Kdtree knn implementation

src/gaknn/core/Instance.java

@@ -1,6 +1,10 @@
 
 package gaknn.core;
 
+
+
+
+
 /**
  * Reprsents an instance of the data set
  * 
@@ -69,11 +73,138 @@ public Instances dataset() {
     public void AddElement(double value, int index){
         m_AttValues[index] = value;
     }
-
+    /** Return number of values in instance.
+    *
+    * 
+    */
+    //@author thimal
+    public int numValues(){
+    	return m_AttValues.length;
+    }
+    /**
+     * Returns the index of the attribute stored at the given position.
+     * Just returns the given value.
+     *
+     * @param position the position 
+     * @return the index of the attribute stored at the given position
+     */
+    //@author thimal
+    public /*@pure@*/ int index(int position) {
+
+      return position;
+    }
+    /**
+     * Returns an instance's attribute value in internal format.
+     * Does exactly the same thing as value() if applied to an Instance.
+     *
+     * @param indexOfIndex the index of the attribute's index
+     * @return the specified value as a double (If the corresponding
+     * attribute is nominal (or a string) then it returns the value's index as a 
+     * double).
+     */
+    //@author thimal
+    public /*@pure@*/ double valueSparse(int indexOfIndex) {
+
+      return m_AttValues[indexOfIndex];
+    } 
+    /**
+     * Tests if a specific value is "missing".
+     *
+     * @param attIndex the attribute's index
+     * @return true if the value is "missing"
+     */
+    //@author thimal
+    public /*@pure@*/ boolean isMissing(int attIndex) {
+
+      if (Double.isNaN(m_AttValues[attIndex])) {
+        return true;
+      }
+      return false;
+    }
+    /**
+     * Tests if the given value codes "missing".
+     *
+     * @param val the value to be tested
+     * @return true if val codes "missing"
+     */
+    //@author thimal
+    public static /*@pure@*/ boolean isMissingValue(double val) {
+
+        return Double.isNaN(val);
+      }
     /** Returns the element at the given position
      *
      * @param index of the elrment.
      */
+    /**
+     * Returns the values of each attribute as an array of doubles.
+     *
+     * @return an array containing all the instance attribute values
+     */
+    //@author thimal
+    public double[] toDoubleArray() {
+
+      double[] newValues = new double[m_AttValues.length];
+      System.arraycopy(m_AttValues, 0, newValues, 0, 
+  		     m_AttValues.length);
+      return newValues;
+    }
+    /**
+     * Clones the attribute vector of the instance and
+     * overwrites it with the clone.
+     */
+    //@author thimal
+    private void freshAttributeVector() {
+
+        m_AttValues = toDoubleArray();
+      }
+    /**
+     * Sets a specific value in the instance to the given value 
+     * (internal floating-point format). Performs a deep copy
+     * of the vector of attribute values before the value is set.
+     *
+     * @param attIndex the attribute's index 
+     * @param value the new attribute value (If the corresponding
+     * attribute is nominal (or a string) then this is the new value's
+     * index as a double).  
+     */
+    //@author thimal
+    public void setValue(int attIndex, double value) {
+
+      freshAttributeVector();
+      m_AttValues[attIndex] = value;
+    }
+    /**
+     * Sets the reference to the dataset. Does not check if the instance
+     * is compatible with the dataset. Note: the dataset does not know
+     * about this instance. If the structure of the dataset's header
+     * gets changed, this instance will not be adjusted automatically.
+     *
+     * @param instances the reference to the dataset 
+     */
+    //@author thimal
+    public final void setDataset(Instances instances) {
+
+      m_Dataset = instances;
+    }
+    /**
+     * Produces a shallow copy of this instance. The copy has
+     * access to the same dataset. (if you want to make a copy
+     * that doesn't have access to the dataset, use 
+     * <code>new Instance(instance)</code>
+     *
+     * @return the shallow copy
+     */
+    //@ also ensures \result != null;
+    //@ also ensures \result instanceof Instance;
+    //@ also ensures ((Instance)\result).m_Dataset == m_Dataset;
+    public /*@pure@*/ Object copy() {
+
+      Instance result = new Instance(this);
+      result.m_Dataset = m_Dataset;
+      return result;
+    }
+
     public double GetElementAt(int index){
         return m_AttValues[index];
     }

src/gaknn/core/Instances.java

@@ -1,5 +1,11 @@
 package gaknn.core;
 
+
+
+
+
+//import Instance;
+
 /**
  * Instances class represents the data.
  *
@@ -39,6 +45,9 @@ public Instances(String name,
         m_RelationName = name;
         m_ClassIndex = -1;
         m_Attributes = attInfo;
+
+        //initialize the m_instances
+        m_Instances=new FastVector();
 
         for (int i=0; i<attInfo.size(); i++ )
         {
@@ -52,6 +61,56 @@ public Instances(String name,
         m_Capacity = CAPACITY;
     }
 
+    /**
+     * Constructor creating an empty set of instances. Copies references to the
+     * header information from the given set of instances. Sets the capacity of
+     * the set of instances to 0 if its negative.
+     * 
+     * @param dataset the instances from which the header information is to be
+     *          taken
+     * @param capacity the capacity of the new dataset
+     */
+    //@author thimal
+    public Instances(/* @non_null@ */Instances dataset, int capacity) {
+      initialize(dataset, capacity);
+    }
+
+    /**
+     * initializes with the header information of the given dataset and sets the
+     * capacity of the set of instances.
+     * 
+     * @param dataset the dataset to use as template
+     * @param capacity the number of rows to reserve
+     */
+    //@author thimal
+    protected void initialize(Instances dataset, int capacity) {
+      if (capacity < 0)
+        capacity = 0;
+
+      // Strings only have to be "shallow" copied because
+      // they can't be modified.
+      m_ClassIndex = dataset.m_ClassIndex;
+      m_RelationName = dataset.m_RelationName;
+      m_Attributes = dataset.m_Attributes;
+      m_Instances = new FastVector(capacity);
+    }
+    /**
+     * Adds one instance to the end of the set. Shallow copies instance before it
+     * is added. Increases the size of the dataset if it is not large enough. Does
+     * not check if the instance is compatible with the dataset. Note: String or
+     * relational values are not transferred.
+     * 
+     * @param instance the instance to be added
+     */
+    //thimal
+    public void add(/* @non_null@ */Instance instance) {
+
+      Instance newInstance = (Instance) instance.copy();
+
+      newInstance.setDataset(this);
+      m_Instances.addElement(newInstance);
+    }
+
     /** Sets the weight vector of the attributes
      *
      * @param weights for the attributes.
@@ -185,6 +244,10 @@ public void AddElement(int RecNo, double[] values, int classIndex){
         if (m_NumAttributes > 0) m_DataSet[RecNo] = values;
         m_ClassIdList[RecNo] = classIndex;
         m_Lines++;
+
+        // set the m_instances
+        Instance ins=new Instance(values);
+       add(ins);
     }
 
 
@@ -225,6 +288,20 @@ private static Object ResizeArray (Object oldArray, int newSize) {
             System.arraycopy (oldArray,0,newArray,0,preserveLength);
         return newArray; 
     }
+
+    /**
+     * Returns the instance at the given position.
+     * 
+     * @param index the instance's index (index starts with 0)
+     * @return the instance at the given position
+     */
+    // @ requires 0 <= index;
+    // @ requires index < numInstances();
+    // @ author thimal
+    public/* @non_null pure@ */Instance instance(int index) {
+
+      return (Instance) m_Instances.elementAt(index);
+    }
 
 
 }

src/gaknn/core/kdtree/AdditionalMeasureProducer.java

@@ -0,0 +1,51 @@
+/*
+ *    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.
+ */
+
+/*
+ *    AdditionalMeasureProducer.java
+ *    Copyright (C) 2000 University of Waikato, Hamilton, New Zealand
+ *
+ */
+
+package gaknn.core.kdtree;
+
+import java.util.*;
+
+/** 
+ * Interface to something that can produce measures other than those
+ * calculated by evaluation modules. 
+ *
+ * @author Mark Hall (mhall@cs.waikato.ac.nz)
+ * @version $Revision: 1.8 $
+ */
+public interface AdditionalMeasureProducer {
+
+  /**
+   * Returns an enumeration of the measure names. Additional measures
+   * must follow the naming convention of starting with "measure", eg.
+   * double measureBlah()
+   * @return an enumeration of the measure names
+   */
+  Enumeration enumerateMeasures();
+
+  /**
+   * Returns the value of the named measure
+   * @param measureName the name of the measure to query for its value
+   * @return the value of the named measure
+   * @exception IllegalArgumentException if the named measure is not supported
+   */
+  double getMeasure(String measureName);
+}