cobweb.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

      }

      return Math.max(m_acuity, stdDev);
    }

    /**
     * Update attribute stats using the supplied instance. 
     *
     * @param updateInstance the instance for updating
     * @param delete true if the values of the supplied instance are
     * to be removed from the statistics
     */
    protected void updateStats(Instance updateInstance, 
			       boolean delete) {

      if (m_attStats == null) {
	m_attStats = new AttributeStats[m_numAttributes];
	for (int i = 0; i < m_numAttributes; i++) {
	  m_attStats[i] = new AttributeStats();
	  if (m_clusterInstances.attribute(i).isNominal()) {
	    m_attStats[i].nominalCounts = 
	      new int [m_clusterInstances.attribute(i).numValues()];
	  } else {
	    m_attStats[i].numericStats = new Stats();
	  }
	}
      }
      for (int i = 0; i < m_numAttributes; i++) {
	if (!updateInstance.isMissing(i)) {
	  double value = updateInstance.value(i);
	  if (m_clusterInstances.attribute(i).isNominal()) {
	    m_attStats[i].nominalCounts[(int)value] += (delete) ? 
	      (-1.0 * updateInstance.weight()) : 
	      updateInstance.weight();
	    m_attStats[i].totalCount += (delete) ?
	      (-1.0 * updateInstance.weight()) :
	      updateInstance.weight();
	  } else {
	    if (delete) {
	      m_attStats[i].numericStats.subtract(value, 
						  updateInstance.weight());
	    } else {
	      m_attStats[i].numericStats.add(value, updateInstance.weight());
	    }
	  }
	}
      }
      m_totalInstances += (delete) 
	? (-1.0 * updateInstance.weight()) 
	: (updateInstance.weight());
    }

    /**
     * Recursively assigns numbers to the nodes in the tree.
     *
     * @param cl_num an <code>int[]</code> value
     * @exception Exception if an error occurs
     */
    private void assignClusterNums(int [] cl_num) throws Exception {
      if (m_children != null && m_children.size() < 2) {
	throw new Exception("assignClusterNums: tree not built correctly!");
      }
      
      m_clusterNum = cl_num[0];
      cl_num[0]++;
      if (m_children != null) {
	for (int i = 0; i < m_children.size(); i++) {
	  CNode child = (CNode) m_children.elementAt(i);
	  child.assignClusterNums(cl_num);
	}
      }
    }

    /**
     * Recursively build a string representation of the Cobweb tree
     *
     * @param depth depth of this node in the tree
     * @param text holds the string representation
     */
    protected void dumpTree(int depth, StringBuffer text) {

      if (m_children == null) {
	text.append("\n");
	for (int j = 0; j < depth; j++) {
	  text.append("|   ");
	}
	text.append("leaf "+m_clusterNum+" ["
		    +m_clusterInstances.numInstances()+"]");
      } else {
	for (int i = 0; i < m_children.size(); i++) {
	  text.append("\n");
	  for (int j = 0; j < depth; j++) {
	    text.append("|   ");
	  }
	  text.append("node "+m_clusterNum+" ["
		      +m_clusterInstances.numInstances()
		      +"]");
	  ((CNode) m_children.elementAt(i)).dumpTree(depth+1, text);
	}
      }
    }

    /**
     * Returns the instances at this node as a string. Appends the cluster
     * number of the child that each instance belongs to.
     *
     * @return a <code>String</code> value
     * @exception Exception if an error occurs
     */
    protected String dumpData() throws Exception {
      if (m_children == null) {
	return m_clusterInstances.toString();
      }

      // construct instances string with cluster numbers attached
      CNode tempNode = new CNode(m_numAttributes);
      tempNode.m_clusterInstances = new Instances(m_clusterInstances, 1);
      for (int i = 0; i < m_children.size(); i++) {
	tempNode.addChildNode((CNode)m_children.elementAt(i));
      }
      Instances tempInst = tempNode.m_clusterInstances;
      tempNode = null;

      StringBuffer instBuff = new StringBuffer();
      Add af = new Add();
      af.setAttributeName("Cluster");
      String labels = "";
      for (int i = 0; i < m_children.size(); i++) {
	CNode temp = (CNode)m_children.elementAt(i);
	labels += ("C"+temp.m_clusterNum);
	if (i < m_children.size()-1) {
	  labels+=",";
	}
      }
      af.setNominalLabels(labels);
      af.setInputFormat(tempInst);
      tempInst = Filter.useFilter(tempInst, af);
      tempInst.setRelationName("Cluster "+m_clusterNum);
      
      int z = 0;
      for (int i = 0; i < m_children.size(); i++) {
	CNode temp = (CNode)m_children.elementAt(i);
	for (int j = 0; j < temp.m_clusterInstances.numInstances(); j++) {
	  tempInst.instance(z).setValue(m_numAttributes, (double)i);
	  z++;
	}
      }
      return tempInst.toString();
    }

    /**
     * Recursively generate the graph string for the Cobweb tree.
     *
     * @param text holds the graph string
     */
    protected void graphTree(StringBuffer text) throws Exception {
      
      text.append("N"+m_clusterNum
		  + " [label=\""+((m_children == null) 
				  ? "leaf " : "node ")
		  +m_clusterNum+" "
		  +" ("+m_clusterInstances.numInstances()
		  +")\" "
		  +((m_children == null) 
		    ? "shape=box style=filled " : "")
		  +(m_saveInstances 
		    ? "data =\n"+dumpData() +"\n,\n"
		    : "")
		  + "]\n");
      if (m_children != null) {
	for (int i = 0; i < m_children.size(); i++) {
	  CNode temp = (CNode)m_children.elementAt(i);
	  text.append("N"+m_clusterNum
		      +"->"
		      +"N" + temp.m_clusterNum
		      + "\n");
	}

	for (int i = 0; i < m_children.size(); i++) {
	  CNode temp = (CNode)m_children.elementAt(i);
	  temp.graphTree(text);
	}
      }
    }
  }

  /**
   * Normal constant.
   */
  protected static final double m_normal = 1.0/(2 * Math.sqrt(Math.PI));

  /**
   * Acuity (minimum standard deviation).
   */
  protected double m_acuity = 1.0;

  /**
   * Cutoff (minimum category utility).
   */
  protected double m_cutoff = 0.01 * Cobweb.m_normal;

  /**
   * Holds the root of the Cobweb tree.
   */
  protected CNode m_cobwebTree = null;

  /**
   * Number of clusters (nodes in the tree).
   */
  protected int m_numberOfClusters = -1;
  
  protected int m_numberSplits;
  protected int m_numberMerges;

  /**
   * Output instances in graph representation of Cobweb tree (Allows
   * instances at nodes in the tree to be visualized in the Explorer).
   */
  protected boolean m_saveInstances = false;

  /**
   * Builds the clusterer.
   *
   * @param data the training instances.
   * @exception Exception if something goes wrong.
   */
  public void buildClusterer(Instances data) throws Exception {
    m_numberOfClusters = -1;
    m_cobwebTree = null;
    m_numberSplits = 0;
    m_numberMerges = 0;

    if (data.checkForStringAttributes()) {
      throw new Exception("Can't handle string attributes!");
    }
    
    // randomize the instances
    data = new Instances(data);
    data.randomize(new Random(42));

    for (int i = 0; i < data.numInstances(); i++) {
      addInstance(data.instance(i));
    }
    
    int [] numClusts = new int [1];
    numClusts[0] = 0;
    m_cobwebTree.assignClusterNums(numClusts);
    m_numberOfClusters = numClusts[0];
  }

  /**
   * Classifies a given instance.
   *
   * @param instance the instance to be assigned to a cluster
   * @return the number of the assigned cluster as an interger
   * if the class is enumerated, otherwise the predicted value
   * @exception Exception if instance could not be classified
   * successfully
   */
  public int clusterInstance(Instance instance) throws Exception {
    CNode host = m_cobwebTree;
    CNode temp = null;
    
    do {
      if (host.m_children == null) {
	temp = null;
	break;
      }

      host.updateStats(instance, false);
      temp = host.findHost(instance, true);
      host.updateStats(instance, true);
      
      if (temp != null) {
	host = temp;
      }
    } while (temp != null);
    
    return host.m_clusterNum;
  }

  /**
   * Returns the number of clusters.
   *
   * @exception Exception if something goes wrong.
   */
  public int numberOfClusters() throws Exception {
    return m_numberOfClusters;
  }

  /**
   * Adds an instance to the Cobweb tree.
   *
   * @param newInstance the instance to be added
   * @exception Exception if something goes wrong
   */
  public void addInstance(Instance newInstance) throws Exception {
    if (m_cobwebTree == null) {
      m_cobwebTree = new CNode(newInstance.numAttributes(), newInstance);
    } else {
      m_cobwebTree.addInstance(newInstance);
    }
  }

  /**
   * Returns an enumeration describing the available options.
   *
   * @return an enumeration of all the available options.
   **/
  public Enumeration listOptions() {
    
    Vector newVector = new Vector(2);
    
    newVector.addElement(new Option("\tAcuity.\n"
				    +"\t(default=1.0)", "A", 1,"-A <acuity>"));
    newVector.addElement(new Option("\tCutoff.\n"
				    +"a\t(default=0.002)", "C", 1,"-C <cutoff>"));
    
    return newVector.elements();
  }

  /**
   * Parses a given list of options.
   *
   * Valid options are:<p>
   *
   * -A <acuity> <br>
   * Acuity. <p>
   *
   * -C <cutoff> <br>
   * Cutoff. <p>
   *
   * @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;

    optionString = Utils.getOption('A', options); 
    if (optionString.length() != 0) {
      Double temp = new Double(optionString);
      setAcuity(temp.doubleValue());
    }
    else {
      m_acuity = 1.0;
    }
    optionString = Utils.getOption('C', options); 
    if (optionString.length() != 0) {
      Double temp = new Double(optionString);
      setCutoff(temp.doubleValue());
    }
    else {
      m_cutoff = 0.01 * Cobweb.m_normal;
    }
  }

  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String acuityTipText() {
    return "set the minimum standard deviation for numeric attributes";
  }

  /**
   * set the acuity.
   * @param a the acuity value
   */
  public void setAcuity(double a) {
    m_acuity = a;
  }

  /**
   * get the acuity value
   * @return the acuity
   */
  public double getAcuity() {
    return m_acuity;
  }

  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String cutoffTipText() {
    return "set the category utility threshold by which to prune nodes";
  }

  /**
   * set the cutoff
   * @param c the cutof
   */
  public void setCutoff(double c) {
    m_cutoff = c;
  }

  /**
   * get the cutoff
   * @return the cutoff
   */
  public double getCutoff() {
    return m_cutoff;
  }
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String saveInstanceDataTipText() {
    return "save instance information for visualization purposes";
  }

  /**
   * Get the value of saveInstances.
   *
   * @return Value of saveInstances.
   */
  public boolean getSaveInstanceData() {
    
    return m_saveInstances;
  }
  
  /**
   * Set the value of saveInstances.
   *
   * @param newsaveInstances Value to assign to saveInstances.
   */
  public void setSaveInstanceData(boolean newsaveInstances) {
    
    m_saveInstances = newsaveInstances;
  }
  

  /**
   * Gets the current settings of Cobweb.
   *
   * @return an array of strings suitable for passing to setOptions()
   */
  public String [] getOptions() {
    
    String [] options = new String [4];
    int current = 0;
    options[current++] = "-A"; 
    options[current++] = "" + m_acuity;
    options[current++] = "-C"; 
    options[current++] = "" + m_cutoff;
    while (current < options.length) {
      options[current++] = "";
    }
    return options;
  }

  /**
   * Returns a description of the clusterer as a string.
   *
   * @return a string describing the clusterer.
   */
  public String toString() { 
    StringBuffer text = new StringBuffer();
    if (m_cobwebTree == null) {
      return "Cobweb hasn't been built yet!";
    }
    else {
      m_cobwebTree.dumpTree(0, text); 
      return "Number of merges: "
	+ m_numberMerges+"\nNumber of splits: "
	+ m_numberSplits+"\nNumber of clusters: "
	+ m_numberOfClusters+"\n"+text.toString()+"\n\n";
     
    }
  }

  /**
   * Generates the graph string of the Cobweb tree
   *
   * @return a <code>String</code> value
   * @exception Exception if an error occurs
   */
  public String graph() throws Exception {
    StringBuffer text = new StringBuffer();
    
    text.append("digraph CobwebTree {\n");
    m_cobwebTree.graphTree(text);
    text.append("}\n");
    return text.toString();
  }

  // Main method for testing this class
  public static void main(String [] argv)
  {
    try {
      System.out.println(ClusterEvaluation.evaluateClusterer(new Cobweb(), 
							     argv));
    }
    catch (Exception e)
      {
	System.out.println(e.getMessage());
	e.printStackTrace();
      }
  }
}