Esempio n. 1
0
  /**
   * Creates a new instance of an object given it's class name and (optional) arguments to pass to
   * it's setOptions method. If the object implements OptionHandler and the options parameter is
   * non-null, the object will have it's options set. Example use:
   *
   * <p><code> <pre>
   * String classifierName = M5StaticUtils.getOption('W', options);
   * Classifier c = (Classifier)M5StaticUtils.forName(Classifier.class,
   *                                          classifierName,
   *                                          options);
   * setClassifier(c);
   * </pre></code>
   *
   * @param classType the class that the instantiated object should be assignable to -- an exception
   *     is thrown if this is not the case
   * @param className the fully qualified class name of the object
   * @param options an array of options suitable for passing to setOptions. May be null. Any options
   *     accepted by the object will be removed from the array.
   * @return the newly created object, ready for use.
   * @exception Exception if the class name is invalid, or if the class is not assignable to the
   *     desired class type, or the options supplied are not acceptable to the object
   */
  public static Object forName(Class classType, String className, String[] options)
      throws Exception {

    Class c = null;
    try {
      c = Class.forName(className);
    } catch (Exception ex) {
      throw new Exception("Can't find class called: " + className);
    }
    if (!classType.isAssignableFrom(c)) {
      throw new Exception(classType.getName() + " is not assignable from " + className);
    }
    Object o = c.newInstance();
    if ((o instanceof M5) && (options != null)) {
      ((M5) o).setOptions(options);
      M5StaticUtils.checkForRemainingOptions(options);
    }
    return o;
  }
  /**
   * Method for testing filters ability to process multiple batches.
   *
   * @param options should contain the following arguments:<br>
   *     -i (first) input file <br>
   *     -o (first) output file <br>
   *     -r (second) input file <br>
   *     -s (second) output file <br>
   *     -c class_index <br>
   *     or -h for help on options
   * @exception Exception if something goes wrong or the user requests help on command options
   */
  public static void batchFilterFile(NominalToBinaryFilter filter, String[] options)
      throws Exception {

    M5Instances firstData = null;
    M5Instances secondData = null;
    Reader firstInput = null;
    Reader secondInput = null;
    PrintWriter firstOutput = null;
    PrintWriter secondOutput = null;
    boolean helpRequest;
    try {
      helpRequest = M5StaticUtils.getFlag('h', options);

      String fileName = M5StaticUtils.getOption('i', options);
      if (fileName.length() != 0) {
        firstInput = new BufferedReader(new FileReader(fileName));
      } else {
        throw new Exception("No first input file given.\n");
      }

      fileName = M5StaticUtils.getOption('r', options);
      if (fileName.length() != 0) {
        secondInput = new BufferedReader(new FileReader(fileName));
      } else {
        throw new Exception("No second input file given.\n");
      }

      fileName = M5StaticUtils.getOption('o', options);
      if (fileName.length() != 0) {
        firstOutput = new PrintWriter(new FileOutputStream(fileName));
      } else {
        firstOutput = new PrintWriter(System.out);
      }

      fileName = M5StaticUtils.getOption('s', options);
      if (fileName.length() != 0) {
        secondOutput = new PrintWriter(new FileOutputStream(fileName));
      } else {
        secondOutput = new PrintWriter(System.out);
      }
      String classIndex = M5StaticUtils.getOption('c', options);

      if (filter instanceof NominalToBinaryFilter) {
        ((NominalToBinaryFilter) filter).setOptions(options);
      }
      M5StaticUtils.checkForRemainingOptions(options);

      if (helpRequest) {
        throw new Exception("Help requested.\n");
      }
      firstData = new M5Instances(firstInput, 1);
      secondData = new M5Instances(secondInput, 1);
      if (!secondData.equalHeaders(firstData)) {
        throw new Exception("Input file formats differ.\n");
      }
      if (classIndex.length() != 0) {
        if (classIndex.equals("first")) {
          firstData.setClassIndex(0);
          secondData.setClassIndex(0);
        } else if (classIndex.equals("last")) {
          firstData.setClassIndex(firstData.numAttributes() - 1);
          secondData.setClassIndex(secondData.numAttributes() - 1);
        } else {
          firstData.setClassIndex(Integer.parseInt(classIndex) - 1);
          secondData.setClassIndex(Integer.parseInt(classIndex) - 1);
        }
      }
    } catch (Exception ex) {
      String filterOptions = "";
      // Output the error and also the valid options
      if (filter instanceof NominalToBinaryFilter) {
        filterOptions += "\nFilter options:\n\n";
        Enumeration enume = ((NominalToBinaryFilter) filter).listOptions();
        while (enume.hasMoreElements()) {
          Information option = (Information) enume.nextElement();
          filterOptions += option.synopsis() + '\n' + option.description() + "\n";
        }
      }

      String genericOptions =
          "\nGeneral options:\n\n"
              + "-h\n"
              + "\tGet help on available options.\n"
              + "-i <filename>\n"
              + "\tThe file containing first input instances.\n"
              + "-o <filename>\n"
              + "\tThe file first output instances will be written to.\n"
              + "-r <filename>\n"
              + "\tThe file containing second input instances.\n"
              + "-s <filename>\n"
              + "\tThe file second output instances will be written to.\n"
              + "-c <class index>\n"
              + "\tThe number of the attribute to use as the class.\n"
              + "\t\"first\" and \"last\" are also valid entries.\n"
              + "\tIf not supplied then no class is assigned.\n";

      throw new Exception('\n' + ex.getMessage() + filterOptions + genericOptions);
    }
    boolean printedHeader = false;
    if (filter.setInputFormat(firstData)) {
      firstOutput.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }

    // Pass all the instances to the filter
    while (firstData.readInstance(firstInput)) {
      if (filter.input(firstData.instance(0))) {
        if (!printedHeader) {
          throw new Error("Filter didn't return true from setInputFormat() " + "earlier!");
        }
        firstOutput.println(filter.output().toString());
      }
      firstData.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (filter.batchFinished()) {
      if (!printedHeader) {
        firstOutput.println(filter.getOutputFormat().toString());
      }
      while (filter.numPendingOutput() > 0) {
        firstOutput.println(filter.output().toString());
      }
    }

    if (firstOutput != null) {
      firstOutput.close();
    }
    printedHeader = false;
    if (filter.isOutputFormatDefined()) {
      secondOutput.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }
    // Pass all the second instances to the filter
    while (secondData.readInstance(secondInput)) {
      if (filter.input(secondData.instance(0))) {
        if (!printedHeader) {
          throw new Error("Filter didn't return true from" + " isOutputFormatDefined() earlier!");
        }
        secondOutput.println(filter.output().toString());
      }
      secondData.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (filter.batchFinished()) {
      if (!printedHeader) {
        secondOutput.println(filter.getOutputFormat().toString());
      }
      while (filter.numPendingOutput() > 0) {
        secondOutput.println(filter.output().toString());
      }
    }
    if (secondOutput != null) {
      secondOutput.close();
    }
  }
Esempio n. 3
0
  /**
   * Main method for testing this class.
   *
   * @param ops some dummy options
   */
  public static void main(String[] ops) {

    double[] doubles = {4.5, 6.7, Double.NaN, 3.4, 4.8, 1.2, 3.4};
    int[] ints = {12, 6, 2, 18, 16, 6, 7, 5};

    try {

      // Option handling
      System.out.println("First option split up:");
      if (ops.length > 0) {
        String[] firstOptionSplitUp = M5StaticUtils.splitOptions(ops[0]);
        for (int i = 0; i < firstOptionSplitUp.length; i++) {
          System.out.println(firstOptionSplitUp[i]);
        }
      }
      System.out.println("Partitioned options: ");
      String[] partitionedOptions = M5StaticUtils.partitionOptions(ops);
      for (int i = 0; i < partitionedOptions.length; i++) {
        System.out.println(partitionedOptions[i]);
      }
      System.out.println("Get flag -f: " + M5StaticUtils.getFlag('f', ops));
      System.out.println("Get option -o: " + M5StaticUtils.getOption('o', ops));
      System.out.println("Checking for remaining options... ");
      M5StaticUtils.checkForRemainingOptions(ops);

      // Statistics
      System.out.println("Original array (doubles): ");
      for (int i = 0; i < doubles.length; i++) {
        System.out.print(doubles[i] + " ");
      }
      System.out.println();
      System.out.println("Original array (ints): ");
      for (int i = 0; i < ints.length; i++) {
        System.out.print(ints[i] + " ");
      }
      System.out.println();
      System.out.println(
          "Correlation: " + M5StaticUtils.correlation(doubles, doubles, doubles.length));
      System.out.println("Mean: " + M5StaticUtils.mean(doubles));
      System.out.println("Variance: " + M5StaticUtils.variance(doubles));
      System.out.println("Sum (doubles): " + M5StaticUtils.sum(doubles));
      System.out.println("Sum (ints): " + M5StaticUtils.sum(ints));
      System.out.println("Max index (doubles): " + M5StaticUtils.maxIndex(doubles));
      System.out.println("Max index (ints): " + M5StaticUtils.maxIndex(ints));
      System.out.println("Min index (doubles): " + M5StaticUtils.minIndex(doubles));
      System.out.println("Min index (ints): " + M5StaticUtils.minIndex(ints));

      // Sorting and normalizing
      System.out.println("Sorted array (doubles): ");
      int[] sorted = M5StaticUtils.sort(doubles);
      for (int i = 0; i < doubles.length; i++) {
        System.out.print(doubles[sorted[i]] + " ");
      }
      System.out.println();
      System.out.println("Normalized array (doubles): ");
      M5StaticUtils.normalize(doubles);
      for (int i = 0; i < doubles.length; i++) {
        System.out.print(doubles[i] + " ");
      }
      System.out.println();
      System.out.println("Normalized again (doubles): ");
      M5StaticUtils.normalize(doubles, M5StaticUtils.sum(doubles));
      for (int i = 0; i < doubles.length; i++) {
        System.out.print(doubles[i] + " ");
      }
      System.out.println();

      // Pretty-printing
      System.out.println("-4.58: " + M5StaticUtils.doubleToString(-4.57826535, 2));
      System.out.println("-6.78: " + M5StaticUtils.doubleToString(-6.78214234, 6, 2));

      // Comparisons
      System.out.println("5.70001 == 5.7 ? " + M5StaticUtils.eq(5.70001, 5.7));
      System.out.println("5.70001 > 5.7 ? " + M5StaticUtils.gr(5.70001, 5.7));
      System.out.println("5.70001 >= 5.7 ? " + M5StaticUtils.grOrEq(5.70001, 5.7));
      System.out.println("5.7 < 5.70001 ? " + M5StaticUtils.sm(5.7, 5.70001));
      System.out.println("5.7 <= 5.70001 ? " + M5StaticUtils.smOrEq(5.7, 5.70001));

      // Math
      System.out.println("Info (ints): " + M5StaticUtils.info(ints));
      System.out.println("log2(4.6): " + M5StaticUtils.log2(4.6));
      System.out.println("5 * log(5): " + M5StaticUtils.xlogx(5));
      System.out.println("5.5 rounded: " + M5StaticUtils.round(5.5));
      System.out.println(
          "5.55555 rounded to 2 decimal places: " + M5StaticUtils.roundDouble(5.55555, 2));
    } catch (Exception e) {
      e.printStackTrace();
    }
  }
  /**
   * Method for testing filters.
   *
   * @param options should contain the following arguments: <br>
   *     -i input_file <br>
   *     -o output_file <br>
   *     -c class_index <br>
   *     or -h for help on options
   * @exception Exception if something goes wrong or the user requests help on command options
   */
  public static void filterFile(NominalToBinaryFilter filter, String[] options) throws Exception {

    boolean debug = false;
    M5Instances data = null;
    Reader input = null;
    PrintWriter output = null;
    boolean helpRequest;

    try {
      helpRequest = M5StaticUtils.getFlag('h', options);

      if (M5StaticUtils.getFlag('d', options)) {
        debug = true;
      }
      String infileName = M5StaticUtils.getOption('i', options);
      String outfileName = M5StaticUtils.getOption('o', options);
      String classIndex = M5StaticUtils.getOption('c', options);

      if (filter instanceof NominalToBinaryFilter) {
        ((NominalToBinaryFilter) filter).setOptions(options);
      }

      M5StaticUtils.checkForRemainingOptions(options);
      if (helpRequest) {
        throw new Exception("Help requested.\n");
      }
      if (infileName.length() != 0) {
        input = new BufferedReader(new FileReader(infileName));
      } else {
        input = new BufferedReader(new InputStreamReader(System.in));
      }
      if (outfileName.length() != 0) {
        output = new PrintWriter(new FileOutputStream(outfileName));
      } else {
        output = new PrintWriter(System.out);
      }

      data = new M5Instances(input, 1);
      if (classIndex.length() != 0) {
        if (classIndex.equals("first")) {
          data.setClassIndex(0);
        } else if (classIndex.equals("last")) {
          data.setClassIndex(data.numAttributes() - 1);
        } else {
          data.setClassIndex(Integer.parseInt(classIndex) - 1);
        }
      }
    } catch (Exception ex) {
      String filterOptions = "";
      // Output the error and also the valid options
      if (filter instanceof NominalToBinaryFilter) {
        filterOptions += "\nFilter options:\n\n";
        Enumeration enuma = ((NominalToBinaryFilter) filter).listOptions();
        while (enuma.hasMoreElements()) {
          Information option = (Information) enuma.nextElement();
          filterOptions += option.synopsis() + '\n' + option.description() + "\n";
        }
      }

      String genericOptions =
          "\nGeneral options:\n\n"
              + "-h\n"
              + "\tGet help on available options.\n"
              + "\t(use -b -h for help on batch mode.)\n"
              + "-i <file>\n"
              + "\tThe name of the file containing input instances.\n"
              + "\tIf not supplied then instances will be read from stdin.\n"
              + "-o <file>\n"
              + "\tThe name of the file output instances will be written to.\n"
              + "\tIf not supplied then instances will be written to stdout.\n"
              + "-c <class index>\n"
              + "\tThe number of the attribute to use as the class.\n"
              + "\t\"first\" and \"last\" are also valid entries.\n"
              + "\tIf not supplied then no class is assigned.\n";

      throw new Exception('\n' + ex.getMessage() + filterOptions + genericOptions);
    }

    if (debug) {
      System.err.println("Setting input format");
    }
    boolean printedHeader = false;
    if (filter.setInputFormat(data)) {
      if (debug) {
        System.err.println("Getting output format");
      }
      output.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }

    // Pass all the instances to the filter
    while (data.readInstance(input)) {
      if (debug) {
        System.err.println("Input instance to filter");
      }
      if (filter.input(data.instance(0))) {
        if (debug) {
          System.err.println("Filter said collect immediately");
        }
        if (!printedHeader) {
          throw new Error("Filter didn't return true from setInputFormat() " + "earlier!");
        }
        if (debug) {
          System.err.println("Getting output instance");
        }
        output.println(filter.output().toString());
      }
      data.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (debug) {
      System.err.println("Setting end of batch");
    }
    if (filter.batchFinished()) {
      if (debug) {
        System.err.println("Filter said collect output");
      }
      if (!printedHeader) {
        if (debug) {
          System.err.println("Getting output format");
        }
        output.println(filter.getOutputFormat().toString());
      }
      if (debug) {
        System.err.println("Getting output instance");
      }
      while (filter.numPendingOutput() > 0) {
        output.println(filter.output().toString());
        if (debug) {
          System.err.println("Getting output instance");
        }
      }
    }
    if (debug) {
      System.err.println("Done");
    }

    if (output != null) {
      output.close();
    }
  }