.#mpckmeans.java.1.106

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	      }
	    } else if (otherIdx == centroidIdx &&
		       pair.linkType == InstancePair.CANNOT_LINK) { 
	      double penalty = m_metrics[centroidIdx].penaltySymmetric(instance1, instance2);
	      m_objCannotLinksCurrPoint +=  m_CLweight *
		(m_maxCLPenalties[centroidIdx] - penalty);
	      if (m_maxCLPenalties[centroidIdx] - penalty < 0) {
		System.out.println("***NEGATIVE*** penalty: " + penalty + " for CL constraint"); 
	      }
	    }
	  }
	}
      }
    }

    double total = m_objVarianceCurrPoint  + m_objCannotLinksCurrPoint 
      + m_objMustLinksCurrPoint + m_objNormalizerCurrPoint;
    if(m_verbose) {
      System.out.println("Final penalty for instance " + instIdx + " and centroid "
			 + centroidIdx + " is: " + total);
    }
    return total;
  }
  

  /** M-step of the KMeans clustering algorithm -- updates cluster centroids
   */
  protected void updateClusterCentroids() throws Exception {
    // M-step: update cluster centroids
    Instances [] tempI = new Instances[m_NumClusters];
    m_ClusterCentroids = new Instances(m_Instances, m_NumClusters);
    
    for (int i = 0; i < m_NumClusters; i++) {
      tempI[i] = new Instances(m_Instances, 0); // tempI[i] stores the cluster instances for cluster i
    }
    for (int i = 0; i < m_Instances.numInstances(); i++) {
      tempI[m_ClusterAssignments[i]].add(m_Instances.instance(i));
    }
    
    // Calculates cluster centroids
    for (int i = 0; i < m_NumClusters; i++) {
      double [] values = new double[m_Instances.numAttributes()];
       
      if (m_isSparseInstance) {
	values = ClusterUtils.meanOrMode(tempI[i]); // uses fast meanOrMode
      }
      else {
	for (int j = 0; j < m_Instances.numAttributes(); j++) {
	  values[j] = tempI[i].meanOrMode(j); // uses usual meanOrMode
	}
      }

      // cluster centroids are dense in SPKMeans
      Instance centroid = new Instance(1.0, values);

      // if we are using a smoothing metric, smooth the centroids
      if (m_metric instanceof SmoothingMetric &&
	  ((SmoothingMetric) m_metric).getUseSmoothing()) { 
	SmoothingMetric smoothingMetric = (SmoothingMetric) m_metric;
	centroid = smoothingMetric.smoothInstance(centroid); 
      }

      m_ClusterCentroids.add(centroid);
      
      // in SPKMeans, cluster centroids need to be normalized
      if (m_metric.doesNormalizeData()) {
	m_metric.normalizeInstanceWeighted(m_ClusterCentroids.instance(i));
      }
    }

    if (m_metric instanceof SmoothingMetric &&
	((SmoothingMetric) m_metric).getUseSmoothing())
      updateSmoothingMetrics();       
    
    for (int i = 0; i < m_NumClusters; i++)
      tempI[i] = null; // free memory
  }


  /** M-step of the KMeans clustering algorithm -- updates metric
   *  weights. Invoked only when we're using non-Potts model
   *  and metric is trainable
   */
  protected void updateMetricWeights() throws Exception {
    if (m_useMultipleMetrics) {
      for (int i = 0; i < m_NumClusters; i++) {
	m_metricLearners[i].trainMetric(i);
      } 
    } else {
      m_metricLearner.trainMetric(-1);
    } 
    InitNormalizerRegularizer();
  }
 

  /** checks for convergence */
  public boolean convergenceCheck(double oldObjective,
				  double newObjective) throws Exception {
    boolean converged = false;

    // Convergence check
    if(Math.abs(oldObjective - newObjective) < m_ObjFunConvergenceDifference) {
      System.out.println("Final objective function is: " + newObjective);
      converged = true;
    }

    // number of iterations check
    if (m_numBlankIterations >= m_maxBlankIterations) {
      System.out.println("Max blank iterations reached ...\n");
      converged = true;
    }
    if (m_Iterations >= m_maxIterations) {
      System.out.println("Max iterations reached ...\n");
      converged = true;
    }

    return converged;
  }

  /** calculates objective function */
  public double calculateObjectiveFunction(boolean isComplete) throws Exception {
    if (m_verbose) {
      System.out.println("Calculating objective function ...");
    }

    // update the oldObjective only if previous estimate of m_Objective
    // was complete
    if (isComplete) {
      m_OldObjective = m_Objective;
    }
    m_Objective = 0;
    m_objVariance = 0;
    m_objMustLinks = 0;
    m_objCannotLinks = 0;
    m_objNormalizer = 0;

    // temporarily halve weights since every constraint is counted twice
    double tempML = m_MLweight;
    double tempCL = m_CLweight;
    m_MLweight = tempML/2;
    m_CLweight = tempCL/2; 
    
    if (m_verbose) {
      System.out.println("Must link weight: " + m_MLweight);
      System.out.println("Cannot link weight: " + m_CLweight);    
    }

    for (int i=0; i<m_Instances.numInstances(); i++) {
      if (m_isOfflineMetric) {
	double dist = m_metric.penalty(m_Instances.instance(i),
				       m_ClusterCentroids.instance(m_ClusterAssignments[i]));
	m_Objective += dist;
	if (m_verbose) {
	  System.out.println("Component for " + i + " = " + dist);
	}
      }
      else {
	m_Objective += penaltyForInstance(i, m_ClusterAssignments[i]);
	m_objVariance += m_objVarianceCurrPoint;
	m_objMustLinks += m_objMustLinksCurrPoint;
	m_objCannotLinks += m_objCannotLinksCurrPoint;
	m_objNormalizer += m_objNormalizerCurrPoint;
      }
    }

    m_Objective -= m_objRegularizer;

    m_MLweight = tempML;
    m_CLweight = tempCL; // reset the values of the constraint weights

    // Oscillation check
    if ((float)m_OldObjective < (float)m_Objective) {
      System.out.println("WHOA!!!  Oscillations => bug in EM step?");
      System.out.println("Old objective:" + (float)m_OldObjective
			 + " < New objective: " + (float)m_Objective); 
    }

    return m_Objective;
  }

  
  /** Actual KMeans function */
  protected void runKMeans() throws Exception {
    boolean converged = false;
    m_Iterations = 0;
    m_numBlankIterations = 0; 
    m_Objective = Double.POSITIVE_INFINITY; 

    if (!m_isOfflineMetric) {
      // initialize normalizer and regularizer
      m_metric.resetMetric();
      // initialize max CL penalties
      if (m_ConstraintsHash.size() > 0) {
	m_maxCLPenalties = calculateMaxCLPenalties();
      }
    }

    while (!converged) {
      m_OldObjective = m_Objective; 
      
      // E-step
      int numMovedPoints = findBestAssignments();

      m_numBlankIterations = (numMovedPoints == 0) ? m_numBlankIterations+1 : 0; 
      {//if (m_verbose) {
	calculateObjectiveFunction(false);
      }
	System.out.println((float)m_Objective + " - Objective function after point assignment(CALC)");
	System.out.println("\tvar=" + ((float)m_objVariance) 
			   + "\tC=" + ((float)m_objCannotLinks) 
			   + "\tM=" + ((float)m_objMustLinks) 
			   + "\tLOG=" + ((float)m_objNormalizer) 
			   + "\tREG=" + ((float)m_objRegularizer));
     

      // M-step
      updateClusterCentroids();

      System.out.println("\n" + m_Iterations + ". Objective function: " + ((float)m_Objective));
      {//if (m_verbose) {
	calculateObjectiveFunction(true);
      }
	System.out.println((float)m_Objective + " - Objective function after centroid estimation");
	System.out.println("\tvar=" + ((float)m_objVariance)
			   + "\tC=" + ((float)m_objCannotLinks)
			   + "\tM=" + ((float)m_objMustLinks)
			   + "\tLOG=" + ((float)m_objNormalizer) 
			   + "\tREG=" + ((float)m_objRegularizer));

      if (m_Trainable == TRAINING_INTERNAL && !m_isOfflineMetric) {

	updateMetricWeights();
	  
	{//if (m_verbose) {
	  calculateObjectiveFunction(true);
	}
	  System.out.println((float)m_Objective + " - Objective function after metric update");
	  System.out.println("\tvar=" + ((float)m_objVariance) + "\tC=" + ((float)m_objCannotLinks) +
			     "\tM=" + ((float)m_objMustLinks)  + "\tLOG=" + ((float)m_objNormalizer) +
			     "\tREG=" + ((float)m_objRegularizer));

	  
	if (m_ConstraintsHash.size() > 0) {
	  m_maxCLPenalties = calculateMaxCLPenalties();
	}
      }

      converged = convergenceCheck(m_OldObjective, m_Objective);
      m_Iterations++;
    }

    if (m_verbose) {
      System.out.println("Done clustering; top cluster features: ");
      for (int i = 0; i < m_NumClusters; i++){
	System.out.println("Centroid " + i);
	TreeMap map = new TreeMap(Collections.reverseOrder());
	Instance centroid= m_ClusterCentroids.instance(i);
	for (int j = 0; j < centroid.numValues(); j++) {
	  Attribute attr = centroid.attributeSparse(j);
	  map.put(new Double(centroid.value(attr)), attr.name());
	}
	Iterator it = map.entrySet().iterator();
	for (int j=0; j < 5 && it.hasNext(); j++) {
	  Map.Entry entry = (Map.Entry) it.next();
	  System.out.println("\t" + entry.getKey() + "\t" + entry.getValue());
	}
      }
    }
  }


  /** reset the value of the objective function and all of its components */ 
  public void resetObjective() { 
    m_Objective = 0;
    m_objVariance = 0;
    m_objCannotLinks = 0;
    m_objMustLinks = 0;
    m_objNormalizer = 0;
    m_objRegularizer = 0;
  }
  
  /** Go through the cannot-link constraints and find the current maximum distance
   * @return an array of maximum weighted distances.  If a single metric is used, maximum distance
   * is calculated over the entire dataset */
  // TODO:  non-datasetWide case is not debugged currently!!!
  protected double[] calculateMaxCLPenalties() throws Exception {
    double [] maxPenalties = null;
    double [][] minValues = null;
    double [][] maxValues = null;
    int[] attrIdxs = null; 

    maxPenalties = new double[m_NumClusters];
    m_maxCLPoints = new Instance[m_NumClusters][2];
    m_maxCLDiffInstances = new Instance[m_NumClusters];

    for (int i = 0; i < m_NumClusters; i++) { 
      m_maxCLPoints[i][0] = new Instance(m_Instances.numAttributes());
      m_maxCLPoints[i][1] = new Instance(m_Instances.numAttributes());
      m_maxCLPoints[i][0].setDataset(m_Instances);
      m_maxCLPoints[i][1].setDataset(m_Instances);
      m_maxCLDiffInstances[i] = new Instance(m_Instances.numAttributes());
      m_maxCLDiffInstances[i].setDataset(m_Instances);
    }

    // TEMPORARY PLUG:  this was supposed to take care of WeightedDotp,
    // but it turns out that with weighting similarity can be > 1. 
//      if (m_metric.m_fixedMaxDistance) {
//        for (int i = 0; i < m_NumClusters; i++) {
//  	maxPenalties[i] = m_metric.getMaxDistance(); 
//        }
//        return maxPenalties; 
//      } 

    
    minValues = new double[m_NumClusters][m_metrics[0].getNumAttributes()];
    maxValues = new double[m_NumClusters][m_metrics[0].getNumAttributes()];
    attrIdxs = m_metrics[0].getAttrIndxs();

    // temporary plug:  if this if the first iteration when no instances were assigned to clusters,
    // dataset-wide (not cluster-wide!) minimum and maximum are used even for the case with
    // multiple metrics
    boolean datasetWide = true;
    if (m_useMultipleMetrics && m_Iterations > 0) { 
      datasetWide = false;
    } 

    // TODO:  Mahalanobis - check with getMaxPoints
    // go through all points
   //   if (m_useMultipleMetrics) {
//        for (int i = 0; i < m_metrics.length; i++) { 
//  	double[][] maxPoints = ((WeightedMahalanobis)m_metrics[i]).getMaxPoints(m_ConstraintsHash, m_Instances);
//  	minValues[i] = maxPoints[0];
//  	  maxValues[i] = maxPoints[1];
//  	  //  	  System.out.println("Max points " + i);
//  	  //  	  for (int j = 0; j < maxPoints[0].length; j++) { System.out.println(maxPoints[0][j] + " - " + maxPoints[1][j]);}
//  	}
//        } else { 
//  	double[][] maxPoints = ((WeightedMahalanobis)m_metric).getMaxPoints(m_ConstraintsHash, m_Instances);
//  	minValues[0] = maxPoints[0];
//  	maxValues[0] = maxPoints[1];
//  	for (int i = 0; i < m_metrics.length; i++) {
//  	  minValues[i] = maxPoints[0];
//  	  maxValues[i] = maxPoints[1];
//  	}
//  	//  	System.out.println("Max points:");
//  	//  	for (int i = 0; i < maxPoints[0].length; i++) { System.out.println(maxPoints[0][i] + " - " + maxPoints[1][i]);}
//        }
//      } else { // find the enclosing hypercube for WeightedEuclidean etc. 
    for (int i = 0; i < m_Instances.numInstances(); i++) {
      Instance instance = m_Instances.instance(i);
      for (int j = 0; j < attrIdxs.length; j++) {
	double val = instance.value(attrIdxs[j]);
	if (datasetWide) {
	  if (val < minValues[0][j]) {
	    minValues[0][j] = val; 
	  }
	  if (val > maxValues[0][j]) {
	    maxValues[0][j] = val; 
	  } 
	} else { // cluster-specific min's and max's  are needed
	  if (val < minValues[m_ClusterAssignments[i]][j]) {
	    minValues[m_ClusterAssignments[i]][j] = val; 
	  }
	  if (val > maxValues[m_ClusterAssignments[i]][j]) {
	    maxValues[m_ClusterAssignments[i]][j] = val; 
	  } 
	} 
      }
    }

    // get the max/min points
    if (datasetWide) {
      for (int i = 0; i < attrIdxs.length; i++) {
	m_maxCLPoints[0][0].setValue(attrIdxs[i], minValues[0][i]);
	m_maxCLPoints[0][1].setValue(attrIdxs[i], maxValues[0][i]);
      }
      // must copy these over all clusters - just for the first iteration
      for (int j = 1; j < m_NumClusters; j++) { 
	for (int i = 0; i < attrIdxs.length; i++) {
	  m_maxCLPoints[j][0].setValue(attrIdxs[i], minValues[0][i]);
	  m_maxCLPoints[j][1].setValue(attrIdxs[i], maxValues[0][i]);
	}
      } 
    } else { // cluster-specific
      for (int j = 0; j < m_NumClusters; j++) { 
	for (int i = 0; i < attrIdxs.length; i++) {
	  m_maxCLPoints[j][0].setValue(attrIdxs[i], minValues[j][i]);
	  m_maxCLPoints[j][1].setValue(attrIdxs[i], maxValues[j][i]);
	}
      }
    }

    // calculate the distances
    if (datasetWide) {
      maxPenalties[0] = m_metrics[0].penaltySymmetric(m_maxCLPoints[0][0],
						      m_maxCLPoints[0][1]);
      m_maxCLDiffInstances[0] = m_metrics[0].createDiffInstance(m_maxCLPoints[0][0], 
								 m_maxCLPoints[0][1]);
      for (int i = 1; i < maxPenalties.length; i++) {
	maxPenalties[i] = maxPenalties[0];
	m_maxCLDiffInstances[i] = m_maxCLDiffInstances[0];
      } 
    } else { // cluster-specific - SHOULD BE FIXED!!!!
      for (int j = 0; j < m_NumClusters; j++) { 
	for (int i = 0; i < attrIdxs.length; i++) {
	  maxPenalties[j] += m_metrics[j].penaltySymmetric(m_maxCLPoints[j][0],