pairedttester.java

Java 编写的多种数据挖掘算法 包括聚类、分类、预处理等

			      + "column " + (m_ResultsetKeyColumns[j] + 1)
			      + "!\n" + current);
	}
      }
      for (int j = 0; j < m_DatasetKeyColumns.length; j++) {
	if (current.isMissing(m_DatasetKeyColumns[j])) {
	  throw new Exception("Instance has missing value in dataset key "
			      + "column " + (m_DatasetKeyColumns[j] + 1)
			      + "!\n" + current);
	}
      }
      boolean found = false;
      for (int j = 0; j < m_Resultsets.size(); j++) {
	Resultset resultset = (Resultset) m_Resultsets.elementAt(j);
	if (resultset.matchesTemplate(current)) {
	  resultset.add(current);
	  found = true;
	  break;
	}
      }
      if (!found) {
	Resultset resultset = new Resultset(current);
	m_Resultsets.addElement(resultset);
      }

      m_DatasetSpecifiers.add(current);
    }

    // Tell each resultset to sort on the run column
    for (int j = 0; j < m_Resultsets.size(); j++) {
      Resultset resultset = (Resultset) m_Resultsets.elementAt(j);
      if (m_FoldColumn >= 0) {
        // sort on folds first in case they are out of order
        resultset.sort(m_FoldColumn);
      }
      resultset.sort(m_RunColumn);
    }

    m_ResultsetsValid = true;
  }

  /**
   * Gets the number of datasets in the resultsets
   *
   * @return the number of datasets in the resultsets
   */
  public int getNumDatasets() {

    if (!m_ResultsetsValid) {
      try {
	prepareData();
      } catch (Exception ex) {
	ex.printStackTrace();
	return 0;
      }
    }
    return m_DatasetSpecifiers.numSpecifiers();
  }

  /**
   * Gets the number of resultsets in the data.
   *
   * @return the number of resultsets in the data
   */
  public int getNumResultsets() {

    if (!m_ResultsetsValid) {
      try {
  prepareData();
      } catch (Exception ex) {
  ex.printStackTrace();
  return 0;
      }
    }
    return m_Resultsets.size();
  }

  /**
   * Gets a string descriptive of the specified resultset.
   *
   * @param index the index of the resultset
   * @return a descriptive string for the resultset
   */
  public String getResultsetName(int index) {

    if (!m_ResultsetsValid) {
      try {
	prepareData();
      } catch (Exception ex) {
	ex.printStackTrace();
	return null;
      }
    }
    return ((Resultset) m_Resultsets.elementAt(index)).templateString();
  }
  
  /**
   * Checks whether the resultset with the given index shall be displayed.
   * 
   * @param index the index of the resultset to check whether it shall be displayed 
   * @return whether the specified resultset is displayed 
   */
  public boolean displayResultset(int index) {
    boolean       result;
    int           i;
    
    result = true;

    if (m_DisplayedResultsets != null) {
      result = false;
      for (i = 0; i < m_DisplayedResultsets.length; i++) {
        if (m_DisplayedResultsets[i] == index) {
          result = true;
          break;
        }
      }
    }
      
    return result;
  }
  
  /**
   * Computes a paired t-test comparison for a specified dataset between
   * two resultsets.
   *
   * @param datasetSpecifier the dataset specifier
   * @param resultset1Index the index of the first resultset
   * @param resultset2Index the index of the second resultset
   * @param comparisonColumn the column containing values to compare
   * @return the results of the paired comparison
   * @throws Exception if an error occurs
   */
  public PairedStats calculateStatistics(Instance datasetSpecifier,
					 int resultset1Index,
					 int resultset2Index,
					 int comparisonColumn) throws Exception {

    if (m_Instances.attribute(comparisonColumn).type()
	!= Attribute.NUMERIC) {
      throw new Exception("Comparison column " + (comparisonColumn + 1)
			  + " ("
			  + m_Instances.attribute(comparisonColumn).name()
			  + ") is not numeric");
    }
    if (!m_ResultsetsValid) {
      prepareData();
    }

    Resultset resultset1 = (Resultset) m_Resultsets.elementAt(resultset1Index);
    Resultset resultset2 = (Resultset) m_Resultsets.elementAt(resultset2Index);
    FastVector dataset1 = resultset1.dataset(datasetSpecifier);
    FastVector dataset2 = resultset2.dataset(datasetSpecifier);
    String datasetName = templateString(datasetSpecifier);
    if (dataset1 == null) {
      throw new Exception("No results for dataset=" + datasetName
			 + " for resultset=" + resultset1.templateString());
    } else if (dataset2 == null) {
      throw new Exception("No results for dataset=" + datasetName
			 + " for resultset=" + resultset2.templateString());
    } else if (dataset1.size() != dataset2.size()) {
      throw new Exception("Results for dataset=" + datasetName
			  + " differ in size for resultset="
			  + resultset1.templateString()
			  + " and resultset="
			  + resultset2.templateString()
			  );
    }
    
    PairedStats pairedStats = new PairedStats(m_SignificanceLevel);

    for (int k = 0; k < dataset1.size(); k ++) {
      Instance current1 = (Instance) dataset1.elementAt(k);
      Instance current2 = (Instance) dataset2.elementAt(k);
      if (current1.isMissing(comparisonColumn)) {
	System.err.println("Instance has missing value in comparison "
			   + "column!\n" + current1);
	continue;
      }
      if (current2.isMissing(comparisonColumn)) {
	System.err.println("Instance has missing value in comparison "
			   + "column!\n" + current2);
	continue;
      }
      if (current1.value(m_RunColumn) != current2.value(m_RunColumn)) {
	System.err.println("Run numbers do not match!\n"
			    + current1 + current2);
      }
      if (m_FoldColumn != -1) {
	if (current1.value(m_FoldColumn) != current2.value(m_FoldColumn)) {
	  System.err.println("Fold numbers do not match!\n"
			     + current1 + current2);
	}
      }
      double value1 = current1.value(comparisonColumn);
      double value2 = current2.value(comparisonColumn);
      pairedStats.add(value1, value2);
    }
    pairedStats.calculateDerived();
    //System.err.println("Differences stats:\n" + pairedStats.differencesStats);
    return pairedStats;

  }
  
  /**
   * Creates a key that maps resultset numbers to their descriptions.
   *
   * @return a value of type 'String'
   */
  public String resultsetKey() {

    if (!m_ResultsetsValid) {
      try {
	prepareData();
      } catch (Exception ex) {
	ex.printStackTrace();
	return ex.getMessage();
      }
    }
    String result = "";
    for (int j = 0; j < getNumResultsets(); j++) {
      result += "(" + (j + 1) + ") " + getResultsetName(j) + '\n';
    }
    return result + '\n';
  }
  
  /**
   * Creates a "header" string describing the current resultsets.
   *
   * @param comparisonColumn a value of type 'int'
   * @return a value of type 'String'
   */
  public String header(int comparisonColumn) {

    if (!m_ResultsetsValid) {
      try {
	prepareData();
      } catch (Exception ex) {
	ex.printStackTrace();
	return ex.getMessage();
      }
    }
    
    initResultMatrix();
    m_ResultMatrix.addHeader("Tester", getClass().getName());
    m_ResultMatrix.addHeader("Analysing", m_Instances.attribute(comparisonColumn).name());
    m_ResultMatrix.addHeader("Datasets", Integer.toString(getNumDatasets()));
    m_ResultMatrix.addHeader("Resultsets", Integer.toString(getNumResultsets()));
    m_ResultMatrix.addHeader("Confidence", getSignificanceLevel() + " (two tailed)");
    m_ResultMatrix.addHeader("Sorted by", getSortColumnName());
    m_ResultMatrix.addHeader("Date", (new SimpleDateFormat()).format(new Date()));

    return m_ResultMatrix.toStringHeader() + "\n";
  }

  /**
   * Carries out a comparison between all resultsets, counting the number
   * of datsets where one resultset outperforms the other.
   *
   * @param comparisonColumn the index of the comparison column
   * @param nonSigWin for storing the non-significant wins
   * @return a 2d array where element [i][j] is the number of times resultset
   * j performed significantly better than resultset i.
   * @throws Exception if an error occurs
   */
  public int [][] multiResultsetWins(int comparisonColumn, int [][] nonSigWin)
    throws Exception {

    int numResultsets = getNumResultsets();
    int [][] win = new int [numResultsets][numResultsets];
    //    int [][] nonSigWin = new int [numResultsets][numResultsets];
    for (int i = 0; i < numResultsets; i++) {
      for (int j = i + 1; j < numResultsets; j++) {
	System.err.print("Comparing (" + (i + 1) + ") with ("
			 + (j + 1) + ")\r");
	System.err.flush();
	for (int k = 0; k < getNumDatasets(); k++) {
	  try {
	    PairedStats pairedStats = 
	      calculateStatistics(m_DatasetSpecifiers.specifier(k), i, j,
				  comparisonColumn);
	    if (pairedStats.differencesSignificance < 0) {
	      win[i][j]++;
	    } else if (pairedStats.differencesSignificance > 0) {
	      win[j][i]++;
	    }

	    if (pairedStats.differencesStats.mean < 0) {
	      nonSigWin[i][j]++;
	    } else if (pairedStats.differencesStats.mean > 0) {
	      nonSigWin[j][i]++;
	    }
	  } catch (Exception ex) {
	    //ex.printStackTrace();
	    System.err.println(ex.getMessage());
	  }
	}
      }
    }
    return win;
  }

  /**
   * clears the content and fills the column and row names according to the
   * given sorting
   */
  protected void initResultMatrix() {
    m_ResultMatrix.setSize(getNumResultsets(), getNumDatasets());
    m_ResultMatrix.setShowStdDev(m_ShowStdDevs);

    for (int i = 0; i < getNumDatasets(); i++)
      m_ResultMatrix.setRowName(i, 
          templateString(m_DatasetSpecifiers.specifier(i)));

    for (int j = 0; j < getNumResultsets(); j++) {
      m_ResultMatrix.setColName(j, getResultsetName(j));
      m_ResultMatrix.setColHidden(j, !displayResultset(j));
    }
  }
  
  /**
   * Carries out a comparison between all resultsets, counting the number
   * of datsets where one resultset outperforms the other. The results
   * are summarized in a table.
   *
   * @param comparisonColumn the index of the comparison column
   * @return the results in a string
   * @throws Exception if an error occurs
   */
  public String multiResultsetSummary(int comparisonColumn)
    throws Exception {
    
    int[][] nonSigWin = new int [getNumResultsets()][getNumResultsets()];
    int[][] win = multiResultsetWins(comparisonColumn, nonSigWin);
    
    initResultMatrix();    
    m_ResultMatrix.setSummary(nonSigWin, win);
    
    return m_ResultMatrix.toStringSummary();
  }

  /**
   * returns a ranking of the resultsets
   * 
   * @param comparisonColumn	the column to compare with
   * @return			the ranking
   * @throws Exception		if something goes wrong
   */
  public String multiResultsetRanking(int comparisonColumn)
    throws Exception {
    
    int[][] nonSigWin = new int [getNumResultsets()][getNumResultsets()];
    int[][] win       = multiResultsetWins(comparisonColumn, nonSigWin);
    
    initResultMatrix();    
    m_ResultMatrix.setRanking(win);

    return m_ResultMatrix.toStringRanking();
  }
				    
  /**
   * Creates a comparison table where a base resultset is compared to the
   * other resultsets. Results are presented for every dataset.
   *
   * @param baseResultset the index of the base resultset
   * @param comparisonColumn the index of the column to compare over
   * @return the comparison table string
   * @throws Exception if an error occurs
   */
  public String multiResultsetFull(int baseResultset,
				   int comparisonColumn) throws Exception {

    int maxWidthMean = 2;
    int maxWidthStdDev = 2;
    
    double[] sortValues = new double[getNumDatasets()];
      
    // determine max field width
    for (int i = 0; i < getNumDatasets(); i++) {
      sortValues[i] = Double.POSITIVE_INFINITY;  // sorts skipped cols to end
      
      for (int j = 0; j < getNumResultsets(); j++) {
        if (!displayResultset(j))
          continue;
	try {
	  PairedStats pairedStats = 
	    calculateStatistics(m_DatasetSpecifiers.specifier(i), 
				baseResultset, j, comparisonColumn);
          if (!Double.isInfinite(pairedStats.yStats.mean) &&
              !Double.isNaN(pairedStats.yStats.mean)) {
            double width = ((Math.log(Math.abs(pairedStats.yStats.mean)) / 
                             Math.log(10))+1);
            if (width > maxWidthMean) {
              maxWidthMean = (int)width;
            }
          }

          if (j == baseResultset) {
            if (getSortColumn() != -1)
              sortValues[i] = calculateStatistics(
                                m_DatasetSpecifiers.specifier(i), 
                                baseResultset, j, getSortColumn()).xStats.mean;
            else
              sortValues[i] = i;
          }
	  
	  if (m_ShowStdDevs &&
              !Double.isInfinite(pairedStats.yStats.stdDev) &&
              !Double.isNaN(pairedStats.yStats.stdDev)) {
	    double width = ((Math.log(Math.abs(pairedStats.yStats.stdDev)) / 
                             Math.log(10))+1);
	    if (width > maxWidthStdDev) {
	      maxWidthStdDev = (int)width;
	    }
	  }
	}  catch (Exception ex) {
	  //ex.printStackTrace();
          System.err.println(ex);
	}
      }
    }

    // sort rows according to sort column
    m_SortOrder = Utils.sort(sortValues);

    // determine column order
    m_ColOrder = new int[getNumResultsets()];
    m_ColOrder[0] = baseResultset;
    int index = 1;
    for (int i = 0; i < getNumResultsets(); i++) {
      if (i == baseResultset)
        continue;
      m_ColOrder[index] = i;
      index++;
    }

    // setup matrix
    initResultMatrix();    
    m_ResultMatrix.setRowOrder(m_SortOrder);
    m_ResultMatrix.setColOrder(m_ColOrder);
    m_ResultMatrix.setMeanWidth(maxWidthMean);
    m_ResultMatrix.setStdDevWidth(maxWidthStdDev);
    m_ResultMatrix.setSignificanceWidth(1);

    // make sure that test base is displayed, even though it might not be
    // selected
    for (int i = 0; i < m_ResultMatrix.getColCount(); i++) {
      if (    (i == baseResultset)
           && (m_ResultMatrix.getColHidden(i)) ) {
        m_ResultMatrix.setColHidden(i, false);
        System.err.println("Note: test base was hidden - set visible!");
      }
    }
    
    // the data
    for (int i = 0; i < getNumDatasets(); i++) {
      m_ResultMatrix.setRowName(i, 
          templateString(m_DatasetSpecifiers.specifier(i)));

      for (int j = 0; j < getNumResultsets(); j++) {
        try {
          // calc stats
          PairedStats pairedStats = 
            calculateStatistics(m_DatasetSpecifiers.specifier(i), 
                baseResultset, j, comparisonColumn);

          // count
          m_ResultMatrix.setCount(i, pairedStats.count);

          // mean
          m_ResultMatrix.setMean(j, i, pairedStats.yStats.mean);
          
          // std dev
          m_ResultMatrix.setStdDev(j, i, pairedStats.yStats.stdDev);

          // significance
          if (pairedStats.differencesSignificance < 0)
            m_ResultMatrix.setSignificance(j, i, ResultMatrix.SIGNIFICANCE_WIN);
          else if (pairedStats.differencesSignificance > 0)
            m_ResultMatrix.setSignificance(j, i, ResultMatrix.SIGNIFICANCE_LOSS);
          else
            m_ResultMatrix.setSignificance(j, i, ResultMatrix.SIGNIFICANCE_TIE);
        }
        catch (Exception e) {
          //e.printStackTrace();
          System.err.println(e);
        }
      }
    }

    // generate output
    StringBuffer result = new StringBuffer(1000);
    try {
      result.append(m_ResultMatrix.toStringMatrix());
    }