps.quantification.QuantifySVMPerf.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = QuantifySVMPerf.class.getName() + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <quantificationModelDirectory>"; Options options = new Options(); OptionBuilder.withArgName("d"); OptionBuilder.withDescription("Dump confidences file"); OptionBuilder.withLongOpt("d"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false);/*w w w . ja v a2 s. c o m*/ options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary files in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfClassifierCustomizer customizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); customizer = new SvmPerfClassifierCustomizer(remainingArgs[0]); if (line.hasOption("v")) customizer.printSvmPerfOutput(true); if (line.hasOption("s")) { System.out.println("Keeping temporary files."); customizer.setDeleteTestFiles(false); customizer.setDeletePredictionsFiles(false); } if (line.hasOption("t")) customizer.setTempPath(line.getOptionValue("t")); } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } if (remainingArgs.length != 3) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[1]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String quantifierFilename = remainingArgs[2]; FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false); indexFssm.open(); IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); indexFssm.close(); FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false); quantifierFssm.open(); SvmPerfDataManager classifierDataManager = new SvmPerfDataManager(customizer); FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false); fssm.open(); IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager, ClassificationMode.PER_CATEGORY); fssm.close(); quantifierFssm.close(); Quantification ccQuantification = quantifiers[0].quantify(test); Quantification paQuantification = quantifiers[1].quantify(test); Quantification accQuantification = quantifiers[2].quantify(test); Quantification maxQuantification = quantifiers[3].quantify(test); Quantification sccQuantification = quantifiers[4].quantify(test); Quantification spaQuantification = quantifiers[5].quantify(test); Quantification trueQuantification = new Quantification("True", test.getClassificationDB()); File quantifierFile = new File(quantifierFilename); String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + ".txt"; BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName)); IShortIterator iterator = test.getCategoryDB().getCategories(); while (iterator.hasNext()) { short category = iterator.next(); String prefix = quantifierFile.getName() + "\t" + indexName + "\t" + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t" + trueQuantification.getQuantification(category) + "\t"; writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category) + "\n"); writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category) + "\n"); writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category) + "\n"); writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category) + "\n"); writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category) + "\n"); writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category) + "\n"); } writer.close(); BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + "_rates.txt")); TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs(); TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleTPRs(); TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs(); TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs(); ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet(); ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]) .getInternalQuantifier()).getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = test.getCategoryDB().getCategoryName(cat); ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat); ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double maxTPR = maxTPRs.get(cat); double maxFPR = maxFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t" + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn() + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:apps.quantification.QuantifySVMLight.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = QuantifySVMLight.class.getName() + " [OPTIONS] <path to svm_light_classify> <testIndexDirectory> <quantificationModelDirectory>"; Options options = new Options(); OptionBuilder.withArgName("d"); OptionBuilder.withDescription("Dump confidences file"); OptionBuilder.withLongOpt("d"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false);/* ww w . j a v a2 s . co m*/ options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary files in svm_light format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmLightClassifierCustomizer customizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); customizer = new SvmLightClassifierCustomizer(remainingArgs[0]); if (line.hasOption("v")) customizer.printSvmLightOutput(true); if (line.hasOption("s")) { System.out.println("Keeping temporary files."); customizer.setDeleteTestFiles(false); customizer.setDeletePredictionsFiles(false); } if (line.hasOption("t")) customizer.setTempPath(line.getOptionValue("t")); } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } if (remainingArgs.length != 3) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[1]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String quantifierFilename = remainingArgs[2]; FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false); indexFssm.open(); IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); indexFssm.close(); FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false); quantifierFssm.open(); SvmLightDataManager classifierDataManager = new SvmLightDataManager(customizer); FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false); fssm.open(); IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager, ClassificationMode.PER_CATEGORY); fssm.close(); quantifierFssm.close(); Quantification ccQuantification = quantifiers[0].quantify(test); Quantification paQuantification = quantifiers[1].quantify(test); Quantification accQuantification = quantifiers[2].quantify(test); Quantification maxQuantification = quantifiers[3].quantify(test); Quantification sccQuantification = quantifiers[4].quantify(test); Quantification spaQuantification = quantifiers[5].quantify(test); Quantification trueQuantification = new Quantification("True", test.getClassificationDB()); File quantifierFile = new File(quantifierFilename); String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + ".txt"; BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName)); IShortIterator iterator = test.getCategoryDB().getCategories(); while (iterator.hasNext()) { short category = iterator.next(); String prefix = quantifierFile.getName() + "\t" + indexName + "\t" + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t" + trueQuantification.getQuantification(category) + "\t"; writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category) + "\n"); writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category) + "\n"); writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category) + "\n"); writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category) + "\n"); writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category) + "\n"); writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category) + "\n"); } writer.close(); BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + "_rates.txt")); TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs(); TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleTPRs(); TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs(); TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs(); ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet(); ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]) .getInternalQuantifier()).getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = test.getCategoryDB().getCategoryName(cat); ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat); ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double maxTPR = maxTPRs.get(cat); double maxFPR = maxFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t" + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn() + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:apps.quantification.LearnQuantificationSVMLight.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = LearnQuantificationSVMLight.class.getName() + " [OPTIONS] <path to svm_light_learn> <path to svm_light_classify> <trainingIndexDirectory> <outputDirectory>"; Options options = new Options(); OptionBuilder.withArgName("f"); OptionBuilder.withDescription("Number of folds"); OptionBuilder.withLongOpt("f"); OptionBuilder.isRequired(true); OptionBuilder.hasArg();/*from w w w. j a v a 2s. c om*/ options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("c"); OptionBuilder.withDescription("The c value for svm_light (default 1)"); OptionBuilder.withLongOpt("c"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("k"); OptionBuilder.withDescription("Kernel type (default 0: linear, 1: polynomial, 2: RBF, 3: sigmoid)"); OptionBuilder.withLongOpt("k"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_light format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmLightLearnerCustomizer classificationLearnerCustomizer = null; SvmLightClassifierCustomizer classificationCustomizer = null; int folds = -1; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); classificationLearnerCustomizer = new SvmLightLearnerCustomizer(remainingArgs[0]); classificationCustomizer = new SvmLightClassifierCustomizer(remainingArgs[1]); folds = Integer.parseInt(line.getOptionValue("f")); if (line.hasOption("c")) classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c"))); if (line.hasOption("k")) { System.out.println("Kernel type: " + line.getOptionValue("k")); classificationLearnerCustomizer.setKernelType(Integer.parseInt(line.getOptionValue("k"))); } if (line.hasOption("v")) classificationLearnerCustomizer.printSvmLightOutput(true); if (line.hasOption("s")) classificationLearnerCustomizer.setDeleteTrainingFiles(false); if (line.hasOption("t")) { classificationLearnerCustomizer.setTempPath(line.getOptionValue("t")); classificationCustomizer.setTempPath(line.getOptionValue("t")); } } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } assert (classificationLearnerCustomizer != null); if (remainingArgs.length != 4) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[2]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String outputPath = remainingArgs[3]; SvmLightLearner classificationLearner = new SvmLightLearner(); classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer); FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false); fssm.open(); IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers"); IOperationStatusListener status = new IOperationStatusListener() { @Override public void operationStatus(double percentage) { progressBar.signal((int) percentage); } }; QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner, classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY, new LogisticFunction(), status); IQuantifier[] quantifiers = quantificationLearner.learn(training); File executableFile = new File(classificationLearnerCustomizer.getSvmLightLearnPath()); IDataManager classifierDataManager = new SvmLightDataManager(new SvmLightClassifierCustomizer( executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_light_classify")); String description = "_SVMLight_C-" + classificationLearnerCustomizer.getC() + "_K-" + classificationLearnerCustomizer.getKernelType(); if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0) description += "_" + classificationLearnerCustomizer.getAdditionalParameters(); String quantifierPrefix = indexName + "_Quantifier-" + folds + description; FileSystemStorageManager fssmo = new FileSystemStorageManager( outputPath + File.separatorChar + quantifierPrefix, true); fssmo.open(); QuantificationLearner.write(quantifiers, fssmo, classifierDataManager); fssmo.close(); BufferedWriter bfs = new BufferedWriter( new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt")); TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs(); TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs(); ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = training.getCategoryDB().getCategoryName(cat); ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:apps.quantification.LearnQuantificationSVMPerf.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = LearnQuantificationSVMPerf.class.getName() + " [OPTIONS] <path to svm_perf_learn> <path to svm_perf_classify> <trainingIndexDirectory> <outputDirectory>"; Options options = new Options(); OptionBuilder.withArgName("f"); OptionBuilder.withDescription("Number of folds"); OptionBuilder.withLongOpt("f"); OptionBuilder.isRequired(true); OptionBuilder.hasArg();//from ww w. java2s.co m options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("c"); OptionBuilder.withDescription("The c value for svm_perf (default 0.01)"); OptionBuilder.withLongOpt("c"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("l"); OptionBuilder.withDescription("The loss function to optimize (default 2):\n" + " 0 Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n" + " 1 F1: 100 minus the F1-score in percent.\n" + " 2 Errorrate: Percentage of errors in prediction vector.\n" + " 3 Prec/Rec Breakeven: 100 minus PRBEP in percent.\n" + " 4 Prec@p: 100 minus precision at p in percent.\n" + " 5 Rec@p: 100 minus recall at p in percent.\n" + " 10 ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea)."); OptionBuilder.withLongOpt("l"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("w"); OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n" + " 0: n-slack algorithm described in [2]\n" + " 1: n-slack algorithm with shrinking heuristic\n" + " 2: 1-slack algorithm (primal) described in [5]\n" + " 3: 1-slack algorithm (dual) described in [5]\n" + " 4: 1-slack algorithm (dual) with constraint cache [5]\n" + " 9: custom algorithm in svm_struct_learn_custom.c"); OptionBuilder.withLongOpt("w"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("p"); OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)"); OptionBuilder.withLongOpt("p"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfLearnerCustomizer classificationLearnerCustomizer = null; SvmPerfClassifierCustomizer classificationCustomizer = null; int folds = -1; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]); classificationCustomizer = new SvmPerfClassifierCustomizer(remainingArgs[1]); folds = Integer.parseInt(line.getOptionValue("f")); if (line.hasOption("c")) classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c"))); if (line.hasOption("w")) classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w"))); if (line.hasOption("p")) classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p"))); if (line.hasOption("l")) classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l"))); if (line.hasOption("v")) classificationLearnerCustomizer.printSvmPerfOutput(true); if (line.hasOption("s")) classificationLearnerCustomizer.setDeleteTrainingFiles(false); if (line.hasOption("t")) { classificationLearnerCustomizer.setTempPath(line.getOptionValue("t")); classificationCustomizer.setTempPath(line.getOptionValue("t")); } } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } assert (classificationLearnerCustomizer != null); if (remainingArgs.length != 4) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[2]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String outputPath = remainingArgs[3]; SvmPerfLearner classificationLearner = new SvmPerfLearner(); classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer); FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false); fssm.open(); IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers"); IOperationStatusListener status = new IOperationStatusListener() { @Override public void operationStatus(double percentage) { progressBar.signal((int) percentage); } }; QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner, classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY, new LogisticFunction(), status); IQuantifier[] quantifiers = quantificationLearner.learn(training); File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath()); IDataManager classifierDataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer( executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify")); String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-" + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL(); if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5) description += "_P-" + classificationLearnerCustomizer.getP(); if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0) description += "_" + classificationLearnerCustomizer.getAdditionalParameters(); String quantifierPrefix = indexName + "_Quantifier-" + folds + description; FileSystemStorageManager fssmo = new FileSystemStorageManager( outputPath + File.separatorChar + quantifierPrefix, true); fssmo.open(); QuantificationLearner.write(quantifiers, fssmo, classifierDataManager); fssmo.close(); BufferedWriter bfs = new BufferedWriter( new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt")); TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs(); TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs(); ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = training.getCategoryDB().getCategoryName(cat); ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:Homework4Execute.java
@SuppressWarnings("static-access") private static Options getCommandLineOptions() { Options options = new Options(); options.addOption(OptionBuilder.isRequired(false).withArgName("task").withLongOpt("task").hasArg(true) .withDescription("trace route task [uname,traceroute,enviroment,cmdWinDir,cmdWinTrace]").create()); options.addOption(OptionBuilder.isRequired(false).withArgName("host").withLongOpt("host").hasArg(true) .withDescription("trace route host on redirect task").create()); options.addOption(OptionBuilder.isRequired(false).withArgName("dir").withLongOpt("dir").hasArg(true) .withDescription("test dir on cmdWinDir task").create()); return options; }
From source file:com.opengamma.integration.tool.config.MultiFileConfigExportTool.java
@SuppressWarnings("static-access") private Option createDirectoryOption() { return OptionBuilder.isRequired(true).hasArg(true).withDescription("Directory to save files to") .withLongOpt("directory").create("d"); }