Changeset 138 for trunk/CrossPare/src

Timestamp:

08/17/16 19:21:07 (8 years ago)

Author:

atrautsch

Message:

Bigger code cleanup, still some work to do in the attribute selection

File:

• trunk/CrossPare/src/de/ugoe/cs/cpdp/training/MetricMatchingTraining.java (modified) (17 diffs)

trunk/CrossPare/src/de/ugoe/cs/cpdp/training/MetricMatchingTraining.java

@@ -40 +40 @@
 import weka.core.Attribute;
 import weka.core.DenseInstance;
-import weka.core.FastVector;
 import weka.core.Instance;
 import weka.core.Instances;
 
 /**
- * Implements Heterogenous Defect Prediction after Nam et al.
+ * Implements Heterogenous Defect Prediction after Nam et al.  2015.
+ * 
+ * We extend WekaBaseTraining because we have to Wrap the Classifier to use MetricMatching.
+ * This also means we can use any Weka Classifier not just LogisticRegression.
  * 
  * TODO:
  * - spacing, coding conventions
- * - we depend on having exactly one class attribute on multiple locations
- * - 
+ * - clean up attribute selection on train data
+ * - percentile test run
  */
 public class MetricMatchingTraining extends WekaBaseTraining implements ISetWiseTestdataAwareTrainingStrategy {
 
     private SetUniqueList<Instances> traindataSet;
-    private MetricMatch mm;
-    private final Classifier classifier = new MetricMatchingClassifier();
+    private MetricMatch mm = null;
+    private Classifier classifier = new MetricMatchingClassifier();
     
     private String method;
@@ -70 +72 @@
     }
 
-
+    /**
+     * Set similarity measure method.
+     */
     @Override
     public void setMethod(String method) {
@@ -76 +80 @@
     }
 
-
+    /**
+     * Set threshold for similarity measure.
+     */
     @Override
     public void setThreshold(String threshold) {
@@ -88 +94 @@
         @Override
         public void apply(SetUniqueList<Instances> traindataSet, Instances testdata) {
-                this.traindataSet = traindataSet;
-
-                double score = 0; // custom ranking score to select the best training data from the set
+
+                double score = 0; // matching score to select the best matching training data from the set
                 int num = 0;
                 int biggest_num = 0;
                 MetricMatch tmp;
-                MetricMatch biggest = null;
-                for (Instances traindata : this.traindataSet) {
+                for (Instances traindata : traindataSet) {
                         num++;
 
@@ -110 +114 @@
                         
                         // we only select the training data from our set with the most matching attributes
-                        if (tmp.getScore() > score) {
+                        if (tmp.getScore() > score && tmp.attributes.size() > 0) {
                                 score = tmp.getScore();
-                                biggest = tmp;
+                                this.mm = tmp;
                                 biggest_num = num;
                         }
                 }
                 
-                if (biggest == null) {
-                    throw new RuntimeException("not enough matching attributes found");
-                }
-
-                // we use the best match according to our matching score
-                this.mm = biggest;
-                Instances ilist = this.mm.getMatchedTrain();
-                Console.traceln(Level.INFO, "Chosing the trainingdata set num "+biggest_num +" with " + score + " matching score, " + ilist.size() + " instances, and " + biggest.attributes.size() + " matched attributes out of a possible set of " + traindataSet.size() + " sets");
-                
-                for(int i = 0; i < this.mm.attributes.size(); i++) {
-                    Console.traceln(Level.INFO, "Matched Attribute: " + this.mm.train.attribute(i).name() + " with " + this.mm.test.attribute((int)this.mm.attributes.get(i)).name());
-                }
-                // replace traindataSEt
-                //traindataSet = new SetUniqueList<Instances>();
-                traindataSet.clear();
-                traindataSet.add(ilist);
-                
-                // we have to build the classifier here:
+                // if we have found a matching instance we use it
+                Instances ilist = null;
+                if (this.mm != null) {
+                ilist = this.mm.getMatchedTrain();
+                Console.traceln(Level.INFO, "[MATCH FOUND] match: ["+biggest_num +"], score: [" + score + "], instances: [" + ilist.size() + "], attributes: [" + this.mm.attributes.size() + "], ilist attrs: ["+ilist.numAttributes()+"]");
+                for(Map.Entry<Integer, Integer> attmatch : this.mm.attributes.entrySet()) {
+                    Console.traceln(Level.INFO, "[MATCHED ATTRIBUTE] source attribute: [" + this.mm.train.attribute(attmatch.getKey()).name() + "], target attribute: [" + this.mm.test.attribute(attmatch.getValue()).name() + "]");
+                }
+                
+                // replace traindataSet
+                //traindataSet.clear();
+                //traindataSet.add(ilist);
+            }
+                
+                // if we have a match we build the special classifier, if not we fall back to FixClass
                 try {
-                    
-                        //
-                    if (this.classifier == null) {
-                        Console.traceln(Level.SEVERE, "Classifier is null");
-                    }
-                        //Console.traceln(Level.INFO, "Building classifier with the matched training data with " + ilist.size() + " instances and "+ ilist.numAttributes() + " attributes");
-                        this.classifier.buildClassifier(ilist);
-                        ((MetricMatchingClassifier) this.classifier).setMetricMatching(this.mm);
+                        if(this.mm != null) {
+                            this.classifier.buildClassifier(ilist);
+                            ((MetricMatchingClassifier) this.classifier).setMetricMatching(this.mm);
+                        }else {
+                            this.classifier = new FixClass();
+                            this.classifier.buildClassifier(ilist);  // this is null, but the FixClass Classifier does not use it anyway
+                        }
                 }catch(Exception e) {
                         e.printStackTrace();
@@ -166 +166 @@
                         this.classifier.buildClassifier(traindata);
                 }
-
+                
+                /**
+                 * Sets the MetricMatch instance so that we can use matched test data later.
+                 * @param mm
+                 */
                 public void setMetricMatching(MetricMatch mm) {
                         this.mm = mm;
@@ -172 +176 @@
                 
                 /**
-                 * Here we can not do the metric matching because we only get one instance
+                 * Here we can not do the metric matching because we only get one instance.
+                 * Therefore we need a MetricMatch instance beforehand to use here.
                  */
                 public double classifyInstance(Instance testdata) {
-                        // todo: maybe we can pull the instance out of our matched testdata?
+                    // get a copy of testdata Instance with only the matched attributes
                         Instance ntest = this.mm.getMatchedTestInstance(testdata);
 
@@ -191 +196 @@
         
         /**
-         * Encapsulates MetricMatching on Instances Arrays
+         * Encapsulates one MetricMatching process.
+         * One source (train) matches against one target (test).
          */
     public class MetricMatch {
@@ -198 +204 @@
                 
                 // used to sum up the matching values of all attributes
-                double p_sum = 0;
+                protected double p_sum = 0;
                 
                 // attribute matching, train -> test
                 HashMap<Integer, Integer> attributes = new HashMap<Integer,Integer>();
-                //double[][] weights;  /* weight matrix, needed to find maximum weighted bipartite matching */
-                 
-                ArrayList<double[]> train_values;
-                ArrayList<double[]> test_values;
-
-                // todo: this constructor does not work
-                public MetricMatch() {
-                }
+                
+                // used for similarity tests
+                protected ArrayList<double[]> train_values;
+                protected ArrayList<double[]> test_values;
+
                  
                 public MetricMatch(Instances train, Instances test) {
-                    // expensive! but we are dropping the attributes so we have to copy all of the data
-                    this.train = new Instances(train);
-                        this.test = new Instances(test);
-                         
-                        // 1. convert metrics of testdata and traindata to later use in test
+                        this.train = train;
+                        this.test = test;
+                        
+                        // convert metrics of testdata and traindata to later use in similarity tests
                         this.train_values = new ArrayList<double[]>();
-                        for (int i = 0; i < this.train.numAttributes()-1; i++) {
-                            this.train_values.add(train.attributeToDoubleArray(i));
+                        for (int i = 0; i < this.train.numAttributes(); i++) {
+                            if(this.train.classIndex() != i) {
+                                this.train_values.add(this.train.attributeToDoubleArray(i));
+                            }
                         }
                         
                         this.test_values = new ArrayList<double[]>();
-                        for (int i=0; i < this.test.numAttributes()-1; i++) {
-                            this.test_values.add(this.test.attributeToDoubleArray(i));
+                        for (int i=0; i < this.test.numAttributes(); i++) {
+                            if(this.test.classIndex() != i) {
+                                this.test_values.add(this.test.attributeToDoubleArray(i));
+                            }
                         }
                 }
@@ -235 +241 @@
                  */
             public double getScore() {
-                int as = this.attributes.size();
+                int as = this.attributes.size();  // # of attributes that were matched
                 
                 // we use thresholding ranking approach for numInstances to influence the matching score
@@ -250 +256 @@
             }
                  
-                 public HashMap<Integer, Integer> getAttributes() {
-                     return this.attributes;
-                 }
+                public HashMap<Integer, Integer> getAttributes() {
+                    return this.attributes;
+                }
                  
-                 public int getNumInstances() {
-                     return this.train_values.get(0).length;
-                 }
+                public int getNumInstances() {
+                    return this.train_values.get(0).length;
+                }
+                
+                /** 
+                 * This creates a new Instance out of the passed Instance and the previously matched attributes.
+                 * We do this because the evaluation phase requires an original Instance with every attribute.
+                 * 
+                 * @param test instance
+                 * @return new instance
+                 */
+                public Instance getMatchedTestInstance(Instance test) {
+                    //create new instance with our matched number of attributes + 1 (the class attribute)
+                        Instances testdata = this.getMatchedTest();
+
+                        Instance ni = new DenseInstance(this.attributes.size()+1);
+                        ni.setDataset(testdata);
+                         
+                for(Map.Entry<Integer, Integer> attmatch : this.attributes.entrySet()) {
+                    ni.setValue(testdata.attribute(attmatch.getKey()), test.value(attmatch.getValue()));
+                }
+                
+                        ni.setClassValue(test.value(test.classAttribute()));
+
+                        return ni;
+        }
+
+        /**
+         * returns a new instances array with the metric matched training data
+         * 
+         * @return instances
+         */
+                public Instances getMatchedTrain() {
+                    return this.getMatchedInstances("train", this.train);
+                }
                  
-                 public Instance getMatchedTestInstance(Instance test) {
-                         // create new instance with our matched number of attributes + 1 (the class attribute)
-                         //Console.traceln(Level.INFO, "getting matched instance");
-                         Instances testdata = this.getMatchedTest();
-                         
-                         //Instance ni = new DenseInstance(this.attmatch.size()+1);
-                         Instance ni = new DenseInstance(this.attributes.size()+1);
-                         ni.setDataset(testdata);
-                         
-                         //Console.traceln(Level.INFO, "Attributes to match: " + this.attmatch.size() + "");
-                         
-                         Iterator it = this.attributes.entrySet().iterator();
-                         int j = 0;
-                         while (it.hasNext()) {
-                                 Map.Entry values = (Map.Entry)it.next();
-                                 ni.setValue(testdata.attribute(j), test.value((int)values.getValue()));
-                                 j++;
-                                 
-                         }
-                         
-                         ni.setClassValue(test.value(test.classAttribute()));
-
-                         return ni;
-                 }
-
-         /**
-          * returns a new instances array with the metric matched training data
-          * 
-          * @return instances
-          */
-                 public Instances getMatchedTrain() {
-                         return this.getMatchedInstances("train", this.train);
-                 }
-                 
-                 /**
-                  * returns a new instances array with the metric matched test data
-                  * 
-                  * @return instances
-                  */
-                 public Instances getMatchedTest() {
-                         return this.getMatchedInstances("test", this.test);
-                 }
-                 
-                 // todo: there must be a better way
-                 // https://weka.wikispaces.com/Programmatic+Use
-                 private Instances getMatchedInstances(String name, Instances data) {
-                         //Console.traceln(Level.INFO, "Constructing instances from: " + name);
-                     // construct our new attributes
-                         Attribute[] attrs = new Attribute[this.attributes.size()+1];
-                         FastVector fwTrain = new FastVector(this.attributes.size());
-                         for (int i=0; i < this.attributes.size(); i++) {
-                                 attrs[i] = new Attribute(String.valueOf(i));
-                                 fwTrain.addElement(attrs[i]);
-                         }
-                         // add our ClassAttribute (which is not numeric!)
-                         ArrayList<String> acl= new ArrayList<String>();
-                         acl.add("0");
-                         acl.add("1");
-                         
-                         fwTrain.addElement(new Attribute("bug", acl));
-                         Instances newTrain = new Instances(name, fwTrain, data.size());
-                         newTrain.setClassIndex(newTrain.numAttributes()-1);
-                         
-                         //Console.traceln(Level.INFO, "data attributes: " + data.numAttributes() + ", this.attributes: "+this.attributes.size());
-                         
-                         for (int i=0; i < data.size(); i++) {
-                                 Instance ni = new DenseInstance(this.attributes.size()+1);
-                                
-                                 Iterator it = this.attributes.entrySet().iterator();
-                                 int j = 0;
-                                 while (it.hasNext()) {
-                                         Map.Entry values = (Map.Entry)it.next();
-                                         int value = (int)values.getValue();
-                                         
-                                         // key ist traindata
-                                         if (name.equals("train")) {
-                                                 value = (int)values.getKey();
-                                         }
-                                         //Console.traceln(Level.INFO, "setting attribute " + j + " with data from instance: " + i);
-                                         ni.setValue(newTrain.attribute(j), data.instance(i).value(value));
-                                         j++;
-                                 }
-                                 ni.setValue(ni.numAttributes()-1, data.instance(i).value(data.classAttribute()));
-                                 
-                                 newTrain.add(ni);
-                         }
-                         
-                    return newTrain;
-        }
-                 
+        /**
+                 * returns a new instances array with the metric matched test data
+                 * 
+                 * @return instances
+                 */
+                public Instances getMatchedTest() {
+                    return this.getMatchedInstances("test", this.test);
+                }
+                
+                /**
+                 * We could drop unmatched attributes from our instances datasets.
+                 * Alas, that would not be nice for the following postprocessing jobs and would not work at all for evaluation.
+                 * We keep this as a warning for future generations.
+                 * 
+                 * @param name
+                 * @param data
+                 */
+                @SuppressWarnings("unused")
+        private void dropUnmatched(String name, Instances data) {
+                    for(int i = 0; i < data.numAttributes(); i++) {
+                        if(data.classIndex() == i) {
+                            continue;
+                        }
+                        
+                        if(name.equals("train") && !this.attributes.containsKey(i)) { 
+                            data.deleteAttributeAt(i);
+                        }
+                        
+                        if(name.equals("test") && !this.attributes.containsValue(i)) {
+                            data.deleteAttributeAt(i);
+                        }
+                    }
+                }
+
+                
+        /**
+         * Returns a deep copy of passed Instances data for Train or Test data.
+         * It only keeps attributes that have been matched.
+         * 
+         * @param name
+         * @param data
+         * @return matched Instances
+         */
+                private Instances getMatchedInstances(String name, Instances data) {
+                    ArrayList<Attribute> attrs = new ArrayList<Attribute>();
+            
+                    // bug attr is a string, really!
+                    ArrayList<String> bug = new ArrayList<String>();
+            bug.add("0");
+            bug.add("1");
+            
+            // add our matched attributes and last the bug
+                    for(Map.Entry<Integer, Integer> attmatch : this.attributes.entrySet()) {
+                        attrs.add(new Attribute(String.valueOf(attmatch.getValue())));
+                    }
+                    attrs.add(new Attribute("bug", bug));
+                    
+                    // create new instances object of the same size (at least for instances)
+                    Instances newInst = new Instances(name, attrs, data.size());
+                    
+                    // set last as class
+                    newInst.setClassIndex(newInst.numAttributes()-1);
+                    
+                    // copy data for matched attributes, this depends if we return train or test data
+            for (int i=0; i < data.size(); i++) {
+                Instance ni = new DenseInstance(this.attributes.size()+1);
+                
+                int j = 0; // new indices!
+                for(Map.Entry<Integer, Integer> attmatch : this.attributes.entrySet()) {
+  
+                    // test attribute match
+                    int value = attmatch.getValue();
+                    
+                    // train attribute match
+                    if(name.equals("train")) {
+                        value = attmatch.getKey();
+                    }
+                    
+                    ni.setValue(newInst.attribute(j), data.instance(i).value(value));
+                    j++;
+                }
+                ni.setValue(ni.numAttributes()-1, data.instance(i).value(data.classAttribute()));
+                newInst.add(ni);
+            }
+
+            return newInst;
+                }
                  
                 /**
@@ -364 +399 @@
                         //Console.traceln(Level.INFO, "-----");
                 }
+                
                 
                 private void attributeSelection(Instances which) throws Exception {
@@ -431 +467 @@
                  
                 
-        
+        /**
+         * Executes the similarity matching between train and test data.
+         * 
+         * After this function is finished we have this.attributes with the correct matching between train and test data attributes.
+         * 
+         * @param type
+         * @param cutoff
+         */
                 public void matchAttributes(String type, double cutoff) {
                     
-
                     MWBMatchingAlgorithm mwbm = new MWBMatchingAlgorithm(this.train.numAttributes(), this.test.numAttributes());
                     
@@ -447 +489 @@
                     }
                     
-                    // resulting maximal match
+                    // resulting maximal match gets assigned to this.attributes
             int[] result = mwbm.getMatching();
             for( int i = 0; i < result.length; i++) {
@@ -468 +510 @@
                     for( int i = 0; i < this.train.numAttributes(); i++ ) {
                 for( int j = 0; j < this.test.numAttributes(); j++ ) {
-                    // negative infinity counts as not present, we do this so we don't have to map between attribute indexs in weka
+                    // negative infinity counts as not present, we do this so we don't have to map between attribute indexes in weka
                     // and the result of the mwbm computation
                     mwbm.setWeight(i, j, Double.NEGATIVE_INFINITY);
@@ -510 +552 @@
                 }
                  
-                 /**
-                  * Calculate Spearmans rank correlation coefficient as matching score
-                  * The number of instances for the source and target needs to be the same so we randomly sample from the bigger one.
-                  * 
-                  * @param cutoff
-                  * @param mwbmatching
-                  */
-                 public void spearmansRankCorrelation(double cutoff, MWBMatchingAlgorithm mwbm) {
-                         double p = 0;
-
-                         SpearmansCorrelation t = new SpearmansCorrelation();
-
-                         // size has to be the same so we randomly sample the number of the smaller sample from the big sample
-                         if (this.train.size() > this.test.size()) {
-                             this.sample(this.train, this.test, this.train_values);
-                         }else if (this.test.size() > this.train.size()) {
-                             this.sample(this.test, this.train, this.test_values);
-                         }
+                /**
+                 * Calculate Spearmans rank correlation coefficient as matching score
+                 * The number of instances for the source and target needs to be the same so we randomly sample from the bigger one.
+                 * 
+                 * @param cutoff
+                 * @param mwbmatching
+                 */
+                public void spearmansRankCorrelation(double cutoff, MWBMatchingAlgorithm mwbm) {
+                    double p = 0;
+
+                        SpearmansCorrelation t = new SpearmansCorrelation();
+
+                        // size has to be the same so we randomly sample the number of the smaller sample from the big sample
+                        if (this.train.size() > this.test.size()) {
+                            this.sample(this.train, this.test, this.train_values);
+                        }else if (this.test.size() > this.train.size()) {
+                            this.sample(this.test, this.train, this.test_values);
+                        }
                         
             // try out possible attribute combinations
@@ -622 +664 @@
                     // this may invoke exactP on small sample sizes which will not terminate in all cases
                                         //p = t.kolmogorovSmirnovTest(this.train_values.get(i), this.test_values.get(j), false);
+
+                    // this uses approximateP everytime
                                         p = t.approximateP(t.kolmogorovSmirnovStatistic(this.train_values.get(i), this.test_values.get(j)), this.train_values.get(i).length, this.test_values.get(j).length);
                                         if (p > cutoff) {