Example usage for java.io File getParent

List of usage examples for java.io File getParent

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Introduction

In this page you can find the example usage for java.io File getParent.

Prototype

public String getParent()

Source Link

Document

Returns the pathname string of this abstract pathname's parent, or null if this pathname does not name a parent directory.

Usage

From source file:MainClass.java

public static void main(String args[]) {
    File f1 = new File("MainClass.java");
    System.out.println("File Name:" + f1.getName());
    System.out.println("Path:" + f1.getPath());
    System.out.println("Abs Path:" + f1.getAbsolutePath());
    System.out.println("Parent:" + f1.getParent());
    System.out.println(f1.exists() ? "exists" : "does not exist");
    System.out.println(f1.canWrite() ? "is writeable" : "is not writeable");
    System.out.println(f1.canRead() ? "is readable" : "is not readable");
    System.out.println("is a directory" + f1.isDirectory());
    System.out.println(f1.isFile() ? "is normal file" : "might be a named pipe");
    System.out.println(f1.isAbsolute() ? "is absolute" : "is not absolute");
    System.out.println("File last modified:" + f1.lastModified());
    System.out.println("File size:" + f1.length() + " Bytes");
}

From source file:FileSample.java

public static void main(String args[]) {
    JFrame frame = new JFrame("JFileChooser Popup");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    Container contentPane = frame.getContentPane();

    final JLabel directoryLabel = new JLabel();
    contentPane.add(directoryLabel, BorderLayout.NORTH);

    final JLabel filenameLabel = new JLabel();
    contentPane.add(filenameLabel, BorderLayout.SOUTH);

    final JButton button = new JButton("Open FileChooser");
    ActionListener actionListener = new ActionListener() {
        public void actionPerformed(ActionEvent actionEvent) {
            Component parent = (Component) actionEvent.getSource();
            JFileChooser fileChooser = new JFileChooser(".");
            fileChooser.setAccessory(new LabelAccessory(fileChooser));
            FileView view = new JavaFileView();
            fileChooser.setFileView(view);
            int status = fileChooser.showOpenDialog(parent);
            if (status == JFileChooser.APPROVE_OPTION) {
                File selectedFile = fileChooser.getSelectedFile();
                directoryLabel.setText(selectedFile.getParent());
                filenameLabel.setText(selectedFile.getName());
            } else if (status == JFileChooser.CANCEL_OPTION) {
                directoryLabel.setText(" ");
                filenameLabel.setText(" ");
            }//from w ww  . ja  va  2 s  .  com
        }
    };
    button.addActionListener(actionListener);
    contentPane.add(button, BorderLayout.CENTER);

    frame.setSize(300, 200);
    frame.setVisible(true);
}

From source file:GuaranteeAFile.java

public static void main(String[] args) {

    String filename = "C:/myFile.txt";
    File aFile = new File(filename);
    if (aFile.isDirectory()) {
        System.out.println("The path " + aFile.getPath() + " does not specify a file. Program aborted.");
        System.exit(1);// www.  j  a v a 2 s.c o  m
    }
    if (!aFile.isFile()) {
        aFile = aFile.getAbsoluteFile();
        File parentDir = new File(aFile.getParent());
        if (!parentDir.exists()) {
            parentDir.mkdirs();
        }
    }
    FileOutputStream outputFile = null;
    try {
        outputFile = new FileOutputStream(aFile, true);
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.err);
    }
}

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);/*from w w  w.j a va2s  .c  om*/
    OptionBuilder.hasArg(false);
    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:FilterSample.java

public static void main(String args[]) {
    JFrame frame = new JFrame("JFileChooser Filter Popup");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    Container contentPane = frame.getContentPane();

    final JLabel directoryLabel = new JLabel();
    contentPane.add(directoryLabel, BorderLayout.NORTH);

    final JLabel filenameLabel = new JLabel();
    contentPane.add(filenameLabel, BorderLayout.SOUTH);

    final JButton button = new JButton("Open FileChooser");
    ActionListener actionListener = new ActionListener() {
        public void actionPerformed(ActionEvent actionEvent) {
            Component parent = (Component) actionEvent.getSource();
            JFileChooser fileChooser = new JFileChooser(".");
            fileChooser.setAccessory(new LabelAccessory(fileChooser));
            FileFilter filter1 = new ExtensionFileFilter(null, new String[] { "JPG", "JPEG" });
            //        fileChooser.setFileFilter(filter1);
            fileChooser.addChoosableFileFilter(filter1);
            FileFilter filter2 = new ExtensionFileFilter("gif", new String[] { "gif" });
            fileChooser.addChoosableFileFilter(filter2);
            fileChooser.setFileView(new JavaFileView());
            int status = fileChooser.showOpenDialog(parent);
            if (status == JFileChooser.APPROVE_OPTION) {
                File selectedFile = fileChooser.getSelectedFile();
                directoryLabel.setText(selectedFile.getParent());
                filenameLabel.setText(selectedFile.getName());
            } else if (status == JFileChooser.CANCEL_OPTION) {
                directoryLabel.setText(" ");
                filenameLabel.setText(" ");
            }/*w  w w  .j a  va2  s  . co m*/
        }
    };
    button.addActionListener(actionListener);
    contentPane.add(button, BorderLayout.CENTER);

    frame.setSize(300, 200);
    frame.setVisible(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);// w  w w.j a v  a  2s.  com
    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;

    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:frankhassanabad.com.github.Jasperize.java

/**
 * Main method to call through Java in order to take a LinkedInProfile on disk and load it.
 *
 * @param args command line arguments where the options are stored
 * @throws FileNotFoundException Thrown if any file its expecting cannot be found.
 * @throws JRException  If there's generic overall Jasper issues.
 * @throws ParseException If there's command line parsing issues.
 *//*from  ww  w .j  a v a  2  s .  c o m*/
public static void main(String[] args) throws IOException, JRException, ParseException {

    Options options = new Options();
    options.addOption("h", "help", false, "Shows the help documentation");
    options.addOption("v", "version", false, "Shows the help documentation");
    options.addOption("cl", "coverLetter", false, "Utilizes a cover letter defined in coverletter.xml");
    options.addOption("sig", true, "Picture of your signature to add to the cover letter.");
    CommandLineParser parser = new GnuParser();
    CommandLine cmd = parser.parse(options, args);
    if (cmd.hasOption("h")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("Jasperize [OPTIONS] [InputJrxmlFile] [OutputExportFile]", options);
        System.exit(0);
    }
    if (cmd.hasOption("v")) {
        System.out.println("Version:" + version);
        System.exit(0);
    }
    boolean useCoverLetter = cmd.hasOption("cl");
    String signatureLocation = cmd.getOptionValue("sig");
    BufferedImage signatureImage = null;
    if (signatureLocation != null) {
        signatureImage = ImageIO.read(new File(signatureLocation));
        ;
    }

    @SuppressWarnings("unchecked")
    List<String> arguments = cmd.getArgList();

    final String jrxmlFile;
    final String jasperOutput;
    if (arguments.size() == 2) {
        jrxmlFile = arguments.get(0);
        jasperOutput = arguments.get(1);
        System.out.println("*Detected* the command line arguments of:");
        System.out.println("    [InputjrxmlFile] " + jrxmlFile);
        System.out.println("    [OutputExportFile] " + jasperOutput);
    } else if (arguments.size() == 3) {
        jrxmlFile = arguments.get(1);
        jasperOutput = arguments.get(2);
        System.out.println("*Detected* the command line arguments of:");
        System.out.println("    [InputjrxmlFile] " + jrxmlFile);
        System.out.println("    [OutputExportFile] " + jasperOutput);
    } else {
        System.out.println("Using the default arguments of:");
        jrxmlFile = "data/jasperTemplates/resume1.jrxml";
        jasperOutput = "data/jasperOutput/linkedInResume.pdf";
        System.out.println("    [InputjrxmlFile] " + jrxmlFile);
        System.out.println("    [OutputExportFile] " + jasperOutput);
    }

    final String compiledMasterFile;
    final String outputType;
    final String jrPrintFile;
    //Split the inputFile
    final String[] inputSplit = jrxmlFile.split("\\.");
    if (inputSplit.length != 2 || !(inputSplit[1].equalsIgnoreCase("jrxml"))) {
        //Error
        System.out.println("Your [InputjrxmlFile] (1st argument) should have a jrxml extension like such:");
        System.out.println("    data/jasperTemplates/resume1.jrxml");
        System.exit(1);
    }
    //Split the outputFile
    final String[] outputSplit = jasperOutput.split("\\.");
    if (outputSplit.length != 2) {
        //Error
        System.out.println("Your [OutputExportFile] (2nd argument) should have a file extension like such:");
        System.out.println("    data/jasperOutput/linkedInResume.pdf");
        System.exit(1);
    }

    File inputFile = new File(inputSplit[0]);
    String inputFileName = inputFile.getName();
    String inputFileParentPath = inputFile.getParent();

    File outputFile = new File(outputSplit[0]);
    String outputFileParentPath = outputFile.getParent();

    System.out.println("Compiling report(s)");
    compileAllJrxmlTemplateFiles(inputFileParentPath, outputFileParentPath);
    System.out.println("Done compiling report(s)");

    compiledMasterFile = outputFileParentPath + File.separator + inputFileName + ".jasper";
    jrPrintFile = outputFileParentPath + File.separator + inputFileName + ".jrprint";

    System.out.println("Filling report: " + compiledMasterFile);
    Reporting.fill(compiledMasterFile, useCoverLetter, signatureImage);
    System.out.println("Done filling reports");
    outputType = outputSplit[1];
    System.out.println("Creating output export file of: " + jasperOutput);
    if (outputType.equalsIgnoreCase("pdf")) {
        Reporting.pdf(jrPrintFile, jasperOutput);
    }
    if (outputType.equalsIgnoreCase("pptx")) {
        Reporting.pptx(jrPrintFile, jasperOutput);
    }
    if (outputType.equalsIgnoreCase("docx")) {
        Reporting.docx(jrPrintFile, jasperOutput);
    }
    if (outputType.equalsIgnoreCase("odt")) {
        Reporting.odt(jrPrintFile, jasperOutput);
    }
    if (outputType.equalsIgnoreCase("xhtml")) {
        Reporting.xhtml(jrPrintFile, jasperOutput);
    }
    System.out.println("Done creating output export file of: " + jasperOutput);
}

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);//from  w w  w . java 2 s . c o  m
    OptionBuilder.hasArg();
    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.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);//from   w  w w.  j  a  v a2  s .  co m
    OptionBuilder.hasArg(false);
    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.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);/*from   w  w w  . j ava 2  s .com*/
    OptionBuilder.hasArg(false);
    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();
}