xmeans.java

wekaUT是 university texas austin 开发的基于weka的半指导学习(semi supervised learning)的分类器

  /**
   * Gets the distance function specification string, which contains the 
   * class name of the distance function class and any options to it
   *
   * @return the distance function specification string
   */
  protected String getDistanceFSpec() {
    
    DistanceFunction d = getDistanceF();
    if (d instanceof OptionHandler) {
      return d.getClass().getName() + " "
	+ Utils.joinOptions(((OptionHandler) d).getOptions());
    }
    return d.getClass().getName();
  }
  /**
   * Sets a file name for a file that has the random vektors stored.
   * Just used for debugging reasons.
   * @param fileName file name for the file to read the random vektors from
   */
  public void setDebugVektorsFile(String fileName) {
    m_DebugVektorsFile = fileName;
  }

  /**
   * Initialises the debug vektor input.
   */
  public void initDebugVektorsInput() throws Exception {
    m_DebugVektorsInput = 
      new BufferedReader(new FileReader(m_DebugVektorsFile));
    m_DebugVektors = new Instances(m_DebugVektorsInput);
    m_DebugVektorsIndex = 0;
  }

  /**
   * Read an instance from debug vektors file.
   * @param model the data model for the instance
   */
  public Instance getNextDebugVektorsInstance(Instances model) 
    throws Exception {
    if (m_DebugVektorsIndex >= m_DebugVektors.numInstances())
      throw new Exception("no more prefabricated Vektors");
    Instance nex = m_DebugVektors.instance(m_DebugVektorsIndex);
    nex.setDataset(model);
    m_DebugVektorsIndex++;
    return nex;
  }

  /**
   * Sets the name of the file to read the list of centers from.
   *
   * @param fileName file name of file to read centers from
   */
  public void setInputCenterFile(String fileName) {
    m_InputCenterFile = fileName;
  }
    
  /**
   * Sets the name of the file to write the list of centers to. 
   *
   * @param fileName file to write centers to
   */
  public void setOutputCenterFile(String fileName) {
    m_OutputCenterFile = fileName;
  }
    
  /**
   * Gets the name of the file to read the list of centers from.
   *
   * @return filename of the file to read the centers from
   */
  public String getInputCenterFile() {
    return m_InputCenterFile;
  }

  /**
   * Gets the name of the file to write the list of centers to. 
   * @return filename of the file to write centers to
   */
  public String getOutputCenterFile() {
    return m_OutputCenterFile;
  }
    
  /**
   * Sets the KDTree class.
   * @param k a KDTree object with all options set
   */
  public void setKDTree(KDTree k) {
    m_KDTree = k;
  }

  /**
   * Gets the KDTree class.
   * @return flag if KDTrees are used
   */
  public KDTree getKDTree() {
    return m_KDTree;
  }

  /**
   * Gets the KDTree specification string, which contains the class name of
   * the KDTree class and any options to the KDTree
   *
   * @return the KDTree string.
   */
  protected String getKDTreeSpec() {
    
    KDTree c = getKDTree();
    if (c instanceof OptionHandler) {
      return c.getClass().getName() + " "
	+ Utils.joinOptions(((OptionHandler)c).getOptions());
    }
    return c.getClass().getName();
  }

  /**
   * Sets the debug level.
   * debug level = 0, means no output
   * @param d debuglevel
   */
  public void setDebugLevel(int d) {
    m_DebugLevel = d;
  }

  /**
   * Gets the debug level.
   * @return debug level
   */
  public int getDebugLevel() {
    return m_DebugLevel;
  }

  /**
   * Gets the minimum number of clusters to generate.
   * @return the minimum number of clusters to generate
   */
  public int getMinNumClusters() {
    return m_MinNumClusters;
  }
    
  /**
   * Gets the maximum number of clusters to generate.
   * @return the maximum number of clusters to generate
   */
  public int getMaxNumClusters() {
    return m_MaxNumClusters;
  }

  /**
   * Returns the tip text for this property.
   * @return tip text for this property 
   */
  public String seedTipText() {
    return "random number seed";
  }

  /**
   * Sets the random number seed.
   * @param s the seed
   */
  public void setSeed(int s) {
    m_Seed = s;
  }


  /**
   * Gets the random number seed.
   * @return the seed
   */
  public int getSeed() {
    return  m_Seed;
  }

  /**
   * Checks the instances.
   * No checks in this KDTree but it calls the check of the distance function.
   */
  private void checkInstances () throws Exception {
    
    m_DistanceF.checkInstances();
  }
  
  /**
   * Parses a given list of options.
   * @param options the list of options as an array of strings
   * @exception Exception if an option is not supported
   *
   **/
  public void setOptions(String[] options)
    throws Exception {

    String optionString = Utils.getOption('I', options);
    if (optionString.length() != 0) {
      setMaxIterations(Integer.parseInt(optionString));
    }
    optionString = Utils.getOption('M', options);
    if (optionString.length() != 0) {
      setMaxKMeans(Integer.parseInt(optionString));
    }
    optionString = Utils.getOption('J', options);
    if (optionString.length() != 0) {
      setMaxKMeansForChildren(Integer.parseInt(optionString));
    }
    optionString = Utils.getOption('L', options);
    if (optionString.length() != 0) {
      setMinNumClusters(Integer.parseInt(optionString));
    }
    optionString = Utils.getOption('H', options);
    if (optionString.length() != 0) {
      setMaxNumClusters(Integer.parseInt(optionString));
    }
    optionString = Utils.getOption('B', options);
    if (optionString.length() != 0) {
      setBinValue(Double.parseDouble(optionString));
    }

    String funcString = Utils.getOption('K', options);
    if (funcString.length() != 0) {
      String [] funcSpec = Utils.splitOptions(funcString);
      if (funcSpec.length == 0) {
	throw new Exception("Invalid function specification string");
      }
      String funcName = funcSpec[0];
      funcSpec[0] = "";
      setKDTree((KDTree) Utils.forName(KDTree.class, funcName, funcSpec));
    }

   optionString = Utils.getOption('C', options);
    if (optionString.length() != 0) {
      setCutOffFactor(Double.parseDouble(optionString));
    }
    funcString = Utils.getOption('D', options);
    if (funcString.length() != 0) {
      String [] funcSpec = Utils.splitOptions(funcString);
      if (funcSpec.length == 0) {
	throw new Exception("Invalid function specification string");
      }
      String funcName = funcSpec[0];
      funcSpec[0] = "";
      setDistanceF((DistanceFunction) Utils.forName(DistanceFunction.class,
						    funcName, funcSpec));
    } 

    optionString  = Utils.getOption('N', options);
    if (optionString.length() != 0) {
      setInputCenterFile(optionString);
      m_CenterInput = 
	new BufferedReader(new FileReader(optionString));
    }

    optionString  = Utils.getOption('O', options);
    if (optionString.length() != 0) {
      setOutputCenterFile(optionString);
      m_CenterOutput = new PrintWriter(new FileOutputStream(optionString));
    }

    optionString = Utils.getOption('S', options);
    if (optionString.length() != 0) {
      setSeed(Integer.parseInt(optionString));
    }


    optionString = Utils.getOption('U', options);
    int debugLevel = 0;
    if (optionString.length() != 0) {
      try {
	debugLevel = Integer.parseInt(optionString);
      } catch (NumberFormatException e) {
	throw new Exception(optionString +
                            "is an illegal value for option D"); 
      }
    }
    setDebugLevel(debugLevel);

    optionString  = Utils.getOption('Y', options);
    if (optionString.length() != 0) {
      setDebugVektorsFile(optionString);
    }
  }
  
  /**
   * Gets the current settings of SimpleKMeans.
   * @return an array of strings suitable for passing to setOptions
   */
  public String[] getOptions() {
    String[] options = new String[27];
    int current = 0;
    
    options[current++] = "-I";
    options[current++] = "" + getMaxIterations();
    options[current++] = "-M";
    options[current++] = "" + getMaxKMeans();
    options[current++] = "-J";
    options[current++] = "" + getMaxKMeansForChildren();
    options[current++] = "-L";
    options[current++] = "" + getMinNumClusters();
    options[current++] = "-H";
    options[current++] = "" + getMaxNumClusters();
    options[current++] = "-B";
    options[current++] = "" + getBinValue();
    if (getKDTree() != null) {
      options[current++] = "-K";
      options[current++] = "" + getKDTreeSpec();
    }
    options[current++] = "-C";
    options[current++] = "" + getCutOffFactor();
    if (getDistanceF() != null) {
      options[current++] = "-D";
      options[current++] = "" + getDistanceFSpec();
    }
    
    options[current++] = "-N";
    options[current++] = "" + getInputCenterFile();
    options[current++] = "-O";
    options[current++] = "" + getOutputCenterFile();
    options[current++] = "-S";
    options[current++] = "" + getSeed();
    int dL = getDebugLevel();
    if (dL > 0) {
      options[current++] = "-U";
      options[current++] = "" + getDebugLevel();
    }
    while (current < options.length) {
      options[current++] = "";
    }

    return  options;
  }

  /**
   * Return a string describing this clusterer.
   * @return a description of the clusterer as a string
   */
  public String toString() {
    StringBuffer temp = new StringBuffer();

    temp.append("\nkMeans\n======\n");

    temp.append("Requested iterations            : " + m_MaxIterations + "\n");
    temp.append("Iterations performed            : " + m_IterationCount+ "\n");
    temp.append("kMeans did not converge\n");
    temp.append("  but was stopped by max-loops " 
		+ m_KMeansStopped + " times (max kMeans-iter) = \n\n");
    temp.append("Splits prepared                 : " + m_NumSplits + "\n");
    temp.append("Splits performed                : " + m_NumSplitsDone + "\n");
    temp.append("Cutoff factor                   : " + m_CutOffFactor + "\n");
    double perc;
    if (m_NumSplitsDone > 0)
      perc = (((double)m_NumSplitsStillDone)/((double) m_NumSplitsDone))
             * 100.0;
    else
      perc = 0.0;
    temp.append("Percentage of splits accepted \n" +
                "by cutoff factor                : " 
		+ Utils.doubleToString(perc,2) + " %\n");
    temp.append("------\n");

    temp.append("Cutoff factor                   : " + m_CutOffFactor + "\n");
    temp.append("------\n");
    temp.append("\nCluster centers                 : " + m_NumClusters + " centers\n");
    for (int i = 0; i < m_NumClusters; i++) {
      temp.append("\nCluster "+i+"\n           ");
      for (int j = 0; j < m_ClusterCenters.numAttributes(); j++) {
	if (m_ClusterCenters.attribute(j).isNominal()) {
	  temp.append(" "+m_ClusterCenters.attribute(j).
		      value((int)m_ClusterCenters.instance(i).value(j)));
	} else {
	  temp.append(" "+m_ClusterCenters.instance(i).value(j));
	}
      }
    }
    if (m_Mle != null)
      temp.append("\n\nDistortion: " + 
		  Utils.doubleToString(Utils.sum(m_Mle),6) + "\n");
    temp.append("BIC-Value : " + Utils.doubleToString(m_Bic,6) + "\n");
    return temp.toString();
  }

  /**
   * Used for debug println's.
   * @param output string that is printed
   */
  private void OOPS(int debugLevel, String output) {
    if (debugLevel == m_DebugLevel)
      System.out.println(output);
  }

  private void OOPS(String output) {
    System.out.println(output);
  }


  /**
   * Print centers for debug.
   * @param debugLevel level that gives according messages
   * @return true if debug level is set
   */
  private void PrCentersFD(int debugLevel) {
    if (debugLevel == m_DebugLevel) {
      for (int i = 0; i < m_ClusterCenters.numInstances(); i++) {
	System.out.println(m_ClusterCenters.instance(i));
      }
    }
  }

  /**
   * Tests on debug status.
   * @param debugLevel level that gives according messages
   * @return true if debug level is set
   */
  private boolean TFD(int debugLevel) {
    return (debugLevel == m_DebugLevel);
  }

  /**
   * Does debug printouts.
   * @param debugLevel level that gives according messages
   * @param output string that is printed
   */
  private void PFD(int debugLevel, String output) {
    if (debugLevel == m_DebugLevel)
      System.out.println(output);
  }
  /**
   * Does debug printouts.
   * @param debugLevel level that gives according messages
   * @param output string that is printed
   */
  private void PFD_CURR(String output)