/** * 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(); } }
/** * 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(); } }