Example usage for java.util.logging Logger getLogger

List of usage examples for java.util.logging Logger getLogger

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Introduction

In this page you can find the example usage for java.util.logging Logger getLogger.

Prototype




@CallerSensitive
public static Logger getLogger(String name)

Source Link

Document

Find or create a logger for a named subsystem.

Usage

From source file:guardar.en.base.de.datos.MainServidor.java

public static void main(String[] args)
        throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException {

    Mongo mongo = new Mongo("localhost", 27017);

    // nombre de la base de datos
    DB database = mongo.getDB("paginas");
    // coleccion de la db
    DBCollection collection = database.getCollection("indice");
    DBCollection collection_textos = database.getCollection("tabla");
    ArrayList<String> lista_textos = new ArrayList();

    try {/*w  w w .  j a  v a2  s. co  m*/
        ServerSocket servidor = new ServerSocket(4545); // Crear un servidor en pausa hasta que un cliente llegue.
        while (true) {
            String aux = new String();
            lista_textos.clear();
            Socket clienteNuevo = servidor.accept();// Si llega se acepta.
            // Queda en pausa otra vez hasta que un objeto llegue.
            ObjectInputStream entrada = new ObjectInputStream(clienteNuevo.getInputStream());

            JSONObject request = (JSONObject) entrada.readObject();
            String b = (String) request.get("id");
            //hacer una query a la base de datos con la palabra que se quiere obtener

            BasicDBObject query = new BasicDBObject("palabra", b);
            DBCursor cursor = collection.find(query);
            ArrayList<DocumentosDB> lista_doc = new ArrayList<>();
            // de la query tomo el campo documentos y los agrego a una lista
            try {
                while (cursor.hasNext()) {
                    //System.out.println(cursor.next());
                    BasicDBList campo_documentos = (BasicDBList) cursor.next().get("documentos");
                    // en el for voy tomando uno por uno los elementos en el campo documentos
                    for (Iterator<Object> it = campo_documentos.iterator(); it.hasNext();) {
                        BasicDBObject dbo = (BasicDBObject) it.next();
                        //DOC tiene id y frecuencia
                        DocumentosDB doc = new DocumentosDB();
                        doc.makefn2(dbo);
                        //int id = (int)doc.getId_documento();
                        //int f = (int)doc.getFrecuencia();

                        lista_doc.add(doc);

                        //*******************************************

                        //********************************************

                        //QUERY A LA COLECCION DE TEXTOS
                        /* BasicDBObject query_textos = new BasicDBObject("id", doc.getId_documento());//query
                         DBCursor cursor_textos = collection_textos.find(query_textos);
                         try {
                        while (cursor_textos.hasNext()) {
                                    
                                    
                            DBObject obj = cursor_textos.next();
                                
                            String titulo = (String) obj.get("titulo");
                            titulo = titulo + "\n\n";
                            String texto = (String) obj.get("texto");
                                
                            String texto_final = titulo + texto;
                            aux = texto_final;
                            lista_textos.add(texto_final);
                        }
                         } finally {
                        cursor_textos.close();
                         }*/
                        //System.out.println(doc.getId_documento());
                        //System.out.println(doc.getFrecuencia());

                    } // end for

                } //end while query

            } finally {
                cursor.close();
            }

            // ordeno la lista de menor a mayor
            Collections.sort(lista_doc, new Comparator<DocumentosDB>() {

                @Override
                public int compare(DocumentosDB o1, DocumentosDB o2) {
                    //throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
                    return o1.getFrecuencia().compareTo(o2.getFrecuencia());
                }
            });
            int tam = lista_doc.size() - 1;
            for (int j = tam; j >= 0; j--) {

                BasicDBObject query_textos = new BasicDBObject("id",
                        (int) lista_doc.get(j).getId_documento().intValue());//query
                DBCursor cursor_textos = collection_textos.find(query_textos);// lo busco
                try {
                    while (cursor_textos.hasNext()) {

                        DBObject obj = cursor_textos.next();
                        String titulo = "*******************************";
                        titulo += (String) obj.get("titulo");
                        int f = (int) lista_doc.get(j).getFrecuencia().intValue();
                        String strinf = Integer.toString(f);
                        titulo += "******************************* frecuencia:" + strinf;
                        titulo = titulo + "\n\n";

                        String texto = (String) obj.get("texto");

                        String texto_final = titulo + texto + "\n\n";
                        aux = aux + texto_final;
                        //lista_textos.add(texto_final);
                    }
                } finally {
                    cursor_textos.close();
                }

            }

            //actualizar el cache
            try {
                Socket cliente_cache = new Socket("localhost", 4500); // nos conectamos con el servidor
                ObjectOutputStream mensaje_cache = new ObjectOutputStream(cliente_cache.getOutputStream()); // get al output del servidor, que es cliente : socket del cliente q se conecto al server
                JSONObject actualizacion_cache = new JSONObject();
                actualizacion_cache.put("actualizacion", 1);
                actualizacion_cache.put("busqueda", b);
                actualizacion_cache.put("respuesta", aux);
                mensaje_cache.writeObject(actualizacion_cache); // envio el msj al servidor
            } catch (Exception ex) {

            }

            //RESPONDER DESDE EL SERVIDORIndex al FRONT
            ObjectOutputStream resp = new ObjectOutputStream(clienteNuevo.getOutputStream());// obtengo el output del cliente para mandarle un msj
            resp.writeObject(aux);
            System.out.println("msj enviado desde el servidor");

        }
    } catch (IOException ex) {
        Logger.getLogger(MainServidor.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:de.weltraumschaf.registermachine.App.java

/**
 * Main entry point for JVM.//from w w w  .  ja  v  a 2  s  .  co  m
 *
 * Catches all {@link Exception exception} and print their message to STDERR and exits with -1.
 *
 * @param args command line arguments
 */
public static void main(final String[] args) {
    final App app = new App(args);

    try {
        InvokableAdapter.main(app, IOStreams.newDefault(), app.isVerbose());
    } catch (UnsupportedEncodingException ex) {
        Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
        app.exit(-1);
    }
}

From source file:view.ViewReportUI.java

/**
 * @param args the command line arguments
 *//*w ww  .j  a v a  2 s  .c o m*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(ViewReportUI.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(ViewReportUI.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(ViewReportUI.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(ViewReportUI.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            try {
                new ViewReportUI().setVisible(true);
            } catch (SQLException ex) {
                Logger.getLogger(ViewReportUI.class.getName()).log(Level.SEVERE, null, ex);
            } catch (ClassNotFoundException ex) {
                Logger.getLogger(ViewReportUI.class.getName()).log(Level.SEVERE, null, ex);
            } catch (ParseException ex) {
                Logger.getLogger(ViewReportUI.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
    });
}

From source file:interfaceTisseoWS.ST4.java

/**
 * @param args the command line arguments
 *//*from   w  ww  . j  a  va2  s .  c o  m*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(ST4.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(ST4.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(ST4.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(ST4.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        @Override
        public void run() {
            try {
                new ST4().setVisible(true);
            } catch (ParseException ex) {
                Logger.getLogger(ST4.class.getName()).log(Level.SEVERE, null, ex);
            } catch (IOException ex) {
                Logger.getLogger(ST4.class.getName()).log(Level.SEVERE, null, ex);
            } catch (URISyntaxException ex) {
                Logger.getLogger(ST4.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
    });
}

From source file:diffhunter.DiffHunter.java

/**
 * @param args the command line arguments
 * @throws org.apache.commons.cli.ParseException
 * @throws java.io.IOException/*from  w w  w  .  ja  va2  s  .  c  o  m*/
 */
public static void main(String[] args) throws ParseException, IOException {

    //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString();

    // TODO code application logic here
    /*args = new String[]
    {
    "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData"
    };*/

    /*args = new String[]
    {
    "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData"
    };*/
    Options options = new Options();

    // add t option
    options.addOption("i", "index", false, "Indexing BED files.");
    options.addOption("b", "bed", true, "bed file to be indexed");
    options.addOption("o", "output", true, "Folder that the index/comparison file will be created.");
    options.addOption("r", "reference", true, "Reference annotation file to be used for indexing");
    options.addOption("c", "compare", false, "Finding differences between two conditions");
    options.addOption("1", "first", true, "First sample index location");
    options.addOption("2", "second", true, "Second sample index location");
    options.addOption("w", "window", true, "Length of window for identifying differences");
    options.addOption("s", "sliding", true, "Length of sliding");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);

    boolean indexing = false;
    boolean comparing = false;

    //Indexing!
    if (cmd.hasOption("i")) {
        //if(cmd.hasOption("1"))
        //System.err.println("sasan");

        //System.out.println("sasa");
        indexing = true;

    } else if (cmd.hasOption("c")) {
        //System.err.println("");
        comparing = true;

    } else {
        //System.err.println("Option is not deteced.");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("diffhunter", options);
        return;
    }

    //Indexing is selected
    //
    if (indexing == true) {
        //Since indexing is true.
        //User have to provide file for indexing.
        if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String bedfile_ = cmd.getOptionValue("b");
        String reference_file = cmd.getOptionValue("r");
        String folder_loc = cmd.getOptionValue("o");

        String sample_name = FilenameUtils.getBaseName(bedfile_);

        try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(
                Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) {
            Indexer indexing_ = new Indexer(reference_file);
            indexing_.Make_Index(B2, bedfile_,
                    Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString());
            B2.close();

        }
    } else if (comparing == true) {
        if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1")
                || cmd.hasOption("2"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String folder_loc = cmd.getOptionValue("o");
        int window_ = Integer.parseInt(cmd.getOptionValue("w"));
        //int window_=600;

        int slide_ = Integer.parseInt(cmd.getOptionValue("s"));

        String first = cmd.getOptionValue("1").replace("_BDB", "");
        String second = cmd.getOptionValue("2").replace("_BDB", "");
        String reference_file = cmd.getOptionValue("r");
        //String folder_loc=cmd.getOptionValue("o");

        String sample_name_first = FilenameUtils.getBaseName(first);
        String sample_name_second = FilenameUtils.getBaseName(second);

        Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first);
        Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second);

        List<String> first_condition_genes = Files
                .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        List<String> second_condition_genes = Files
                .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        System.out.println("First and second condition are loaded!!! ");
        List<String> intersection_ = new ArrayList<>(first_condition_genes);
        intersection_.retainAll(second_condition_genes);

        BufferedWriter output = new BufferedWriter(
                new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt")
                        .toAbsolutePath().toString(), false));
        List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>());
        Worker_New worker_class = new Worker_New();
        worker_class.Read_Reference(reference_file);

        while (!intersection_.isEmpty()) {
            List<String> selected_genes = new ArrayList<>();
            //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));}
            //else selected_genes.addAll(intersection_.subList(0, 10000));
            if (intersection_.size() <= intersection_.size()) {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            } else {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            }
            intersection_.removeAll(selected_genes);
            //System.out.println("Intersection count is:"+intersection_.size());
            //final List<Result_Window> resultssss_=new ArrayList<>();
            IntStream.range(0, selected_genes.size()).parallel().forEach(i -> {
                System.out.println(selected_genes.get(i) + "\tprocessing......");
                String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2";
                int start = worker_class.dic_genes.get(gene_of_interest).start_loc;
                int end = worker_class.dic_genes.get(gene_of_interest).end_loc;

                Map<Integer, Integer> first_ = Collections.EMPTY_MAP;
                try {
                    first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }

                Map<Integer, Integer> second_ = Collections.EMPTY_MAP;
                try {
                    second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }
                List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_);
                List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_);
                //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i));
                // System.out.println("top_window_first_Count\t"+top_windows_first.size());
                // System.out.println("top_window_second_Count\t"+top_windows_second.size());
                if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) {
                    return;
                }

                List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start,
                        end, top_windows_first, top_windows_second, second_, first_, sample_name_first,
                        sample_name_second, 0.01);
                if (!res_temp.isEmpty()) {
                    final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01));

                } //System.out.println(selected_genes.get(i)+"\tprocessed.");

            });

            /*selected_genes.parallelStream().forEach(i ->
             {
                    
                    
             });*/
            List<Double> pvals = new ArrayList<>();

            for (int i = 0; i < final_results.size(); i++) {
                pvals.add(final_results.get(i).p_value);
            }
            List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals);

            System.out.println("Writing to file...");
            output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR");
            output.newLine();

            for (int i = 0; i < final_results.size(); i++) {
                Result_Window item = final_results.get(i);
                output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t"
                        + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value
                        + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
                output.newLine();
            }

            /* for (Result_Window item : final_results)
             {
            output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
            output.newLine();
             }
               */
            final_results.clear();

        }
        output.close();

    }
    System.out.println("Done.");

}

From source file:di.uniba.it.tee2.gui.TEEgui.java

/**
 * @param args the command line arguments
 *//*ww  w.  j  av  a 2  s .c o m*/
public static void main(String args[]) {

    try {
        CommandLine cmd = cmdParser.parse(options, args);
        if (cmd.hasOption("l") && cmd.hasOption("d")) {
            language = cmd.getOptionValue("l");
            maindir = cmd.getOptionValue("d");
            /* Set the Nimbus look and feel */
            //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
            /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
                 * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
                 */
            try {
                for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager
                        .getInstalledLookAndFeels()) {
                    if ("Nimbus".equals(info.getName())) {
                        javax.swing.UIManager.setLookAndFeel(info.getClassName());
                        break;
                    }
                }
            } catch (ClassNotFoundException ex) {
                java.util.logging.Logger.getLogger(TEEgui.class.getName()).log(java.util.logging.Level.SEVERE,
                        null, ex);
            } catch (InstantiationException ex) {
                java.util.logging.Logger.getLogger(TEEgui.class.getName()).log(java.util.logging.Level.SEVERE,
                        null, ex);
            } catch (IllegalAccessException ex) {
                java.util.logging.Logger.getLogger(TEEgui.class.getName()).log(java.util.logging.Level.SEVERE,
                        null, ex);
            } catch (javax.swing.UnsupportedLookAndFeelException ex) {
                java.util.logging.Logger.getLogger(TEEgui.class.getName()).log(java.util.logging.Level.SEVERE,
                        null, ex);
            }
            //</editor-fold>

            /* Create and display the form */
            java.awt.EventQueue.invokeLater(new Runnable() {
                public void run() {
                    try {
                        new TEEgui().setVisible(true);
                    } catch (IOException ex) {
                        Logger.getLogger(TEEgui.class.getName()).log(Level.SEVERE, null, ex);
                    }
                }
            });
        } else {
            HelpFormatter helpFormatter = new HelpFormatter();
            helpFormatter.printHelp("Run GUI", options, true);
        }
    } catch (ParseException ex) {
        Logger.getLogger(TEEgui.class.getName()).log(Level.SEVERE, null, ex);
    }
    //</editor-fold>
}

From source file:javadepchecker.Main.java

/**
 * @param args the command line arguments
 *//* w ww.j a v a2s  . c  om*/
public static void main(String[] args) throws IOException {
    int exit = 0;
    try {
        CommandLineParser parser = new PosixParser();
        Options options = new Options();
        options.addOption("h", "help", false, "print help");
        options.addOption("i", "image", true, "image directory");
        options.addOption("v", "verbose", false, "print verbose output");
        CommandLine line = parser.parse(options, args);
        String[] files = line.getArgs();
        if (line.hasOption("h") || files.length == 0) {
            HelpFormatter h = new HelpFormatter();
            h.printHelp("java-dep-check [-i <image>] <package.env>+", options);
        } else {
            image = line.getOptionValue("i", "");

            for (String arg : files) {
                if (line.hasOption('v')) {
                    System.out.println("Checking " + arg);
                }
                if (!checkPkg(new File(arg))) {
                    exit = 1;
                }
            }
        }
    } catch (ParseException ex) {
        Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
    System.exit(exit);
}

From source file:com.pawandubey.griffin.Griffin.java

/**
 * @param args the command line arguments
 * @throws java.io.IOException the exception
 * @throws java.lang.InterruptedException the exception
 *///from  w w  w.  ja va2s .co m
public static void main(String[] args) throws IOException, InterruptedException {
    try {
        Griffin griffin = new Griffin();

        CmdLineParser parser = new CmdLineParser(griffin, ParserProperties.defaults().withUsageWidth(120));
        parser.parseArgument(args);

        if (griffin.help || griffin.version || args.length == 0) {
            griffin.printHelpMessage();
            parser.printUsage(System.out);
        } else {
            griffin.commands.execute();
        }
    } catch (CmdLineException ex) {
        Logger.getLogger(Griffin.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:it.unipd.dei.ims.falcon.CmdLine.java

public static void main(String[] args) {

    // last argument is always index path
    Options options = new Options();
    // one of these actions has to be specified
    OptionGroup actionGroup = new OptionGroup();
    actionGroup.addOption(new Option("i", true, "perform indexing")); // if dir, all files, else only one file
    actionGroup.addOption(new Option("q", true, "perform a single query"));
    actionGroup.addOption(new Option("b", false, "perform a query batch (read from stdin)"));
    actionGroup.setRequired(true);//from   w ww. j  a  va2 s. c om
    options.addOptionGroup(actionGroup);

    // other options
    options.addOption(new Option("l", "segment-length", true, "length of a segment (# of chroma vectors)"));
    options.addOption(
            new Option("o", "segment-overlap", true, "overlap portion of a segment (# of chroma vectors)"));
    options.addOption(new Option("Q", "quantization-level", true, "quantization level for chroma vectors"));
    options.addOption(new Option("k", "min-kurtosis", true, "minimum kurtosis for indexing chroma vectors"));
    options.addOption(new Option("s", "sub-sampling", true, "sub-sampling of chroma features"));
    options.addOption(new Option("v", "verbose", false, "verbose output (including timing info)"));
    options.addOption(new Option("T", "transposition-estimator-strategy", true,
            "parametrization for the transposition estimator strategy"));
    options.addOption(new Option("t", "n-transp", true,
            "number of transposition; if not specified, no transposition is performed"));
    options.addOption(new Option("f", "force-transp", true, "force transposition by an amount of semitones"));
    options.addOption(new Option("p", "pruning", false,
            "enable query pruning; if -P is unspecified, use default strategy"));
    options.addOption(new Option("P", "pruning-custom", true, "custom query pruning strategy"));

    // parse
    HelpFormatter formatter = new HelpFormatter();
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
        if (cmd.getArgs().length != 1)
            throw new ParseException("no index path was specified");
    } catch (ParseException ex) {
        System.err.println("ERROR - parsing command line:");
        System.err.println(ex.getMessage());
        formatter.printHelp("falcon -{i,q,b} [options] index_path", options);
        return;
    }

    // default values
    final float[] DEFAULT_TRANSPOSITION_ESTIMATOR_STRATEGY = new float[] { 0.65192807f, 0.0f, 0.0f, 0.0f,
            0.3532628f, 0.4997167f, 0.0f, 0.41703504f, 0.0f, 0.16297342f, 0.0f, 0.0f };
    final String DEFAULT_QUERY_PRUNING_STRATEGY = "ntf:0.340765*[0.001694,0.995720];ndf:0.344143*[0.007224,0.997113];"
            + "ncf:0.338766*[0.001601,0.995038];nmf:0.331577*[0.002352,0.997884];"; // TODO not the final one

    int hashes_per_segment = Integer.parseInt(cmd.getOptionValue("l", "150"));
    int overlap_per_segment = Integer.parseInt(cmd.getOptionValue("o", "50"));
    int nranks = Integer.parseInt(cmd.getOptionValue("Q", "3"));
    int subsampling = Integer.parseInt(cmd.getOptionValue("s", "1"));
    double minkurtosis = Float.parseFloat(cmd.getOptionValue("k", "-100."));
    boolean verbose = cmd.hasOption("v");
    int ntransp = Integer.parseInt(cmd.getOptionValue("t", "1"));
    TranspositionEstimator tpe = null;
    if (cmd.hasOption("t")) {
        if (cmd.hasOption("T")) {
            // TODO this if branch is yet to test
            Pattern p = Pattern.compile("\\d\\.\\d*");
            LinkedList<Double> tokens = new LinkedList<Double>();
            Matcher m = p.matcher(cmd.getOptionValue("T"));
            while (m.find())
                tokens.addLast(new Double(cmd.getOptionValue("T").substring(m.start(), m.end())));
            float[] strategy = new float[tokens.size()];
            if (strategy.length != 12) {
                System.err.println("invalid transposition estimator strategy");
                System.exit(1);
            }
            for (int i = 0; i < strategy.length; i++)
                strategy[i] = new Float(tokens.pollFirst());
        } else {
            tpe = new TranspositionEstimator(DEFAULT_TRANSPOSITION_ESTIMATOR_STRATEGY);
        }
    } else if (cmd.hasOption("f")) {
        int[] transps = parseIntArray(cmd.getOptionValue("f"));
        tpe = new ForcedTranspositionEstimator(transps);
        ntransp = transps.length;
    }
    QueryPruningStrategy qpe = null;
    if (cmd.hasOption("p")) {
        if (cmd.hasOption("P")) {
            qpe = new StaticQueryPruningStrategy(cmd.getOptionValue("P"));
        } else {
            qpe = new StaticQueryPruningStrategy(DEFAULT_QUERY_PRUNING_STRATEGY);
        }
    }

    // action
    if (cmd.hasOption("i")) {
        try {
            Indexing.index(new File(cmd.getOptionValue("i")), new File(cmd.getArgs()[0]), hashes_per_segment,
                    overlap_per_segment, subsampling, nranks, minkurtosis, tpe, verbose);
        } catch (IndexingException ex) {
            Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex);
        } catch (IOException ex) {
            Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
    if (cmd.hasOption("q")) {
        String queryfilepath = cmd.getOptionValue("q");
        doQuery(cmd, queryfilepath, hashes_per_segment, overlap_per_segment, nranks, subsampling, tpe, ntransp,
                minkurtosis, qpe, verbose);
    }
    if (cmd.hasOption("b")) {
        try {
            long starttime = System.currentTimeMillis();
            BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
            String line = null;
            while ((line = in.readLine()) != null && !line.trim().isEmpty())
                doQuery(cmd, line, hashes_per_segment, overlap_per_segment, nranks, subsampling, tpe, ntransp,
                        minkurtosis, qpe, verbose);
            in.close();
            long endtime = System.currentTimeMillis();
            System.out.println(String.format("total time: %ds", (endtime - starttime) / 1000));
        } catch (IOException ex) {
            Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

From source file:com.guns.media.tools.yuv.MediaTool.java

/**
 * @param args the command line arguments
 *///from  w  w w .j  a v a2  s  .  co  m
public static void main(String[] args) throws IOException {

    try {
        Options options = getOptions();
        CommandLine cmd = null;
        int offset = 0;
        CommandLineParser parser = new GnuParser();
        cmd = parser.parse(options, args);

        if (cmd.hasOption("help")) {
            printHelp(options);
            exit(1);
        }

        if (cmd.hasOption("offset")) {
            offset = new Integer(cmd.getOptionValue("offset"));
        }
        int frame = new Integer(cmd.getOptionValue("f"));

        //  int scale = new Integer(args[2]);
        BufferedInputStream if1 = new BufferedInputStream(new FileInputStream(cmd.getOptionValue("if1")));
        BufferedInputStream if2 = new BufferedInputStream(new FileInputStream(cmd.getOptionValue("if2")));

        DataStorage.create(new Integer(cmd.getOptionValue("f")));

        int width = new Integer(cmd.getOptionValue("w"));
        int height = new Integer(cmd.getOptionValue("h"));
        LookUp.initSSYUV(width, height);
        //  int[][] frame1 = new int[width][height];
        //  int[][] frame2 = new int[width][height];
        int nRead;
        int fRead;
        byte[] data = new byte[width * height + ((width * height) / 2)];
        byte[] data1 = new byte[width * height + ((width * height) / 2)];
        int frames = 0;
        long start_ms = System.currentTimeMillis() / 1000L;
        long end_ms = start_ms;

        if (offset > 0) {
            if1.skip(((width * height + ((width * height) / 2)) * offset));
        } else if (offset < 0) {
            if2.skip(((width * height + ((width * height) / 2)) * (-1 * offset)));
        }

        if (cmd.hasOption("psnr")) {
            ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newCachedThreadPool();
            while ((nRead = if1.read(data)) != -1 && ((fRead = if2.read(data1)) != -1) && frames < frame) {
                byte[] data_out = data.clone();
                byte[] data1_out = data1.clone();

                PSNRCalculatorThread wt = new PSNRCalculatorThread(data_out, data1_out, frames, width, height);
                executor.execute(wt);
                frames++;

            }
            executor.shutdown();
            end_ms = System.currentTimeMillis();

            System.out.println("Frame Rate :" + frames * 1000 / ((end_ms - start_ms)));
            for (int i = 0; i < frames; i++) {
                System.out.println(
                        i + "," + 10 * Math.log10((255 * 255) / (DataStorage.getFrame(i) / (width * height))));

            }
        }
        if (cmd.hasOption("sub")) {

            RandomAccessFile raf = new RandomAccessFile(cmd.getOptionValue("o"), "rw");

            ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newCachedThreadPool();
            while ((nRead = if1.read(data)) != -1 && ((fRead = if2.read(data1)) != -1)) {
                byte[] data_out = data.clone();
                byte[] data1_out = data1.clone();

                ImageSubstractThread wt = new ImageSubstractThread(data_out, data1_out, frames, width, height,
                        raf);
                //wt.run();
                executor.execute(wt);

                frames++;

            }
            executor.shutdown();
            end_ms = System.currentTimeMillis() / 1000L;
            System.out.println("Frame Rate :" + frames / ((end_ms - start_ms)));

            raf.close();
        }
        if (cmd.hasOption("ss") && !cmd.getOptionValue("o").matches("-")) {

            RandomAccessFile raf = new RandomAccessFile(cmd.getOptionValue("o"), "rw");

            // RandomAccessFile ra =  new RandomAccessFile(cmd.getOptionValue("o"), "rw");
            // MappedByteBuffer raf = new RandomAccessFile(cmd.getOptionValue("o"), "rw").getChannel().map(FileChannel.MapMode.READ_WRITE, 0, ((width*height)+(width*height/2))*frame);
            ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newCachedThreadPool();
            while ((nRead = if1.read(data)) != -1 && ((fRead = if2.read(data1)) != -1) && frames < frame) {
                byte[] data_out = data.clone();
                byte[] data1_out = data1.clone();

                SidebySideImageThread wt = new SidebySideImageThread(data_out, data1_out, frames, width, height,
                        raf);
                // MPSidebySideImageThread wt = new MPSidebySideImageThread(data_out, data1_out, frames, width, height, ra);
                frames++;
                // wt.run();

                executor.execute(wt);
            }
            executor.shutdown();
            end_ms = System.currentTimeMillis() / 1000L;

            while (!executor.isTerminated()) {

            }

            raf.close();
        }
        if (cmd.hasOption("ss") && cmd.getOptionValue("o").matches("-")) {

            PrintStream stdout = new PrintStream(System.out);

            // RandomAccessFile ra =  new RandomAccessFile(cmd.getOptionValue("o"), "rw");
            // MappedByteBuffer raf = new RandomAccessFile(cmd.getOptionValue("o"), "rw").getChannel().map(FileChannel.MapMode.READ_WRITE, 0, ((width*height)+(width*height/2))*frame);
            // ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newCachedThreadPool();
            while ((nRead = if1.read(data)) != -1 && ((fRead = if2.read(data1)) != -1) && frames < frame) {
                byte[] data_out = data.clone();
                byte[] data1_out = data1.clone();

                SidebySideImageThread wt = new SidebySideImageThread(data_out, data1_out, frames, width, height,
                        stdout);
                // MPSidebySideImageThread wt = new MPSidebySideImageThread(data_out, data1_out, frames, width, height, ra);
                frames++;
                // wt.run();

                wt.run();
            }

            end_ms = System.currentTimeMillis() / 1000L;
            System.out.println("Frame Rate :" + frames / ((end_ms - start_ms)));

            stdout.close();
        }
        if (cmd.hasOption("image")) {

            System.setProperty("java.awt.headless", "true");
            //ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newCachedThreadPool();
            ThreadPoolExecutor executor = (ThreadPoolExecutor) Executors.newFixedThreadPool(10);
            while ((nRead = if1.read(data)) != -1 && ((fRead = if2.read(data1)) != -1)) {

                if (frames == frame) {
                    byte[] data_out = data.clone();
                    byte[] data1_out = data1.clone();

                    Frame f1 = new Frame(data_out, width, height, Frame.YUV420);
                    Frame f2 = new Frame(data1_out, width, height, Frame.YUV420);
                    //       System.out.println(cmd.getOptionValue("o"));
                    ExtractImageThread wt = new ExtractImageThread(f1, frames,
                            cmd.getOptionValue("if1") + "frame1-" + cmd.getOptionValue("o"));
                    ExtractImageThread wt1 = new ExtractImageThread(f2, frames,
                            cmd.getOptionValue("if2") + "frame2-" + cmd.getOptionValue("o"));
                    //   executor.execute(wt);
                    executor.execute(wt);
                    executor.execute(wt1);
                }
                frames++;

            }
            executor.shutdown();
            //  executor.shutdown();
            end_ms = System.currentTimeMillis() / 1000L;
            System.out.println("Frame Rate :" + frames / ((end_ms - start_ms)));
        }

    } catch (ParseException ex) {
        Logger.getLogger(MediaTool.class.getName()).log(Level.SEVERE, null, ex);
    }
}