content: /*
   *    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.
   */
  
  /*
   *    NumericTransform.java
   *    Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
   *
   */
  
  package weka.filters.unsupervised.attribute;
  
  import weka.core.Capabilities;
  import weka.core.Instance; 
  import weka.core.DenseInstance;
  import weka.core.Instances;
  import weka.core.Option;
  import weka.core.OptionHandler;
  import weka.core.Range;
  import weka.core.RevisionUtils;
  import weka.core.SparseInstance;
  import weka.core.Utils;
  import weka.core.Capabilities.Capability;
  import weka.filters.Filter;
  import weka.filters.StreamableFilter;
  import weka.filters.UnsupervisedFilter;
  
  import java.lang.reflect.InvocationTargetException;
  import java.lang.reflect.Method;
  import java.util.Enumeration;
  import java.util.Vector;
  
  /** 
   <!-- globalinfo-start -->
   * Transforms numeric attributes using a given transformation method.
   * <p/>
   <!-- globalinfo-end -->
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -R &lt;index1,index2-index4,...&gt;
   *  Specify list of columns to transform. First and last are
   *  valid indexes (default none). Non-numeric columns are 
   *  skipped.</pre>
   * 
   * <pre> -V
   *  Invert matching sense.</pre>
   * 
   * <pre> -C &lt;string&gt;
   *  Sets the class containing transformation method.
   *  (default java.lang.Math)</pre>
   * 
   * <pre> -M &lt;string&gt;
   *  Sets the method. (default abs)</pre>
   * 
   <!-- options-end -->
   *
   * @author Eibe Frank (eibe@cs.waikato.ac.nz) 
   * @version $Revision: 5987 $
   */
  public class NumericTransform 
    extends Filter
    implements UnsupervisedFilter, StreamableFilter, OptionHandler {
    
    /** for serialization */
    static final long serialVersionUID = -8561413333351366934L;
  
    /** Stores which columns to transform. */
    private Range m_Cols = new Range();
  
    /** Class containing transformation method. */
    private String m_Class;
  
    /** Transformation method. */
    private String m_Method;
  
    /**
     * Returns a string describing this filter
     *
     * @return a description of the filter suitable for
     * displaying in the explorer/experimenter gui
     */
    public String globalInfo() {
  
      return "Transforms numeric attributes using a given transformation method.";
    }
  
    /**
     * Default constructor -- sets the default transform method
     * to java.lang.Math.abs().
     */
    public NumericTransform() {
  
      m_Class = "java.lang.Math";
      m_Method = "abs";
    }
  
    /** 
     * 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 {
  
      if (m_Class == null) {
        throw new IllegalStateException("No class has been set.");
      }
      if (m_Method == null) {
        throw new IllegalStateException("No method has been set.");
      }
      super.setInputFormat(instanceInfo);
      m_Cols.setUpper(instanceInfo.numAttributes() - 1);
      setOutputFormat(instanceInfo);
      return true;
    }
  
    /**
     * Input an instance for filtering. The instance is processed
     * and made available for output immediately.
     *
     * @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.
     * @throws InvocationTargetException if there is a problem applying
     * the configured transform method.
     */
    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;
      }
  
      Method m = (Class.forName(m_Class)).getMethod(m_Method, new Class[] {Double.TYPE});
  
      double []vals = new double[instance.numAttributes()];
      Double []params = new Double[1];
      Double newVal;
      for(int i = 0; i < instance.numAttributes(); i++) {
        if (instance.isMissing(i)) {
  	vals[i] = Utils.missingValue();
        } else {
  	if (m_Cols.isInRange(i) &&
  	    instance.attribute(i).isNumeric()) {
  	  params[0] = new Double(instance.value(i));
  	  newVal = (Double) m.invoke(null, (Object[])params);
  	  if (newVal.isNaN() || newVal.isInfinite()) {
  	    vals[i] = Utils.missingValue();
  	  } else {
  	    vals[i] = newVal.doubleValue(); 
  	  }
  	} else {
  	  vals[i] = instance.value(i);
  	}
        }
      }
      Instance inst = null;
      if (instance instanceof SparseInstance) {
        inst = new SparseInstance(instance.weight(), vals);
      } else {
        inst = new DenseInstance(instance.weight(), vals);
      }
      inst.setDataset(instance.dataset());
      push(inst);
      return true;
    }
  
    /**
     * Returns an enumeration describing the available options.
     *
     * @return an enumeration of all the available options.
     */
    public Enumeration listOptions() {
  
      Vector newVector = new Vector(4);
  
      newVector.addElement(new Option(
                "\tSpecify list of columns to transform. First and last are\n"
  	      + "\tvalid indexes (default none). Non-numeric columns are \n"
  	      + "\tskipped.",
                "R", 1, "-R <index1,index2-index4,...>"));
  
      newVector.addElement(new Option(
  	      "\tInvert matching sense.",
                "V", 0, "-V"));
  
      newVector.addElement(new Option(
                "\tSets the class containing transformation method.\n"+
                "\t(default java.lang.Math)",
                "C", 1, "-C <string>"));
  
      newVector.addElement(new Option(
                "\tSets the method. (default abs)",
                "M", 1, "-M <string>"));
  
      return newVector.elements();
    }
  
  
    /**
     * Parses a given list of options. <p/>
     * 
     <!-- options-start -->
     * Valid options are: <p/>
     * 
     * <pre> -R &lt;index1,index2-index4,...&gt;
     *  Specify list of columns to transform. First and last are
     *  valid indexes (default none). Non-numeric columns are 
     *  skipped.</pre>
     * 
     * <pre> -V
     *  Invert matching sense.</pre>
     * 
     * <pre> -C &lt;string&gt;
     *  Sets the class containing transformation method.
     *  (default java.lang.Math)</pre>
     * 
     * <pre> -M &lt;string&gt;
     *  Sets the method. (default abs)</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 {
      
      setAttributeIndices(Utils.getOption('R', options));
      setInvertSelection(Utils.getFlag('V', options));
      String classString = Utils.getOption('C', options);
      if (classString.length() != 0) {
        setClassName(classString);
      }
      String methodString = Utils.getOption('M', options);
      if (methodString.length() != 0) {
        setMethodName(methodString);
      }
  
      if (getInputFormat() != null) {
        setInputFormat(getInputFormat());
      }
    }
  
    /**
     * Gets the current settings of the filter.
     *
     * @return an array of strings suitable for passing to setOptions
     */
    public String [] getOptions() {
  
      String [] options = new String [7];
      int current = 0;
  
      if (getInvertSelection()) {
        options[current++] = "-V";
      }
      if (!getAttributeIndices().equals("")) {
        options[current++] = "-R"; options[current++] = getAttributeIndices();
      }
      if (m_Class != null) {
        options[current++] = "-C"; options[current++] = getClassName();
      }
      if (m_Method != null) {
        options[current++] = "-M"; options[current++] = getMethodName();
      }
  
      while (current < options.length) {
        options[current++] = "";
      }
      return options;
    }
  
    /**
     * Returns the tip text for this property
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String classNameTipText() {
      return "Name of the class containing the method used for the transformation.";
    }
  
    /**
     * Get the class containing the transformation method.
     *
     * @return string describing the class
     */
    public String getClassName() {
  
      return m_Class;
    }
   
    /**
     * Sets the class containing the transformation method.
     *
     * @param name the name of the class
     * @throws ClassNotFoundException if class can't be found
     */
    public void setClassName(String name) throws ClassNotFoundException {
    
      m_Class = name;
    }
  
    /**
     * Returns the tip text for this property
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String methodNameTipText() {
      return "Name of the method used for the transformation.";
    }
   
    /**
     * Get the transformation method.
     *
     * @return string describing the transformation method.
     */
    public String getMethodName() {
  
      return m_Method;
    }
  
    /**
     * Set the transformation method.
     *
     * @param name the name of the method
     * @throws NoSuchMethodException if method can't be found in class
     */
    public void setMethodName(String name) throws NoSuchMethodException {
  
      m_Method = name;
    }
  
    /**
     * 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 "Whether to process the inverse of the given attribute ranges.";
    }
  
    /**
     * Get whether the supplied columns are to be transformed or not
     *
     * @return true if the supplied columns will be kept
     */
    public boolean getInvertSelection() {
  
      return m_Cols.getInvert();
    }
  
    /**
     * Set whether selected columns should be transformed or not. 
     *
     * @param invert the new invert setting
     */
    public void setInvertSelection(boolean invert) {
  
      m_Cols.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 attributeIndicesTipText() {
      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 getAttributeIndices() {
  
      return m_Cols.getRanges();
    }
  
    /**
     * Set which attributes are to be transformed (or kept if invert is true). 
     *
     * @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
     * @throws InvalidArgumentException if an invalid range list is supplied
     */
  
    public void setAttributeIndices(String rangeList) {
  
      m_Cols.setRanges(rangeList);
    }
  
    /**
     * Set which attributes are to be transformed (or kept if invert is true)
     *
     * @param attributes an array containing indexes of attributes to select.
     * Since the array will typically come from a program, attributes are indexed
     * from 0.
     * @throws InvalidArgumentException if an invalid set of ranges is supplied
     */
    public void setAttributeIndicesArray(int [] attributes) {
  
      setAttributeIndices(Range.indicesToRangeList(attributes));
    }
    
    /**
     * 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 NumericTransform(), argv);
    }
  }
  