Examples of weka.classifiers.CostMatrix

weka.classifiers.CostMatrix
Class for storing and manipulating a misclassification cost matrix. The element at position i,j in the matrix is the penalty for classifying an instance of class j as class i. Cost values can be fixed or computed on a per-instance basis (cost sensitive evaluation only) from the value of an attribute or an expression involving attribute(s). @author Mark Hall @author Richard Kirkby (rkirkby@cs.waikato.ac.nz) @version $Revision: 1.17 $

  File selectedFile = m_fileChooser.getSelectedFile();
  Reader reader = null;
  try {
    reader = new BufferedReader(new FileReader(selectedFile));
    m_matrix = 
      new CostMatrix(reader);
    reader.close();
    matrixChanged();
  } catch (Exception ex) {
    JOptionPane.showMessageDialog(this, 
        Messages.getInstance().getString("CostMatrixEditor_OpenMatrix_JOptionPaneShowMessageDialog_Text_First")

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    MetaCost cl = new MetaCost();
    
    // load costmatrix
    try {
      cl.setCostMatrix(
          new CostMatrix(
            new InputStreamReader(ClassLoader.getSystemResourceAsStream(
                  "weka/classifiers/data/ClassifierTest.cost"))));
    }
    catch (Exception e) {
      e.printStackTrace();

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    CostSensitiveClassifier cl = new CostSensitiveClassifier();
    
    // load costmatrix
    try {
      cl.setCostMatrix(
          new CostMatrix(
            new InputStreamReader(ClassLoader.getSystemResourceAsStream(
                  "weka/classifiers/data/ClassifierTest.cost"))));
    }
    catch (Exception e) {
      e.printStackTrace();

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      && (!m_EvalWRTCostsBut.isSelected())) {
    m_SetCostsFrame.setVisible(false);
  }
      }
    });
    m_CostMatrixEditor.setValue(new CostMatrix(1));
    m_SetCostsBut.setEnabled(m_EvalWRTCostsBut.isSelected());
    m_SetCostsBut.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent e) {
  m_SetCostsBut.setEnabled(false);
  if (m_SetCostsFrame == null) {
    if (PropertyDialog.getParentDialog(ClassifierPanel.this) != null)
      m_SetCostsFrame = new PropertyDialog(
    PropertyDialog.getParentDialog(ClassifierPanel.this), 
    m_CostMatrixEditor, 100, 100);
    else
      m_SetCostsFrame = new PropertyDialog(
    PropertyDialog.getParentFrame(ClassifierPanel.this), 
    m_CostMatrixEditor, 100, 100);
    m_SetCostsFrame.setTitle(Messages.getInstance().getString("ClassifierPanel_SetCostsFrame_SetTitle_Text"));
    //  pd.setSize(250,150);
    m_SetCostsFrame.addWindowListener(new java.awt.event.WindowAdapter() {
      public void windowClosing(java.awt.event.WindowEvent p) {
        m_SetCostsBut.setEnabled(m_EvalWRTCostsBut.isSelected());
        if ((m_SetCostsFrame != null) 
      && (!m_EvalWRTCostsBut.isSelected())) {
    m_SetCostsFrame.setVisible(false);
        }
      }
    });
    m_SetCostsFrame.setVisible(true);
  }
  
  // do we need to change the size of the matrix?
  int classIndex = m_ClassCombo.getSelectedIndex();
  int numClasses = m_Instances.attribute(classIndex).numValues();
  if (numClasses != ((CostMatrix) m_CostMatrixEditor.getValue()).numColumns())
    m_CostMatrixEditor.setValue(new CostMatrix(numClasses));
  
  m_SetCostsFrame.setVisible(true);
      }
    });

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      }
      m_RunThread = new Thread() {
  public void run() {
    // Copy the current state of things
    m_Log.statusMessage(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Log_StatusMessage_Text_First"));
    CostMatrix costMatrix = null;
    Instances inst = new Instances(m_Instances);
    DataSource source = null;
          Instances userTestStructure = null;
    // additional vis info (either shape type or point size)
    FastVector plotShape = new FastVector();
    FastVector plotSize = new FastVector();
    Instances predInstances = null;
   
    // for timing
    long trainTimeStart = 0, trainTimeElapsed = 0;


          try {
            if (m_TestLoader != null && m_TestLoader.getStructure() != null) {
              m_TestLoader.reset();
              source = new DataSource(m_TestLoader);
              userTestStructure = source.getStructure();
            }
          } catch (Exception ex) {
            ex.printStackTrace();
          }
    if (m_EvalWRTCostsBut.isSelected()) {
      costMatrix = new CostMatrix((CostMatrix) m_CostMatrixEditor
          .getValue());
    }
    boolean outputModel = m_OutputModelBut.isSelected();
    boolean outputConfusion = m_OutputConfusionBut.isSelected();
    boolean outputPerClass = m_OutputPerClassBut.isSelected();
    boolean outputSummary = true;
          boolean outputEntropy = m_OutputEntropyBut.isSelected();
    boolean saveVis = m_StorePredictionsBut.isSelected();
    boolean outputPredictionsText = m_OutputPredictionsTextBut.isSelected();
    if (m_OutputAdditionalAttributesText.getText().equals("")) {
      m_OutputAdditionalAttributesRange = null;
    }
    else {
      m_OutputAdditionalAttributesRange = new Range(m_OutputAdditionalAttributesText.getText());
      m_OutputAdditionalAttributesRange.setUpper(inst.numAttributes() - 1);
    }


    String grph = null;


    int testMode = 0;
    int numFolds = 10;
          double percent = 66;
    int classIndex = m_ClassCombo.getSelectedIndex();
    Classifier classifier = (Classifier) m_ClassifierEditor.getValue();
    Classifier template = null;
    try {
      template = Classifier.makeCopy(classifier);
    } catch (Exception ex) {
      m_Log.logMessage(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Log_LogMessage_Text_First") + ex.getMessage());
    }
    Classifier fullClassifier = null;
    StringBuffer outBuff = new StringBuffer();
    String name = (new SimpleDateFormat("HH:mm:ss - "))
    .format(new Date());
    String cname = classifier.getClass().getName();
    if (cname.startsWith("weka.classifiers.")) {
      name += cname.substring("weka.classifiers.".length());
    } else {
      name += cname;
    }
          String cmd = m_ClassifierEditor.getValue().getClass().getName();
          if (m_ClassifierEditor.getValue() instanceof OptionHandler)
            cmd += " " + Utils.joinOptions(((OptionHandler) m_ClassifierEditor.getValue()).getOptions());
    Evaluation eval = null;
    try {
      if (m_CVBut.isSelected()) {
        testMode = 1;
        numFolds = Integer.parseInt(m_CVText.getText());
        if (numFolds <= 1) {
    throw new Exception(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Exception_Text_First"));
        }
      } else if (m_PercentBut.isSelected()) {
        testMode = 2;
        percent = Double.parseDouble(m_PercentText.getText());
        if ((percent <= 0) || (percent >= 100)) {
    throw new Exception(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Exception_Text_Second"));
        }
      } else if (m_TrainBut.isSelected()) {
        testMode = 3;
      } else if (m_TestSplitBut.isSelected()) {
        testMode = 4;
        // Check the test instance compatibility
        if (source == null) {
    throw new Exception(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Exception_Text_Third"));
        }
        if (!inst.equalHeaders(userTestStructure)) {
    throw new Exception(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Exception_Text_Fourth"));
        }
              userTestStructure.setClassIndex(classIndex);
      } else {
        throw new Exception(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Exception_Text_Fifth"));
      }
      inst.setClassIndex(classIndex);


      // set up the structure of the plottable instances for 
      // visualization
            if (saveVis) {
              predInstances = setUpVisualizableInstances(inst);
              predInstances.setClassIndex(inst.classIndex()+1);
            } 


      // Output some header information
      m_Log.logMessage(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Log_LogMessage_Text_Second") + cname);
      m_Log.logMessage(Messages.getInstance().getString("ClassifierPanel_StartClassifier_Log_LogMessage_Text_Third") + cmd);
      if (m_Log instanceof TaskLogger) {
        ((TaskLogger)m_Log).taskStarted();
      }
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_First"));
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Second") + cname);
      if (classifier instanceof OptionHandler) {
        String [] o = ((OptionHandler) classifier).getOptions();
        outBuff.append(" " + Utils.joinOptions(o));
      }
      outBuff.append("\n");
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Fourth") + inst.relationName() + '\n');
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Sixth") + inst.numInstances() + '\n');
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Eigth") + inst.numAttributes() + '\n');
      if (inst.numAttributes() < 100) {
        for (int i = 0; i < inst.numAttributes(); i++) {
    outBuff.append("              " + inst.attribute(i).name()
             + '\n');
        }
      } else {
        outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Twelveth"));
      }


      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Thirteenth"));
      switch (testMode) {
        case 3: // Test on training
    outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Fourteenth"));
    break;
        case 1: // CV mode
    outBuff.append("" + numFolds + Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Sixteenth"));
    break;
        case 2: // Percent split
    outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Seventeenth") + percent
        + Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Eighteenth"));
    break;
        case 4: // Test on user split
    if (source.isIncremental())
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Nineteenth"));
    else
      outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_Twentyth")
          + source.getDataSet().numInstances() + Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_TwentyFirst"));
    break;
      }
            if (costMatrix != null) {
               outBuff.append(Messages.getInstance().getString("ClassifierPanel_StartClassifier_OutBuffer_Text_TwentySecond"))
               .append(costMatrix.toString()).append("\n");
            }
      outBuff.append("\n");
      m_History.addResult(name, outBuff);
      m_History.setSingle(name);

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            // additional vis info (either shape type or point size)
            FastVector plotShape = new FastVector();
            FastVector plotSize = new FastVector();
            Instances predInstances = null;


            CostMatrix costMatrix = null;
            if (m_EvalWRTCostsBut.isSelected()) {
              costMatrix = new CostMatrix((CostMatrix) m_CostMatrixEditor
                                          .getValue());
            }    
            boolean outputConfusion = m_OutputConfusionBut.isSelected();
            boolean outputPerClass = m_OutputPerClassBut.isSelected();
            boolean outputSummary = true;

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    String costName = train.relationName() + CostMatrix.FILE_EXTENSION;
    File costFile = new File(getOnDemandDirectory(), costName);
    if (!costFile.exists()) {
      throw new Exception("On-demand cost file doesn't exist: " + costFile);
    }
    CostMatrix costMatrix = new CostMatrix(new BufferedReader(
    new FileReader(costFile)));
    
    Evaluation eval = new Evaluation(train, costMatrix);    
    m_Classifier = Classifier.makeCopy(m_Template);

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    String costName = train.relationName() + CostMatrix.FILE_EXTENSION;
    File costFile = new File(getOnDemandDirectory(), costName);
    if (!costFile.exists()) {
      throw new Exception("On-demand cost file doesn't exist: " + costFile);
    }
    CostMatrix costMatrix = new CostMatrix(new BufferedReader(
    new FileReader(costFile)));
    
    Evaluation eval = new Evaluation(train, costMatrix);    
    m_Classifier = Classifier.makeCopy(m_Template);

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    setMinimizeExpectedCost(Utils.getFlag('M', options));


    String costFile = Utils.getOption('C', options);
    if (costFile.length() != 0) {
      try {
  setCostMatrix(new CostMatrix(new BufferedReader(
             new FileReader(costFile))));
      } catch (Exception ex) {
  // now flag as possible old format cost matrix. Delay cost matrix
  // loading until buildClassifer is called
  setCostMatrix(null);
      }
      setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED,
                                          TAGS_MATRIX_SOURCE));
      m_CostFile = costFile;
    } else {
      setCostMatrixSource(new SelectedTag(MATRIX_ON_DEMAND, 
                                          TAGS_MATRIX_SOURCE));
    }
    
    String demandDir = Utils.getOption('N', options);
    if (demandDir.length() != 0) {
      setOnDemandDirectory(new File(demandDir));
    }


    String cost_matrix = Utils.getOption("cost-matrix", options);
    if (cost_matrix.length() != 0) {
      StringWriter writer = new StringWriter();
      CostMatrix.parseMatlab(cost_matrix).write(writer);
      setCostMatrix(new CostMatrix(new StringReader(writer.toString())));
      setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED,
                                          TAGS_MATRIX_SOURCE));
    }
    
    super.setOptions(options);

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      String costName = data.relationName() + CostMatrix.FILE_EXTENSION;
      File costFile = new File(getOnDemandDirectory(), costName);
      if (!costFile.exists()) {
        throw new Exception("On-demand cost file doesn't exist: " + costFile);
      }
      setCostMatrix(new CostMatrix(new BufferedReader(
                                   new FileReader(costFile))));
    } else if (m_CostMatrix == null) {
      // try loading an old format cost file
      m_CostMatrix = new CostMatrix(data.numClasses());
      m_CostMatrix.readOldFormat(new BufferedReader(
             new FileReader(m_CostFile)));
    }


    if (!m_MinimizeExpectedCost) {

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