source: branches/MetisMQI/src/main/java/weka/filters/unsupervised/attribute/MathExpression.java

/*
 *    This program is free software; you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation; either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    This program is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with this program; if not, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 *    MathExpression.java
 *    Copyright (C) 2004 Prados Julien
 *    Copyright (C) 2002 University of Waikato, Hamilton, New Zealand
 */

package weka.filters.unsupervised.attribute;

import weka.core.AttributeStats;
import weka.core.Capabilities;
import weka.core.Instance; 
import weka.core.DenseInstance;
import weka.core.Instances;
import weka.core.MathematicalExpression;
import weka.core.Option;
import weka.core.Range;
import weka.core.RevisionUtils;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import weka.core.mathematicalexpression.Parser;
import weka.core.mathematicalexpression.Scanner;
import java_cup.runtime.DefaultSymbolFactory;
import java_cup.runtime.SymbolFactory;
import weka.filters.UnsupervisedFilter;

import java.io.ByteArrayInputStream;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Vector;

/** 
 <!-- globalinfo-start -->
 * Modify numeric attributes according to a given expression
 * <p/>
 <!-- globalinfo-end -->
 * 
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -unset-class-temporarily
 *  Unsets the class index temporarily before the filter is
 *  applied to the data.
 *  (default: no)</pre>
 * 
 * <pre> -E &lt;expression&gt;
 *  Specify the expression to apply. Eg. pow(A,6)/(MEAN+MAX)
 *  Supported operators are +, -, *, /, pow, log,
 *  abs, cos, exp, sqrt, tan, sin, ceil, floor, rint, (, ), 
 *  MEAN, MAX, MIN, SD, COUNT, SUM, SUMSQUARED, ifelse</pre>
 * 
 * <pre> -R &lt;index1,index2-index4,...&gt;
 *  Specify list of columns to ignore. First and last are valid
 *  indexes. (default none)</pre>
 * 
 * <pre> -V
 *  Invert matching sense (i.e. only modify specified columns)</pre>
 * 
 <!-- options-end -->
 *
 * @author Eibe Frank (eibe@cs.waikato.ac.nz) 
 * @author Prados Julien (julien.prados@cui.unige.ch) 
 * @version $Revision: 5987 $
 * @see MathematicalExpression
 */
public class MathExpression 
  extends PotentialClassIgnorer 
  implements UnsupervisedFilter {
  
  /** for serialization */
  static final long serialVersionUID = -3713222714671997901L;
  
  /** Stores which columns to select as a funky range */
  protected Range m_SelectCols = new Range();
    
  /** The default modification expression */
  public static final String m_defaultExpression = "(A-MIN)/(MAX-MIN)";

  /** The modification expression */
  private String m_expression = m_defaultExpression;
  
  /** Attributes statistics */
  private AttributeStats[] m_attStats;
  
  /**
   * Constructor
   */
  public MathExpression() {
    super();
    setInvertSelection(false);
  }  
  
  /**
   * Returns a string describing this filter
   *
   * @return a description of the filter suitable for
   * displaying in the explorer/experimenter gui
   */
  public String globalInfo() {

    return "Modify numeric attributes according to a given expression ";
  }

  /** 
   * Returns the Capabilities of this filter.
   *
   * @return            the capabilities of this object
   * @see               Capabilities
   */
  public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();

    // attributes
    result.enableAllAttributes();
    result.enable(Capability.MISSING_VALUES);
    
    // class
    result.enableAllClasses();
    result.enable(Capability.MISSING_CLASS_VALUES);
    result.enable(Capability.NO_CLASS);
    
    return result;
  }
  
  /**
   * Sets the format of the input instances.
   *
   * @param instanceInfo an Instances object containing the input 
   * instance structure (any instances contained in the object are 
   * ignored - only the structure is required).
   * @return true if the outputFormat may be collected immediately
   * @throws Exception if the input format can't be set 
   * successfully
   */
  public boolean setInputFormat(Instances instanceInfo) 
       throws Exception {
    m_SelectCols.setUpper(instanceInfo.numAttributes() - 1);
    super.setInputFormat(instanceInfo);
    setOutputFormat(instanceInfo);
    m_attStats = null;
    return true;
  }

  /**
   * Input an instance for filtering. Filter requires all
   * training instances be read before producing output.
   *
   * @param instance the input instance
   * @return true if the filtered instance may now be
   * collected with output().
   * @throws IllegalStateException if no input format has been set.
   */
  public boolean input(Instance instance) throws Exception {

    if (getInputFormat() == null) {
      throw new IllegalStateException("No input instance format defined");
    }
    if (m_NewBatch) {
      resetQueue();
      m_NewBatch = false;
    }
    if (m_attStats == null) {
      bufferInput(instance);
      return false;
    } else {
      convertInstance(instance);
      return true;
    }
  }

  /**
   * Signify that this batch of input to the filter is finished. 
   * If the filter requires all instances prior to filtering,
   * output() may now be called to retrieve the filtered instances.
   *
   * @return true if there are instances pending output
   * @throws IllegalStateException if no input structure has been defined
   */
  public boolean batchFinished() throws Exception {

    if (getInputFormat() == null) {
      throw new IllegalStateException("No input instance format defined");
    }
    if (m_attStats == null) {
      Instances input = getInputFormat();

      m_attStats = new AttributeStats [input.numAttributes()];
      
      for (int i = 0; i < input.numAttributes(); i++) {
        if (input.attribute(i).isNumeric() &&
            (input.classIndex() != i)) {
          m_attStats[i] = input.attributeStats(i);
        }
      }

      // Convert pending input instances
      for(int i = 0; i < input.numInstances(); i++) {
        convertInstance(input.instance(i));
      }
    } 
    // Free memory
    flushInput();

    m_NewBatch = true;
    return (numPendingOutput() != 0);
  }
  
  /**
   * Evaluates the symbols.
   * 
   * @param symbols     the symbols to use for evaluation
   * @return            the calculated value, Double.NaN in case of an error
   */
  protected double eval(HashMap symbols) {
    SymbolFactory               sf;
    ByteArrayInputStream        parserInput;
    Parser                      parser;
    double                      result;
    
    try {
      sf          = new DefaultSymbolFactory();
      parserInput = new ByteArrayInputStream(m_expression.getBytes());
      parser      = new Parser(new Scanner(parserInput, sf), sf);
      parser.setSymbols(symbols);
      parser.parse();
      result = parser.getResult();
    }
    catch (Exception e) {
      result = Double.NaN;
      e.printStackTrace();
    }
    
    return result;
  }
  
  /**
   * Convert a single instance over. The converted instance is 
   * added to the end of the output queue.
   *
   * @param instance the instance to convert
   * @throws Exception if instance cannot be converted
   */
  private void convertInstance(Instance instance) throws Exception {
  
    Instance inst = null;
    HashMap symbols = new HashMap(5);
    if (instance instanceof SparseInstance) {
      double[] newVals = new double[instance.numAttributes()];
      int[] newIndices = new int[instance.numAttributes()];
      double[] vals = instance.toDoubleArray();
      int ind = 0;
      double value;
      for (int j = 0; j < instance.numAttributes(); j++) {
        if (m_SelectCols.isInRange(j)) {          
          if (instance.attribute(j).isNumeric() &&
            (!Utils.isMissingValue(vals[j])) &&
            (getInputFormat().classIndex() != j)) {
              symbols.put("A", new Double(vals[j]));  
              symbols.put("MAX", new Double(m_attStats[j].numericStats.max));
              symbols.put("MIN", new Double(m_attStats[j].numericStats.min));
              symbols.put("MEAN", new Double(m_attStats[j].numericStats.mean));
              symbols.put("SD", new Double(m_attStats[j].numericStats.stdDev));
              symbols.put("COUNT", new Double(m_attStats[j].numericStats.count));
              symbols.put("SUM", new Double(m_attStats[j].numericStats.sum));
              symbols.put("SUMSQUARED", new Double(m_attStats[j].numericStats.sumSq));
              value = eval(symbols);
              if (Double.isNaN(value) || Double.isInfinite(value)) {
                  System.err.println("WARNING:Error in evaluating the expression: missing value set");
                  value = Utils.missingValue();
              }
              if (value != 0.0) {
                newVals[ind] = value;
                newIndices[ind] = j;
                ind++;
              }
              
          }
        } else {
          value = vals[j];
          if (value != 0.0) {
            newVals[ind] = value;
            newIndices[ind] = j;
            ind++;
          }
        }
      } 
      double[] tempVals = new double[ind];
      int[] tempInd = new int[ind];
      System.arraycopy(newVals, 0, tempVals, 0, ind);
      System.arraycopy(newIndices, 0, tempInd, 0, ind);
      inst = new SparseInstance(instance.weight(), tempVals, tempInd,
                                instance.numAttributes());
    } else {
      double[] vals = instance.toDoubleArray();
      for (int j = 0; j < getInputFormat().numAttributes(); j++) {
        if (m_SelectCols.isInRange(j)) {
          if (instance.attribute(j).isNumeric() &&
              (!Utils.isMissingValue(vals[j])) &&
              (getInputFormat().classIndex() != j)) {
              symbols.put("A", new Double(vals[j]));  
              symbols.put("MAX", new Double(m_attStats[j].numericStats.max));
              symbols.put("MIN", new Double(m_attStats[j].numericStats.min));
              symbols.put("MEAN", new Double(m_attStats[j].numericStats.mean));
              symbols.put("SD", new Double(m_attStats[j].numericStats.stdDev));
              symbols.put("COUNT", new Double(m_attStats[j].numericStats.count));
              symbols.put("SUM", new Double(m_attStats[j].numericStats.sum));
              symbols.put("SUMSQUARED", new Double(m_attStats[j].numericStats.sumSq));
              vals[j] = eval(symbols);
              if (Double.isNaN(vals[j]) || Double.isInfinite(vals[j])) {
                  System.err.println("WARNING:Error in Evaluation the Expression: missing value set");
                  vals[j] = Utils.missingValue();
              }
          }
        }
      }
      inst = new DenseInstance(instance.weight(), vals);
    }
    inst.setDataset(instance.dataset());
    push(inst);
  }

  /**
   * Parses a given list of options. <p/>
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -unset-class-temporarily
   *  Unsets the class index temporarily before the filter is
   *  applied to the data.
   *  (default: no)</pre>
   * 
   * <pre> -E &lt;expression&gt;
   *  Specify the expression to apply. Eg. pow(A,6)/(MEAN+MAX)
   *  Supported operators are +, -, *, /, pow, log,
   *  abs, cos, exp, sqrt, tan, sin, ceil, floor, rint, (, ), 
   *  MEAN, MAX, MIN, SD, COUNT, SUM, SUMSQUARED, ifelse</pre>
   * 
   * <pre> -R &lt;index1,index2-index4,...&gt;
   *  Specify list of columns to ignore. First and last are valid
   *  indexes. (default none)</pre>
   * 
   * <pre> -V
   *  Invert matching sense (i.e. only modify specified columns)</pre>
   * 
   <!-- options-end -->
   *
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  public void setOptions(String[] options) throws Exception {
    super.setOptions(options);

    String expString = Utils.getOption('E', options);
    if (expString.length() != 0) {
      setExpression(expString);
    } else {
      setExpression(m_defaultExpression);
    }
    
    String ignoreList = Utils.getOption('R', options);
    if (ignoreList.length() != 0) {
      setIgnoreRange(ignoreList);
    }

    setInvertSelection(Utils.getFlag('V', options));
  }
  
  /**
   * Gets the current settings of the filter.
   *
   * @return an array of strings suitable for passing to setOptions
   */
  public String [] getOptions() {
    Vector        result;
    String[]      options;
    int           i;

    result = new Vector();

    options = super.getOptions();
    for (i = 0; i < options.length; i++)
      result.add(options[i]);

    result.add("-E");
    result.add(getExpression());
    
    if (getInvertSelection())
      result.add("-V");

    if (!getIgnoreRange().equals("")) {
      result.add("-R");
      result.add(getIgnoreRange());
    }

    return (String[]) result.toArray(new String[result.size()]);
  }
  
  /**
   * Returns an enumeration describing the available options.
   *
   * @return an enumeration of all the available options.
   */
  public Enumeration listOptions() {
    Vector result = new Vector();
    Enumeration enm = super.listOptions();
    while (enm.hasMoreElements())
      result.add(enm.nextElement());
      
    result.addElement(new Option(
        "\tSpecify the expression to apply. Eg. pow(A,6)/(MEAN+MAX)"
        +"\n\tSupported operators are +, -, *, /, pow, log,"
        +"\n\tabs, cos, exp, sqrt, tan, sin, ceil, floor, rint, (, ), "
        +"\n\tMEAN, MAX, MIN, SD, COUNT, SUM, SUMSQUARED, ifelse",
        "E",1,"-E <expression>"));
    
    result.addElement(new Option(
        "\tSpecify list of columns to ignore. First and last are valid\n"
        +"\tindexes. (default none)",
        "R", 1, "-R <index1,index2-index4,...>"));
    
    result.addElement(new Option(
        "\tInvert matching sense (i.e. only modify specified columns)",
        "V", 0, "-V"));
    
    return result.elements();
  }
  
  /**
   * Returns the tip text for this property
   *
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String expressionTipText() {
    return "Specify the expression to apply. The 'A' letter"
             + "refers to the attribute value. MIN,MAX,MEAN,SD"
             + "refer respectively to minimum, maximum, mean and"
             + "standard deviation of the attribute."
             +"\n\tSupported operators are +, -, *, /, pow, log,"
             +"abs, cos, exp, sqrt, tan, sin, ceil, floor, rint, (, ),"
             +"A,MEAN, MAX, MIN, SD, COUNT, SUM, SUMSQUARED, ifelse"
             +"\n\tEg. pow(A,6)/(MEAN+MAX)*ifelse(A<0,0,sqrt(A))+ifelse(![A>9 && A<15])";
  }
  
  /**
   * Set the expression to apply
   * @param expr a mathematical expression to apply
   */
  public void setExpression(String expr) {
    m_expression = expr;
  }

  /**
   * Get the expression
   * @return the expression
   */
  public String getExpression() {
    return m_expression;
  }
  
    /**
   * Returns the tip text for this property
   *
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String invertSelectionTipText() {

    return "Determines whether action is to select or unselect."
      + " If set to true, only the specified attributes will be modified;"
      + " If set to false, specified attributes will not be modified.";
  }

  /**
   * Get whether the supplied columns are to be select or unselect
   *
   * @return true if the supplied columns will be kept
   */
  public boolean getInvertSelection() {

    return !m_SelectCols.getInvert();
  }

  /**
   * Set whether selected columns should be select or unselect. If true the 
   * selected columns are modified. If false the selected columns are not
   * modified.
   *
   * @param invert the new invert setting
   */
  public void setInvertSelection(boolean invert) {

    m_SelectCols.setInvert(!invert);
  }

  /**
   * Returns the tip text for this property
   *
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String ignoreRangeTipText() {

    return "Specify range of attributes to act on."
      + " This is a comma separated list of attribute indices, with"
      + " \"first\" and \"last\" valid values. Specify an inclusive"
      + " range with \"-\". E.g: \"first-3,5,6-10,last\".";
  }

  /**
   * Get the current range selection.
   *
   * @return a string containing a comma separated list of ranges
   */
  public String getIgnoreRange() {

    return m_SelectCols.getRanges();
  }

  /**
   * Set which attributes are to be ignored
   *
   * @param rangeList a string representing the list of attributes.  Since
   * the string will typically come from a user, attributes are indexed from
   * 1. <br/>
   * eg: first-3,5,6-last
   */
  public void setIgnoreRange(String rangeList) {

    m_SelectCols.setRanges(rangeList);
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 5987 $");
  }
  
  /**
   * Main method for testing this class.
   *
   * @param argv should contain arguments to the filter: 
   * use -h for help
   */
  public static void main(String [] argv) {
    runFilter(new MathExpression(), argv);
  }
}