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.
   */
  
  /*
   *    FirstOrder.java
   *    Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
   *
   */
  
  
  package weka.filters.unsupervised.attribute;
  
  import weka.core.Attribute;
  import weka.core.Capabilities;
  import weka.core.FastVector;
  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.UnsupportedAttributeTypeException;
  import weka.core.Utils;
  import weka.core.Capabilities.Capability;
  import weka.filters.Filter;
  import weka.filters.StreamableFilter;
  import weka.filters.UnsupervisedFilter;
  
  import java.util.Enumeration;
  import java.util.Vector;
  
  /** 
   <!-- globalinfo-start -->
   * This instance filter takes a range of N numeric attributes and replaces them with N-1 numeric attributes, the values of which are the difference between consecutive attribute values from the original instance. eg: <br/>
   * <br/>
   * Original attribute values<br/>
   * <br/>
   *    0.1, 0.2, 0.3, 0.1, 0.3<br/>
   * <br/>
   * New attribute values<br/>
   * <br/>
   *    0.1, 0.1, -0.2, 0.2<br/>
   * <br/>
   * The range of attributes used is taken in numeric order. That is, a range spec of 7-11,3-5 will use the attribute ordering 3,4,5,7,8,9,10,11 for the differences, NOT 7,8,9,10,11,3,4,5.
   * <p/>
   <!-- globalinfo-end -->
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -R &lt;index1,index2-index4,...&gt;
   *  Specify list of columns to take the differences between.
   *  First and last are valid indexes.
   *  (default none)</pre>
   * 
   <!-- options-end -->
   *
   * @author Len Trigg (trigg@cs.waikato.ac.nz)
   * @version $Revision: 5987 $
   */
  public class FirstOrder 
    extends Filter
    implements UnsupervisedFilter, StreamableFilter, OptionHandler {
  
    /** for serialization */
    static final long serialVersionUID = -7500464545400454179L;
    
    /** Stores which columns to take differences between */
    protected Range m_DeltaCols = new Range();
  
    /**
     * Returns a string describing this filter
     *
     * @return a description of the filter suitable for
     * displaying in the explorer/experimenter gui
     */
    public String globalInfo() {
  
      return "This instance filter takes a range of N numeric attributes and replaces "
        + "them with N-1 numeric attributes, the values of which are the difference "
        + "between consecutive attribute values from the original instance. eg: \n\n"
        + "Original attribute values\n\n"
        + "   0.1, 0.2, 0.3, 0.1, 0.3\n\n"
        + "New attribute values\n\n"
        + "   0.1, 0.1, -0.2, 0.2\n\n"
        + "The range of attributes used is taken in numeric order. That is, a range "
        + "spec of 7-11,3-5 will use the attribute ordering 3,4,5,7,8,9,10,11 for the "
        + "differences, NOT 7,8,9,10,11,3,4,5.";
    }
  
    /**
     * Returns an enumeration describing the available options.
     *
     * @return an enumeration of all the available options.
     */
    public Enumeration listOptions() {
  
      Vector newVector = new Vector(1);
  
      newVector.addElement(new Option(
                "\tSpecify list of columns to take the differences between.\n"
  	      + "\tFirst and last are valid indexes.\n"
  	      + "\t(default none)",
                "R", 1, "-R <index1,index2-index4,...>"));
  
      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 take the differences between.
     *  First and last are valid indexes.
     *  (default none)</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 deltaList = Utils.getOption('R', options);
      if (deltaList.length() != 0) {
        setAttributeIndices(deltaList);
      } else {
        setAttributeIndices("");
      }
      
      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 [2];
      int current = 0;
  
      if (!getAttributeIndices().equals("")) {
        options[current++] = "-R"; options[current++] = getAttributeIndices();
      }
  
      while (current < options.length) {
        options[current++] = "";
      }
      return options;
    }
  
    /** 
     * 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 UnsupportedAttributeTypeException if any of the
     * selected attributes are not numeric 
     * @throws Exception if only one attribute has been selected.
     */
    public boolean setInputFormat(Instances instanceInfo) throws Exception {
  
      super.setInputFormat(instanceInfo);
  
      m_DeltaCols.setUpper(getInputFormat().numAttributes() - 1);
      int selectedCount = 0;
      for (int i = getInputFormat().numAttributes() - 1; i >= 0; i--) {
        if (m_DeltaCols.isInRange(i)) {
          selectedCount++;
          if (!getInputFormat().attribute(i).isNumeric()) {
            throw new UnsupportedAttributeTypeException("Selected attributes must be all numeric");
          }
        }
      }
      if (selectedCount == 1) {
        throw new Exception("Cannot select only one attribute.");
      }
  
      // Create the output buffer
      FastVector newAtts = new FastVector();
      boolean inRange = false;
      String foName = null;
      int clsIndex = -1;
      for(int i = 0; i < instanceInfo.numAttributes(); i++) {
        if (m_DeltaCols.isInRange(i) && (i != instanceInfo.classIndex())) {
  	if (inRange) {
  	  Attribute newAttrib = new Attribute(foName);
            newAtts.addElement(newAttrib);
  	}
          foName = instanceInfo.attribute(i).name();
          foName = "'FO " + foName.replace('\'', ' ').trim() + '\'';
          inRange = true;
        } else {
  	newAtts.addElement((Attribute)instanceInfo.attribute(i).copy());
  	if ((i == instanceInfo.classIndex()))
  	  clsIndex = newAtts.size() - 1;
        }      
      }
      Instances data = new Instances(instanceInfo.relationName(), newAtts, 0);
      data.setClassIndex(clsIndex);
      setOutputFormat(data);
      return true;
    }
    
  
    /**
     * Input an instance for filtering. Ordinarily the instance is processed
     * and made available for output immediately. Some filters require all
     * 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 defined.
     */
    public boolean input(Instance instance) {
  
      if (getInputFormat() == null) {
        throw new IllegalStateException("No input instance format defined");
      }
      if (m_NewBatch) {
        resetQueue();
        m_NewBatch = false;
      }
  
      Instances outputFormat = outputFormatPeek();
      double[] vals = new double[outputFormat.numAttributes()];
      boolean inRange = false;
      double lastVal = Utils.missingValue();
      int i, j;
      for(i = 0, j = 0; j < outputFormat.numAttributes(); i++) {
        if (m_DeltaCols.isInRange(i) && (i != instance.classIndex())) {
  	if (inRange) {
  	  if (Utils.isMissingValue(lastVal) || instance.isMissing(i)) {
  	    vals[j++] = Utils.missingValue();
  	  } else {
  	    vals[j++] = instance.value(i) - lastVal;
  	  }
  	} else {
  	  inRange = true;
  	}
  	lastVal = instance.value(i);
        } else {
  	vals[j++] = 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(getOutputFormat());
      copyValues(inst, false, instance.dataset(), getOutputFormat());
      inst.setDataset(getOutputFormat());
      push(inst);
      return true;
    }
  
  
    /**
     * 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_DeltaCols.getRanges();
    }
  
    /**
     * Set which attributes are to be deleted (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 Exception if an invalid range list is supplied
     */
    public void setAttributeIndices(String rangeList) throws Exception {
  
      m_DeltaCols.setRanges(rangeList);
    }
  
    /**
     * Set which attributes are to be deleted (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 Exception if an invalid set of ranges is supplied
     */
    public void setAttributeIndicesArray(int [] attributes) throws Exception {
  
      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 FirstOrder(), argv);
    }
  }
  