Example usage for java.util Arrays toString

List of usage examples for java.util Arrays toString

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Introduction

In this page you can find the example usage for java.util Arrays toString.

Prototype

public static String toString(Object[] a)

Source Link

Document

Returns a string representation of the contents of the specified array.

Usage

From source file:deck36.storm.plan9.nodejs.ExtendedKittenRobbersTopology.java

public static void main(String[] args) throws Exception {

    String env = null;// ww  w  .j a v a  2 s . c  o m

    if (args != null && args.length > 0) {
        env = args[0];
    }

    if (!"dev".equals(env))
        if (!"prod".equals(env)) {
            System.out.println("Usage: $0 (dev|prod)\n");
            System.exit(1);
        }

    // Topology config
    Config conf = new Config();

    // Load parameters and add them to the Config
    Map configMap = YamlLoader.loadYamlFromResource("storm_" + env + ".yml");

    conf.putAll(configMap);

    log.info(JSONValue.toJSONString((conf)));

    // Set topology loglevel to DEBUG
    conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug"));

    // Create Topology builder
    TopologyBuilder builder = new TopologyBuilder();

    // if there are not special reasons, start with parallelism hint of 1
    // and multiple tasks. By that, you can scale dynamically later on.
    int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint");
    int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks");

    String badgeName = ExtendedKittenRobbersTopology.class.getSimpleName();

    // Create Stream from RabbitMQ messages
    // bind new queue with name of the topology
    // to the main plan9 exchange (from properties config)
    // consuming only CBT-related events by using the rounting key 'cbt.#'

    String rabbitQueueName = badgeName; // use topology class name as name for the queue
    String rabbitExchangeName = JsonPath.read(conf,
            "$.deck36_storm.ExtendedKittenRobbersBolt.rabbitmq.exchange");
    String rabbitRoutingKey = JsonPath.read(conf,
            "$.deck36_storm.ExtendedKittenRobbersBolt.rabbitmq.routing_key");

    // Get JSON deserialization scheme
    Scheme rabbitScheme = new SimpleJSONScheme();

    // Setup a Declarator to configure exchange/queue/routing key
    RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName,
            rabbitRoutingKey);

    // Create Configuration for the Spout
    ConnectionConfig connectionConfig = new ConnectionConfig(
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"),
            (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"),
            (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat"));

    ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName)
            .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail()
            .build();

    // add global parameters to topology config - the RabbitMQSpout will read them from there
    conf.putAll(spoutConfig.asMap());

    // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch
    // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md
    if ("prod".equals(env)) {
        conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING,
                (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch"));
    }

    // Add RabbitMQ spout to topology
    builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint)
            .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks"));

    // construct command to invoke the external bolt implementation
    ArrayList<String> command = new ArrayList(15);

    // Add main execution program (php, hhvm, zend, ..) and parameters
    command.add((String) JsonPath.read(conf, "$.deck36_storm.nodejs.executor"));

    // Add main route to be invoked and its parameters
    command.add((String) JsonPath.read(conf, "$.deck36_storm.ExtendedKittenRobbersBolt.main"));
    List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.ExtendedKittenRobbersBolt.params");
    if (boltParams != null)
        command.addAll(boltParams);

    // Log the final command
    log.info("Command to start bolt for Extended Kitten Robbers From Outer Space: "
            + Arrays.toString(command.toArray()));

    // CODE1
    /* We need to use the tick tuple adapter instead of the general adapter:
            
    // Add constructed external bolt command to topology using MultilangAdapterTickTupleBolt
    builder.setBolt("badge",
        new MultilangAdapterTickTupleBolt(
                command,
                (Integer) JsonPath.read(conf, "$.deck36_storm.ExtendedKittenRobbersBolt.robber_frequency"),
                "badge"
        ),
        parallelism_hint)
        .setNumTasks(num_tasks)
        .shuffleGrouping("incoming");
            
    */

    builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt(
            (String) JsonPath.read(conf, "$.deck36_storm.ExtendedKittenRobbersBolt.rabbitmq.target_exchange"),
            "KittenRobbers" // RabbitMQ routing key
    ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge");

    builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks)
            .shuffleGrouping("rabbitmq_router");

    if ("dev".equals(env)) {
        LocalCluster cluster = new LocalCluster();
        cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology());
        Thread.sleep(2000000);
    }

    if ("prod".equals(env)) {
        StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf,
                builder.createTopology());
    }

}

From source file:deck36.storm.plan9.php.DeludedKittenRobbersTopology.java

public static void main(String[] args) throws Exception {

    String env = null;//from  w ww  .  j  av  a2s .  c o  m

    if (args != null && args.length > 0) {
        env = args[0];
    }

    if (!"dev".equals(env))
        if (!"prod".equals(env)) {
            System.out.println("Usage: $0 (dev|prod)\n");
            System.exit(1);
        }

    // Topology config
    Config conf = new Config();

    // Load parameters and add them to the Config
    Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml");

    conf.putAll(configMap);

    log.info(JSONValue.toJSONString((conf)));

    // Set topology loglevel to DEBUG
    conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug"));

    // Create Topology builder
    TopologyBuilder builder = new TopologyBuilder();

    // if there are not special reasons, start with parallelism hint of 1
    // and multiple tasks. By that, you can scale dynamically later on.
    int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint");
    int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks");

    // Create Stream from RabbitMQ messages
    // bind new queue with name of the topology
    // to the main plan9 exchange (from properties config)
    // consuming only CBT-related events by using the rounting key 'cbt.#'

    String badgeName = DeludedKittenRobbersTopology.class.getSimpleName();

    String rabbitQueueName = badgeName; // use topology class name as name for the queue
    String rabbitExchangeName = JsonPath.read(conf,
            "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.exchange");
    String rabbitRoutingKey = JsonPath.read(conf,
            "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.routing_key");

    // Get JSON deserialization scheme
    Scheme rabbitScheme = new SimpleJSONScheme();

    // Setup a Declarator to configure exchange/queue/routing key
    RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName,
            rabbitRoutingKey);

    // Create Configuration for the Spout
    ConnectionConfig connectionConfig = new ConnectionConfig(
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"),
            (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"),
            (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"),
            (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat"));

    ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName)
            .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail()
            .build();

    // add global parameters to topology config - the RabbitMQSpout will read them from there
    conf.putAll(spoutConfig.asMap());

    // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch
    // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md
    if ("prod".equals(env)) {
        conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING,
                (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch"));
    }

    // Add RabbitMQ spout to topology
    builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint)
            .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks"));

    // construct command to invoke the external bolt implementation
    ArrayList<String> command = new ArrayList(15);

    // Add main execution program (php, hhvm, zend, ..) and parameters
    command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor"));
    command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params"));

    // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.)
    command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main"));
    command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params"));

    // Add main route to be invoked and its parameters
    command.add((String) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.main"));
    List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.params");
    if (boltParams != null)
        command.addAll(boltParams);

    // Log the final command
    log.info("Command to start bolt for Deluded Kitten Robbers: " + Arrays.toString(command.toArray()));

    // Add constructed external bolt command to topology using MultilangAdapterTickTupleBolt
    builder.setBolt("badge", new MultilangAdapterTickTupleBolt(command,
            (Integer) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.attack_frequency_secs"),
            "badge"), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("incoming");

    builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt(
            (String) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.target_exchange"),
            "DeludedKittenRobbers" // RabbitMQ routing key
    ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge");

    builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks)
            .shuffleGrouping("rabbitmq_router");

    if ("dev".equals(env)) {
        LocalCluster cluster = new LocalCluster();
        cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology());
        Thread.sleep(2000000);
    }

    if ("prod".equals(env)) {
        StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf,
                builder.createTopology());
    }

}

From source file:PartitionLR.java

public static void main(String[] args) {

    if (args.length < 6) {
        System.err.println("Usage: JavaHdfsLR <master> <file> <iters> <L> <D> <use FPGA?> (<testing file>)");
        System.exit(1);/*from  w ww .ja  v a 2s .c o  m*/
    }
    int ITERATIONS = Integer.parseInt(args[2]);
    System.out.println("iterations: " + ITERATIONS);
    L = Integer.parseInt(args[3]);
    System.out.println("L: " + L);
    D = Integer.parseInt(args[4]);
    System.out.println("D: " + D);
    useFPGA = Integer.parseInt(args[5]);
    System.out.println("use FPGA: " + useFPGA);

    JavaSparkContext sc = new JavaSparkContext(args[0], "PartitionLR", System.getenv("SPARK_HOME"),
            "target/simple-project-1.0.jar");
    JavaRDD<String> lines = sc.textFile(args[1]);
    JavaRDD<DataPoint> points = lines.map(new ParsePoint()).repartition(32).cache();

    float[][] w = new float[L][D];
    for (int i = 0; i < L; i++) {
        for (int j = 0; j < D; j++) {
            w[i][j] = 0.0f;
        }
    }

    System.out.print("Initial w: ");
    printWeights(w);

    for (int k = 1; k <= ITERATIONS; k++) {
        System.out.println("On iteration " + k);

        long tic = System.nanoTime();
        float[][] gradient = points.mapPartitions(new BackwardLR(w)).reduce(new VectorSum());
        System.out.println("elapsed time: " + (System.nanoTime() - tic) / 1e9);

        for (int i = 0; i < L; i++) {
            for (int j = 0; j < D; j++) {
                w[i][j] -= gradient[i][j];
            }
        }

    }

    System.out.print("Final w: ");
    printWeights(w);

    lines = sc.textFile(args.length < 7 ? args[1] : args[6]);
    System.out.println("first prediction");
    System.out.println(Arrays
            .toString(lines.map(new ParsePoint()).repartition(32).mapPartitions(new ForwardLR(w)).first()));

    System.exit(0);
}

From source file:eu.fbk.utils.twm.FormPageSearcher.java

public static void main(final String args[]) throws Exception {
    String logConfig = System.getProperty("log-config");
    if (logConfig == null) {
        logConfig = "configuration/log-config.txt";
    }//from  www .j a  va2s.  c  o  m

    PropertyConfigurator.configure(logConfig);
    final Options options = new Options();
    try {
        OptionBuilder.withArgName("index");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("open an index with the specified name");
        OptionBuilder.isRequired();
        OptionBuilder.withLongOpt("index");
        final Option indexNameOpt = OptionBuilder.create("i");
        OptionBuilder.withArgName("interactive-mode");
        OptionBuilder.withDescription("enter in the interactive mode");
        OptionBuilder.withLongOpt("interactive-mode");
        final Option interactiveModeOpt = OptionBuilder.create("t");
        OptionBuilder.withArgName("search");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("search for the specified key");
        OptionBuilder.withLongOpt("search");
        final Option searchOpt = OptionBuilder.create("s");
        OptionBuilder.withArgName("key-freq");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("read the keys' frequencies from the specified file");
        OptionBuilder.withLongOpt("key-freq");
        final Option freqFileOpt = OptionBuilder.create("f");
        OptionBuilder.withArgName("minimum-freq");
        // Option keyFieldNameOpt =
        // OptionBuilder.withArgName("key-field-name").hasArg().withDescription("use the specified name for the field key").withLongOpt("key-field-name").create("k");
        // Option valueFieldNameOpt =
        // OptionBuilder.withArgName("value-field-name").hasArg().withDescription("use the specified name for the field value").withLongOpt("value-field-name").create("v");
        final Option minimumKeyFreqOpt = OptionBuilder.hasArg()
                .withDescription("minimum key frequency of cached values (default is " + DEFAULT_MIN_FREQ + ")")
                .withLongOpt("minimum-freq").create("m");
        OptionBuilder.withArgName("int");
        final Option notificationPointOpt = OptionBuilder.hasArg()
                .withDescription(
                        "receive notification every n pages (default is " + DEFAULT_NOTIFICATION_POINT + ")")
                .withLongOpt("notification-point").create("b");
        options.addOption("h", "help", false, "print this message");
        options.addOption("v", "version", false, "output version information and exit");

        options.addOption(indexNameOpt);
        options.addOption(interactiveModeOpt);
        options.addOption(searchOpt);
        options.addOption(freqFileOpt);
        // options.addOption(keyFieldNameOpt);
        // options.addOption(valueFieldNameOpt);
        options.addOption(minimumKeyFreqOpt);
        options.addOption(notificationPointOpt);

        final CommandLineParser parser = new PosixParser();
        final CommandLine line = parser.parse(options, args);

        if (line.hasOption("help") || line.hasOption("version")) {
            throw new ParseException("");
        }

        int minFreq = DEFAULT_MIN_FREQ;
        if (line.hasOption("minimum-freq")) {
            minFreq = Integer.parseInt(line.getOptionValue("minimum-freq"));
        }

        int notificationPoint = DEFAULT_NOTIFICATION_POINT;
        if (line.hasOption("notification-point")) {
            notificationPoint = Integer.parseInt(line.getOptionValue("notification-point"));
        }

        final FormPageSearcher pageFormSearcher = new FormPageSearcher(line.getOptionValue("index"));
        pageFormSearcher.setNotificationPoint(notificationPoint);
        /*
         * logger.debug(line.getOptionValue("key-field-name") + "\t" +
         * line.getOptionValue("value-field-name")); if (line.hasOption("key-field-name")) {
         * pageFormSearcher.setKeyFieldName(line.getOptionValue("key-field-name")); } if
         * (line.hasOption("value-field-name")) {
         * pageFormSearcher.setValueFieldName(line.getOptionValue("value-field-name")); }
         */
        if (line.hasOption("key-freq")) {
            pageFormSearcher.loadCache(line.getOptionValue("key-freq"), minFreq);
        }
        if (line.hasOption("search")) {
            logger.debug("searching " + line.getOptionValue("search") + "...");
            final FreqSetSearcher.Entry[] result = pageFormSearcher.search(line.getOptionValue("search"));
            logger.info(Arrays.toString(result));
        }
        if (line.hasOption("interactive-mode")) {
            pageFormSearcher.interactive();
        }
    } catch (final ParseException e) {
        // oops, something went wrong
        if (e.getMessage().length() > 0) {
            System.out.println("Parsing failed: " + e.getMessage() + "\n");
        }
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(400,
                "java -cp dist/thewikimachine.jar org.fbk.cit.hlt.thewikimachine.index.FormPageSearcher", "\n",
                options, "\n", true);
    }
}

From source file:fr.inria.atlanmod.atl_mr.utils.NeoEMFHBaseMigrator.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file, both of xmi and zxmi extensions are supported");
    inputOpt.setArgs(1);//from ww  w  .  j a v  a2  s  . c  o m
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output HBase resource URI");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(E_PACKAGE);
    inClassOpt.setArgName("METAMODEL");
    inClassOpt.setDescription("URI of the ecore Metamodel");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = URI.createURI(commandLine.getOptionValue(OUT));
        URI metamodelUri = URI.createFileURI(commandLine.getOptionValue(E_PACKAGE));

        NeoEMFHBaseMigrator.class.getClassLoader().loadClass(commandLine.getOptionValue(E_PACKAGE))
                .getMethod("init").invoke(null);
        //org.eclipse.gmt.modisco.java.kyanos.impl.JavaPackageImpl.init();

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("ecore",
                new EcoreResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(KyanosURI.KYANOS_HBASE_SCHEME,
                KyanosResourceFactory.eINSTANCE);

        //Registering the metamodel
        //         Resource MMResource = resourceSet.createResource(metamodelUri);
        //         MMResource.load(Collections.EMPTY_MAP);
        //         ATLMRUtils.registerPackages(resourceSet, MMResource);
        //Loading the XMI resource
        Resource sourceResource = resourceSet.createResource(sourceUri);
        Map<String, Object> loadOpts = new HashMap<String, Object>();

        if ("zxmi".equals(sourceUri.fileExtension())) {
            loadOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        }

        Runtime.getRuntime().gc();
        long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory before loading: {0}",
                ATLMRUtils.byteCountToDisplaySize(initialUsedMemory)));
        LOG.log(Level.INFO, "Loading source resource");
        sourceResource.load(loadOpts);
        LOG.log(Level.INFO, "Source resource loaded");
        Runtime.getRuntime().gc();
        long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory after loading: {0}",
                ATLMRUtils.byteCountToDisplaySize(finalUsedMemory)));
        LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                ATLMRUtils.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));

        Resource targetResource = resourceSet.createResource(targetUri);

        Map<String, Object> saveOpts = new HashMap<String, Object>();
        targetResource.save(saveOpts);

        LOG.log(Level.INFO, "Start moving elements");
        targetResource.getContents().clear();
        targetResource.getContents().addAll(sourceResource.getContents());
        LOG.log(Level.INFO, "End moving elements");
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saved");

        if (targetResource instanceof KyanosHbaseResourceImpl) {
            KyanosHbaseResourceImpl.shutdownWithoutUnload((KyanosHbaseResourceImpl) targetResource);
        } else {
            targetResource.unload();
        }

    } catch (ParseException e) {
        ATLMRUtils.showError(e.toString());
        ATLMRUtils.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        ATLMRUtils.showError(e.toString());
        e.printStackTrace();
    }
}

From source file:kishida.cnn.NeuralNetwork.java

public static void main(String[] args) throws IOException {
    NeuralNetwork nn = new NeuralNetwork();
    nn.getLayers()/*from w w  w .j a  v a 2 s  .  c  om*/
            .addAll(Arrays.asList(new InputLayer(20, 20), new ConvolutionLayer("conv1", 3, 7, 2, 1, true),
                    new MaxPoolingLayer("pool", 3, 2), new MultiNormalizeLayer("norm1", 5, .0001f, true),
                    new FullyConnect("test", 3, 0, 1, new LogisticFunction(), true)));
    nn.init();
    nn.random.nextInt();
    StringWriter sw = new StringWriter();
    nn.writeAsJson(sw);
    System.out.println(sw);

    // ??????????????
    StringReader sr0 = new StringReader(sw.toString());
    NeuralNetwork nn0 = nn.readFromJson(sr0);
    nn0.init();
    ConvolutionLayer conv1o = (ConvolutionLayer) nn.findLayerByName("conv1").get();
    ConvolutionLayer conv1r = (ConvolutionLayer) nn0.findLayerByName("conv1").get();
    System.out.println("org:" + Arrays.toString(conv1o.getFilter()));
    System.out.println("red:" + Arrays.toString(conv1r.getFilter()));
    double loss = IntStream.range(0, conv1o.getFilter().length)
            .mapToDouble(i -> (conv1o.getFilter()[i] - conv1r.getFilter()[i])
                    * (conv1o.getFilter()[i] - conv1r.getFilter()[i]))
            .sum();
    System.out.println(Math.sqrt(loss));

    NeuralNetwork v = NeuralNetwork.readFromJson(new StringReader("{\n" + "  \"weightDecay\" : 5.0E-4,\n"
            + "  \"miniBatch\" : 128,\n" + "  \"random\" : \"c3EAfgAAAT/wWGBKFyCXAAATnQ6sF654\",\n"
            + "  \"imageRandom\" : \"c3EAfgAAAAAAAAAAAAAAAAAABd7s70R4\",\n" + "  \"momentam\" : 0.9,\n"
            + "  \"layers\" : [ {\n" + "    \"InputLayer\" : {\n" + "      \"width\" : 250,\n"
            + "      \"height\" : 220,\n" + "      \"name\" : \"input\"\n" + "    }\n" + "  }, {\n"
            + "    \"ConvolutionLayer\" : {\n" + "      \"name\" : \"conv1\",\n" + "      \"filter\" : null,\n"
            + "      \"bias\" : [ 1.0, 1.0, 1.0 ],\n" + "      \"filterDelta\" : null,\n"
            + "      \"biasDelta\" : [ 0.0, 0.0, 0.0 ],\n" + "      \"stride\" : 2,\n"
            + "      \"filterSize\" : 7,\n" + "      \"useGpu\" : true\n" + "    }\n" + "  }, {\n"
            + "    \"MaxPoolingLayer\" : {\n" + "      \"name\" : \"pool\",\n" + "      \"size\" : 3,\n"
            + "      \"stride\" : 2\n" + "    }\n" + "  }, {\n" + "    \"MultiNormalizeLayer\" : {\n"
            + "      \"name\" : \"norm1\",\n" + "      \"size\" : 5,\n" + "      \"threshold\" : 1.0E-4,\n"
            + "      \"useGpu\" : true\n" + "    }\n" + "  }, {\n" + "    \"FullyConnect\" : {\n"
            + "      \"name\" : \"test\",\n" + "      \"outputSize\" : 3,\n"
            + "      \"weight\" : [ 0.0014115907, 0.0043465886, 0.01138472, -0.0013297468, "
            + "-0.0060525155, -0.0109255025, -0.015493984, 0.011872963, -0.0015145391 ],\n"
            + "      \"initBias\" : 0.5, " + "      \"bias\" : [ 0.0, 0.2, 0.4 ],\n"
            + "      \"weightDelta\" : [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ],\n"
            + "      \"biasDelta\" : [ 0.0, 0.0, 0.0 ],\n" + "      \"dropoutRate\" : 1.0,\n"
            + "      \"activation\" : \"LogisticFunction\",\n" + "      \"useGpu\" : true\n" + "    }\n"
            + "  } ],\n" + "  \"learningRate\" : 0.01\n" + "}"));
    System.out.println(nn.random.nextInt());
    System.out.println(v.random.nextInt());
    v.findLayerByName("test").ifPresent(layer -> {
        FullyConnect f = (FullyConnect) layer;
        System.out.println(f.getActivation().getClass());
        System.out.println(Arrays.toString(f.getBias()));
    });
    v.init();
    v.findLayerByName("test").ifPresent(layer -> {
        FullyConnect f = (FullyConnect) layer;
        System.out.println(f.getActivation().getClass());
        System.out.println(Arrays.toString(f.getBias()));
    });
}

From source file:hu.bme.mit.sette.run.Run.java

public static void main(String[] args) {
    LOG.debug("main() called");

    // parse properties
    Properties prop = new Properties();
    InputStream is = null;// w  ww .j  av a2  s  . c  o m

    try {
        is = new FileInputStream(SETTE_PROPERTIES);
        prop.load(is);
    } catch (IOException e) {
        System.err.println("Parsing  " + SETTE_PROPERTIES + " has failed");
        e.printStackTrace();
        System.exit(1);
    } finally {
        IOUtils.closeQuietly(is);
    }

    String[] basedirs = StringUtils.split(prop.getProperty("basedir"), '|');
    String snippetDir = prop.getProperty("snippet-dir");
    String snippetProject = prop.getProperty("snippet-project");
    String catgPath = prop.getProperty("catg");
    String catgVersionFile = prop.getProperty("catg-version-file");
    String jPETPath = prop.getProperty("jpet");
    String jPETDefaultBuildXml = prop.getProperty("jpet-default-build.xml");
    String jPETVersionFile = prop.getProperty("jpet-version-file");
    String spfPath = prop.getProperty("spf");
    String spfDefaultBuildXml = prop.getProperty("spf-default-build.xml");
    String spfVersionFile = prop.getProperty("spf-version-file");
    String outputDir = prop.getProperty("output-dir");

    Validate.notEmpty(basedirs, "At least one basedir must be specified in " + SETTE_PROPERTIES);
    Validate.notBlank(snippetDir, "The property snippet-dir must be set in " + SETTE_PROPERTIES);
    Validate.notBlank(snippetProject, "The property snippet-project must be set in " + SETTE_PROPERTIES);
    Validate.notBlank(catgPath, "The property catg must be set in " + SETTE_PROPERTIES);
    Validate.notBlank(jPETPath, "The property jpet must be set in " + SETTE_PROPERTIES);
    Validate.notBlank(spfPath, "The property spf must be set in " + SETTE_PROPERTIES);
    Validate.notBlank(outputDir, "The property output-dir must be set in " + SETTE_PROPERTIES);

    String basedir = null;
    for (String bd : basedirs) {
        bd = StringUtils.trimToEmpty(bd);

        if (bd.startsWith("~")) {
            // Linux home
            bd = System.getProperty("user.home") + bd.substring(1);
        }

        FileValidator v = new FileValidator(new File(bd));
        v.type(FileType.DIRECTORY);

        if (v.isValid()) {
            basedir = bd;
            break;
        }
    }

    if (basedir == null) {
        System.err.println("basedir = " + Arrays.toString(basedirs));
        System.err.println("ERROR: No valid basedir was found, please check " + SETTE_PROPERTIES);
        System.exit(2);
    }

    BASEDIR = new File(basedir);
    SNIPPET_DIR = new File(basedir, snippetDir);
    SNIPPET_PROJECT = snippetProject;
    OUTPUT_DIR = new File(basedir, outputDir);

    try {
        String catgVersion = readToolVersion(new File(BASEDIR, catgVersionFile));
        if (catgVersion != null) {
            new CatgTool(new File(BASEDIR, catgPath), catgVersion);
        }

        String jPetVersion = readToolVersion(new File(BASEDIR, jPETVersionFile));
        if (jPetVersion != null) {
            new JPetTool(new File(BASEDIR, jPETPath), new File(BASEDIR, jPETDefaultBuildXml), jPetVersion);
        }

        String spfVersion = readToolVersion(new File(BASEDIR, spfVersionFile));
        if (spfVersion != null) {
            new SpfTool(new File(BASEDIR, spfPath), new File(BASEDIR, spfDefaultBuildXml), spfVersion);
        }

        // TODO stuff
        stuff(args);
    } catch (Exception e) {
        System.err.println(ExceptionUtils.getStackTrace(e));

        ValidatorException vex = (ValidatorException) e;

        for (ValidationException v : vex.getValidator().getAllExceptions()) {
            v.printStackTrace();
        }

        // System.exit(0);

        e.printStackTrace();
        System.err.println("==========");
        e.printStackTrace();

        if (e instanceof ValidatorException) {
            System.err.println("Details:");
            System.err.println(((ValidatorException) e).getFullMessage());
        } else if (e.getCause() instanceof ValidatorException) {
            System.err.println("Details:");
            System.err.println(((ValidatorException) e.getCause()).getFullMessage());
        }
    }
}

From source file:eqtlmappingpipeline.util.ModuleEqtlGeuvadisReplication.java

/**
 * @param args the command line arguments
 *///  www  .j  a v  a  2  s .  co m
public static void main(String[] args) throws IOException, LdCalculatorException {

    System.out.println(HEADER);
    System.out.println();
    System.out.flush(); //flush to make sure header is before errors
    try {
        Thread.sleep(25); //Allows flush to complete
    } catch (InterruptedException ex) {
    }

    CommandLineParser parser = new PosixParser();
    final CommandLine commandLine;
    try {
        commandLine = parser.parse(OPTIONS, args, true);
    } catch (ParseException ex) {
        System.err.println("Invalid command line arguments: " + ex.getMessage());
        System.err.println();
        new HelpFormatter().printHelp(" ", OPTIONS);
        System.exit(1);
        return;
    }

    final String[] genotypesBasePaths = commandLine.getOptionValues("g");
    final RandomAccessGenotypeDataReaderFormats genotypeDataType;
    final String replicationQtlFilePath = commandLine.getOptionValue("e");
    final String interactionQtlFilePath = commandLine.getOptionValue("i");
    final String outputFilePath = commandLine.getOptionValue("o");
    final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld"));
    final int window = Integer.parseInt(commandLine.getOptionValue("w"));

    System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths));
    System.out.println("Interaction file: " + interactionQtlFilePath);
    System.out.println("Replication file: " + replicationQtlFilePath);
    System.out.println("Output: " + outputFilePath);
    System.out.println("LD: " + ldCutoff);
    System.out.println("Window: " + window);

    try {
        if (commandLine.hasOption("G")) {
            genotypeDataType = RandomAccessGenotypeDataReaderFormats
                    .valueOf(commandLine.getOptionValue("G").toUpperCase());
        } else {
            if (genotypesBasePaths[0].endsWith(".vcf")) {
                System.err.println(
                        "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file.");
                System.exit(1);
                return;
            }
            try {
                genotypeDataType = RandomAccessGenotypeDataReaderFormats
                        .matchFormatToPath(genotypesBasePaths[0]);
            } catch (GenotypeDataException e) {
                System.err
                        .println("Unable to determine input 1 type based on specified path. Please specify -G");
                System.exit(1);
                return;
            }
        }
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G")
                + "\" is not a valid input data format");
        System.exit(1);
        return;
    }

    final RandomAccessGenotypeData genotypeData;

    try {
        genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null,
                0.8);
    } catch (TabixFileNotFoundException e) {
        LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n"
                + "Please see README on how to create a tabix file");
        System.exit(1);
        return;
    } catch (IOException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (IncompatibleMultiPartGenotypeDataException e) {
        LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (GenotypeDataException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    }

    ChrPosTreeMap<ArrayList<EQTL>> replicationQtls = new QTLTextFile(replicationQtlFilePath, false)
            .readQtlsAsTreeMap();

    int interactionSnpNotInGenotypeData = 0;
    int noReplicationQtlsInWindow = 0;
    int noReplicationQtlsInLd = 0;
    int multipleReplicationQtlsInLd = 0;
    int replicationTopSnpNotInGenotypeData = 0;

    final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0');
    final String[] outputLine = new String[14];
    int c = 0;
    outputLine[c++] = "Chr";
    outputLine[c++] = "Pos";
    outputLine[c++] = "SNP";
    outputLine[c++] = "Gene";
    outputLine[c++] = "Module";
    outputLine[c++] = "DiscoveryZ";
    outputLine[c++] = "ReplicationZ";
    outputLine[c++] = "DiscoveryZCorrected";
    outputLine[c++] = "ReplicationZCorrected";
    outputLine[c++] = "DiscoveryAlleleAssessed";
    outputLine[c++] = "ReplicationAlleleAssessed";
    outputLine[c++] = "bestLd";
    outputLine[c++] = "bestLd_dist";
    outputLine[c++] = "nextLd";
    outputWriter.writeNext(outputLine);

    HashSet<String> notFound = new HashSet<>();

    CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t');
    interactionQtlReader.readNext();//skip header
    String[] interactionQtlLine;
    while ((interactionQtlLine = interactionQtlReader.readNext()) != null) {

        String snp = interactionQtlLine[1];
        String chr = interactionQtlLine[2];
        int pos = Integer.parseInt(interactionQtlLine[3]);
        String gene = interactionQtlLine[4];
        String alleleAssessed = interactionQtlLine[9];
        String module = interactionQtlLine[12];
        double discoveryZ = Double.parseDouble(interactionQtlLine[10]);

        GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos);

        if (interactionQtlVariant == null) {
            System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos);
            ++interactionSnpNotInGenotypeData;
            continue;
        }

        EQTL bestMatch = null;
        double bestMatchR2 = Double.NaN;
        Ld bestMatchLd = null;
        double nextBestR2 = Double.NaN;

        ArrayList<EQTL> sameSnpQtls = replicationQtls.get(chr, pos);

        if (sameSnpQtls != null) {
            for (EQTL sameSnpQtl : sameSnpQtls) {
                if (sameSnpQtl.getProbe().equals(gene)) {
                    bestMatch = sameSnpQtl;
                    bestMatchR2 = 1;
                }
            }
        }

        NavigableMap<Integer, ArrayList<EQTL>> potentionalReplicationQtls = replicationQtls.getChrRange(chr,
                pos - window, true, pos + window, true);

        for (ArrayList<EQTL> potentialReplicationQtls : potentionalReplicationQtls.values()) {

            for (EQTL potentialReplicationQtl : potentialReplicationQtls) {

                if (!potentialReplicationQtl.getProbe().equals(gene)) {
                    continue;
                }

                GeneticVariant potentialReplicationQtlVariant = genotypeData.getSnpVariantByPos(
                        potentialReplicationQtl.getRsChr().toString(), potentialReplicationQtl.getRsChrPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getRsChr().toString() + ":"
                            + potentialReplicationQtl.getRsChrPos());
                    ++replicationTopSnpNotInGenotypeData;
                    continue;
                }

                Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant);
                double r2 = ld.getR2();

                if (r2 > 1) {
                    r2 = 1;
                }

                if (bestMatch == null) {
                    bestMatch = potentialReplicationQtl;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                } else if (r2 > bestMatchR2) {
                    bestMatch = potentialReplicationQtl;
                    nextBestR2 = bestMatchR2;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                }

            }
        }

        double replicationZ = Double.NaN;
        double replicationZCorrected = Double.NaN;
        double discoveryZCorrected = Double.NaN;

        String replicationAlleleAssessed = null;

        if (bestMatch != null) {
            replicationZ = bestMatch.getZscore();
            replicationAlleleAssessed = bestMatch.getAlleleAssessed();

            if (pos != bestMatch.getRsChrPos()) {

                String commonHap = null;
                double commonHapFreq = -1;
                for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) {

                    double f = hapFreq.getValue();

                    if (f > commonHapFreq) {
                        commonHapFreq = f;
                        commonHap = hapFreq.getKey();
                    }

                }

                String[] commonHapAlleles = StringUtils.split(commonHap, '/');

                discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1;
                replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            } else {

                discoveryZCorrected = discoveryZ;
                replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            }

        }

        c = 0;
        outputLine[c++] = chr;
        outputLine[c++] = String.valueOf(pos);
        outputLine[c++] = snp;
        outputLine[c++] = gene;
        outputLine[c++] = module;
        outputLine[c++] = String.valueOf(discoveryZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected);
        outputLine[c++] = alleleAssessed;
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAlleleAssessed());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getRsChrPos()));
        outputLine[c++] = String.valueOf(nextBestR2);
        outputWriter.writeNext(outputLine);

    }

    outputWriter.close();

    for (String e : notFound) {
        System.err.println("Not found: " + e);
    }

    System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData);
    System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow);
    System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd);
    System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd);
    System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData);

}

From source file:net.bobah.mail.Dupes.java

public static void main(String[] args) throws Exception {
    installDefaultUncaughtExceptionHandler(log);

    final CommandLineParser parser = new PosixParser();
    final Options options = new Options()
            .addOption("j", "threads", true, "number of parallel threads to use for analyzing")
            .addOption("hash", true,
                    "hash function to use, possible values: " + Arrays.toString(Hashes.values()))
            .addOption("dir", true, "add directory to search");
    final CommandLine cmdline = parser.parse(options, args);

    final int threads = Integer.valueOf(
            cmdline.getOptionValue("threads", String.valueOf(Runtime.getRuntime().availableProcessors())));
    final HashFunction hash = Hashes.valueOf(cmdline.getOptionValue("hash", "adler32")).hashfunc;
    final File[] dirs = Collections2
            .transform(Arrays.asList(cmdline.getOptionValues("dir")), new Function<String, File>() {
                @Override//from   w w  w  .  j  a va  2  s  . c  o m
                public File apply(String from) {
                    return new File(from);
                }
            }).toArray(new File[] {});

    log.info("hash: {}, threads: {}, dirs: {} in total", hash, threads, dirs.length);
    try {
        new Dupes(threads, hash, dirs).run();
    } finally {
        Utils.shutdownLogger();
    }
}

From source file:alluxio.yarn.Client.java

/**
 * @param args Command line arguments//from w w  w .  j  a  v  a2  s  .co m
 */
public static void main(String[] args) {
    try {
        Client client = new Client();
        System.out.println("Initializing Client");
        if (!client.parseArgs(args)) {
            System.out.println("Cannot parse commandline: " + Arrays.toString(args));
            System.exit(0);
        }
        System.out.println("Starting Client");
        client.run();
    } catch (Exception e) {
        System.err.println("Error running Client " + e);
        System.exit(1);
    }
}