mathexpression.java

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/*
 *    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 Eibe Frank
 */

package weka.filters.unsupervised.attribute;

import weka.core.AttributeStats;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.SparseInstance;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.UnsupervisedFilter;

import java.io.IOException;
import java.io.Reader;
import java.io.Serializable;
import java.io.StreamTokenizer;
import java.io.StringReader;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;

/** 
 <!-- globalinfo-start -->
 * Modify numeric attributes according to a given expression
 * <p/>
 <!-- globalinfo-end -->
 * 
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <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 ([e-mail]) 
 * @author Prados Julien ([e-mail]) 
 * @version $Revision: 1.4 $
 */
public class MathExpression 
  extends PotentialClassIgnorer 
  implements UnsupervisedFilter, OptionHandler {
  
  /** 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;
  
  /** The expression tree*/
  private Parser.TreeNode m_expTree = null;
  
  /** Attributes statistics*/
  private AttributeStats[] m_attStats;
  
  
  /**Constructor*/
  public MathExpression() {
      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 ";
  }
  
  /**
   * 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;
    m_expTree = 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
   * @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_expTree = Parser.parse(getExpression());
      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);
  }
  
  /**
   * 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;
      for (int j = 0; j < instance.numAttributes(); j++) {
        if (m_SelectCols.isInRange(j)) {          
	  double value;
	  if (instance.attribute(j).isNumeric() &&
	    (!Instance.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 = m_expTree.eval(symbols);
              if (Double.isNaN(value) || Double.isInfinite(value)) {
                  System.err.println("WARNING:Error in evaluating the expression: missing value set");
                  value = Instance.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() &&
	      (!Instance.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] = m_expTree.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] = Instance.missingValue();
              }
	  }
        }
      }
      inst = new Instance(instance.weight(), vals);
    }
    inst.setDataset(instance.dataset());
    push(inst);
  }

  /**
   * Parses a given list of options. <p/>
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <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 {
    String expString = Utils.getOption('E', options);
    if (expString.length() != 0) {
      setExpression(expString);
    } else {
      setExpression(m_defaultExpression);
    }
    
    String ignoreList = Utils.getOption('R', options);