distance map

src/algorithms/Classifier1NNNareshKumarMS.java

-package algorithms;
-
-import Jama.EigenvalueDecomposition;
-import Jama.Matrix;
-import objects.Template;
-
-public class Classifier1NNNareshKumarMS extends Classifier {
-
-    public Classifier1NNNareshKumarMS() {
-        DecisionKNN decision = new DecisionKNN(1);
-        decision.setDistanceTemplates(new DistanceTemplatesNareshKumarMS());
-        setDecision(decision);
-    }
-
-    public final class DistanceTemplatesNareshKumarMS extends DistanceTemplates {
-
-        public DistanceTemplatesNareshKumarMS() {
-        }
-
-        @Override
-        public String getDescription() {
-            return "NareshKumarMS";
-        }
-
-        @Override
-        public double getDistance(Template template1, Template template2) {
-            double sum = 0.0;
-            double[] generalizedEigenvalues = new EigenvalueDecomposition(getCovarianceMatrix(template2).inverse().times(getCovarianceMatrix(template1))).getRealEigenvalues();
-            for (int l = 0; l < generalizedEigenvalues.length; l++) {
-                sum += Math.pow(Math.log(Math.abs(generalizedEigenvalues[l])), 2);
-            }
-            return Math.sqrt(sum);
-        }
-
-        private Matrix getCovarianceMatrix(Template template) {
-            Matrix matrix = template.getMatrix();
-            int rows = matrix.getRowDimension();
-            int columns = matrix.getColumnDimension();
-            Matrix covarianceMatrix = new Matrix(columns, columns);
-            for (int r = 0; r < rows; r++) {
-                Matrix d = matrix.getMatrix(r, r, 0, columns - 1);
-                Matrix u = getDistanceTemplatesMatrix().getMatrix(r, r, 0, columns - 1);
-                Matrix diff = d.minus(u);
-                covarianceMatrix.plusEquals((diff.transpose().times(diff)).times((double) 1 / (rows - 1)));
-            }
-            return covarianceMatrix;
-        }
-    }
-}
+package algorithms;
+
+public class Classifier1NNNareshKumarMS extends Classifier {
+
+    public Classifier1NNNareshKumarMS() {
+        DecisionKNN decision = new DecisionKNN(1);
+        decision.setDistanceTemplates(new DistanceTemplatesNareshKumarMS());
+        setDecision(decision);
+    }
+}

src/algorithms/ClassifierTransform1NNMMCMahalanobis.java

@@ -39,8 +39,15 @@ public class ClassifierTransform1NNMMCMahalanobis extends ClassifierTransform {
             double[] column = (getMeanMatrix(samplesOfClass).minus(meanSampleMatrix)).times(Math.sqrt((double) samplesOfClass.size() / numberOfSamples)).getColumnPackedCopy();
             Upsilon.setMatrix(0, dimension - 1, c, c, new Matrix(column, column.length));
         }
-        SingularValueDecomposition svdChi = new SingularValueDecomposition(Chi);
-        Matrix Omega = svdChi.getU();
+        SingularValueDecomposition svdChi;
+        Matrix Omega;
+        if (dimension < numberOfSamples) {
+            svdChi = new SingularValueDecomposition(Chi.transpose());
+            Omega = svdChi.getV().transpose();
+        } else {
+            svdChi = new SingularValueDecomposition(Chi);
+            Omega = svdChi.getU();
+        }
         Matrix ThetaInverseSquareRoot = svdChi.getS();
         int dim = Math.min(ThetaInverseSquareRoot.getRowDimension(), ThetaInverseSquareRoot.getColumnDimension());
         for (int d = 0; d < dim; d++) {

src/algorithms/Clustering.java → src/algorithms/Clusterer.java

-package algorithms;
-
-import java.util.List;
-import objects.Template;
-
-public abstract class Clustering extends Retriever {
-
-    public Clustering() {
-    }
-
-    public abstract List<List<Template>> cluster(List<Template> templatesGallery);
-    
-    public Template getCentroid(List<Template> templates) {
-        Template centroid = new Template(null, null);
-        if (templates.isEmpty()) {
-            System.out.println("empty class");
-        } else {
-            double minSum = Double.MAX_VALUE;
-            for (Template centroidCandidate : templates) {
-                double sum = 0;
-                for (Template template : templates) {
-                    sum += getDistance(template, centroidCandidate);
-                }
-                if (minSum > sum) {
-                    minSum = sum;
-                    centroid = centroidCandidate;
-                }
-            }
-        }
-        return centroid;
-    }
-}
+package algorithms;
+
+import java.util.List;
+import objects.Template;
+
+public abstract class Clusterer extends Retriever {
+
+    public Clusterer() {
+    }
+
+    public abstract List<List<Template>> cluster(List<Template> templatesGallery);
+    
+    public Template getCentroid(List<Template> templates) {
+        Template centroid = new Template(null, null);
+        if (templates.isEmpty()) {
+            System.out.println("empty class");
+        } else {
+            double minSum = Double.MAX_VALUE;
+            for (Template centroidCandidate : templates) {
+                double sum = 0;
+                for (Template template : templates) {
+                    sum += getDistance(template, centroidCandidate);
+                }
+                if (minSum > sum) {
+                    minSum = sum;
+                    centroid = centroidCandidate;
+                }
+            }
+        }
+        return centroid;
+    }
+}

src/algorithms/ClusteringAgglomerativeHierarchical.java → src/algorithms/ClustererAgglomerativeHierarchical.java

-package algorithms;
-
-import java.util.ArrayList;
-import java.util.List;
-import objects.Template;
-
-public class ClusteringAgglomerativeHierarchical extends Clustering {
-
-    private final int k;
-    private final double d;
-
-    public ClusteringAgglomerativeHierarchical(int k) {
-        this.k = k;
-        this.d = Double.MAX_VALUE;
-    }
-
-    public ClusteringAgglomerativeHierarchical(double d) {
-        this.k = Integer.MAX_VALUE;
-        this.d = d;
-    }
-
-    @Override
-    public List<List<Template>> cluster(List<Template> templatesGallery) {
-        int numberOfTemplates = templatesGallery.size();
-        if (numberOfTemplates < k) {
-            System.out.println(numberOfTemplates + " < " + k);
-        }
-        List<List<Template>> clusters = new ArrayList();
-        List<Template> centroids = new ArrayList();
-        for (Template template : templatesGallery) {
-            List<Template> cluster = new ArrayList();
-            cluster.add(template);
-            clusters.add(cluster);
-            centroids.add(template);
-        }
-        double minDistance = 0;
-        while (clusters.size() > k && minDistance < d) {
-            int numberOfClusters = clusters.size();
-            List<Template> clusterI = clusters.get(0);
-            List<Template> clusterJ = clusters.get(0);
-            Template centroidI = centroids.get(0);
-            Template centroidJ = centroids.get(0);
-            minDistance = Double.MAX_VALUE;
-            for (int i = 0; i < numberOfClusters - 1; i++) {
-                for (int j = i + 1; j < numberOfClusters; j++) {
-                    double distance;
-                    distance = getDistance(centroids.get(i), centroids.get(j));
-                    if (minDistance > distance) {
-                        minDistance = distance;
-                        clusterI = clusters.get(i);
-                        clusterJ = clusters.get(j);
-                        centroidI = centroids.get(i);
-                        centroidJ = centroids.get(j);
-                    }
-                }
-            }
-            clusters.remove(clusterI);
-            clusters.remove(clusterJ);
-            centroids.remove(centroidI);
-            centroids.remove(centroidJ);
-            clusterI.addAll(clusterJ);
-            clusters.add(clusterI);
-            centroids.add(getCentroid(clusterI));
-        }
-        return clusters;
-    }
-}
+package algorithms;
+
+import java.util.ArrayList;
+import java.util.List;
+import objects.Template;
+
+public class ClustererAgglomerativeHierarchical extends Clusterer {
+
+    private final int k;
+    private final double d;
+
+    public ClustererAgglomerativeHierarchical(int k) {
+        this.k = k;
+        this.d = Double.MAX_VALUE;
+    }
+
+    public ClustererAgglomerativeHierarchical(double d) {
+        this.k = Integer.MAX_VALUE;
+        this.d = d;
+    }
+
+    @Override
+    public List<List<Template>> cluster(List<Template> templatesGallery) {
+        int numberOfTemplates = templatesGallery.size();
+        if (numberOfTemplates < k) {
+            System.out.println(numberOfTemplates + " < " + k);
+        }
+        List<List<Template>> clusters = new ArrayList();
+        List<Template> centroids = new ArrayList();
+        for (Template template : templatesGallery) {
+            List<Template> cluster = new ArrayList();
+            cluster.add(template);
+            clusters.add(cluster);
+            centroids.add(template);
+        }
+        double minDistance = 0;
+        while (clusters.size() > k && minDistance < d) {
+            int numberOfClusters = clusters.size();
+            List<Template> clusterI = clusters.get(0);
+            List<Template> clusterJ = clusters.get(0);
+            Template centroidI = centroids.get(0);
+            Template centroidJ = centroids.get(0);
+            minDistance = Double.MAX_VALUE;
+            for (int i = 0; i < numberOfClusters - 1; i++) {
+                for (int j = i + 1; j < numberOfClusters; j++) {
+                    double distance;
+                    distance = getDistance(centroids.get(i), centroids.get(j));
+                    if (minDistance > distance) {
+                        minDistance = distance;
+                        clusterI = clusters.get(i);
+                        clusterJ = clusters.get(j);
+                        centroidI = centroids.get(i);
+                        centroidJ = centroids.get(j);
+                    }
+                }
+            }
+            clusters.remove(clusterI);
+            clusters.remove(clusterJ);
+            centroids.remove(centroidI);
+            centroids.remove(centroidJ);
+            clusterI.addAll(clusterJ);
+            clusters.add(clusterI);
+            centroids.add(getCentroid(clusterI));
+        }
+        return clusters;
+    }
+}

src/algorithms/ClusteringKmeans.java → src/algorithms/ClustererKmeans.java

-package algorithms;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Random;
-import objects.Template;
-
-public class ClusteringKmeans extends Clustering {
-
-    private final int k;
-
-    public ClusteringKmeans(int k) {
-        this.k = k;
-    }
-
-    @Override
-    public List<List<Template>> cluster(List<Template> templatesGallery) {
-        int numberOfTemplates = templatesGallery.size();
-        if (numberOfTemplates < k) {
-            System.out.println(numberOfTemplates + " < " + k);
-            return null;
-        }
-        Random random = new Random();
-        List<Integer> seeds = new ArrayList();
-        for (int i = 0; i < k; i++) {
-            int seed = random.nextInt(numberOfTemplates);
-            while (seeds.contains(seed)) {
-                seed = random.nextInt(numberOfTemplates);
-            }
-            seeds.add(seed);
-        }
-        List<Template> centroids = new ArrayList();
-        for (int i = 0; i < k; i++) {
-            centroids.add(templatesGallery.get(seeds.get(i)));
-        }
-        List<List<Template>> clusters = new ArrayList();
-        boolean done = false;
-        while (!done) {//CHANGE
-            done = true;
-            clusters = new ArrayList();
-            for (int i = 0; i < k; i++) {
-                clusters.add(new ArrayList());
-            }
-            for (Template template : templatesGallery) {
-                double minDistance = Double.MAX_VALUE;
-                int closestCentroidIndex = 0;
-                for (int i = 0; i < k; i++) {
-                    double distance = getDistance(template, centroids.get(i));
-                    if (minDistance > distance) {
-                        minDistance = distance;
-                        closestCentroidIndex = i;
-                    }
-                }
-                clusters.get(closestCentroidIndex).add(template);
-            }
-            for (int i = 0; i < k; i++) {
-                Template centroidOld = centroids.get(i);
-                Template centroidNew = getCentroid(clusters.get(i));
-                centroids.set(i, centroidNew);
-                if(!centroidOld.equals(centroidNew)){
-                    done = false;
-                }
-            }
-        }
-        return clusters;
-    }
-}
+package algorithms;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+import objects.Template;
+
+public class ClustererKmeans extends Clusterer {
+
+    private final int k;
+
+    public ClustererKmeans(int k) {
+        this.k = k;
+    }
+
+    @Override
+    public List<List<Template>> cluster(List<Template> templatesGallery) {
+        int numberOfTemplates = templatesGallery.size();
+        if (numberOfTemplates < k) {
+            System.out.println(numberOfTemplates + " < " + k);
+            return null;
+        }
+        Random random = new Random();
+        List<Integer> seeds = new ArrayList();
+        for (int i = 0; i < k; i++) {
+            int seed = random.nextInt(numberOfTemplates);
+            while (seeds.contains(seed)) {
+                seed = random.nextInt(numberOfTemplates);
+            }
+            seeds.add(seed);
+        }
+        List<Template> centroids = new ArrayList();
+        for (int i = 0; i < k; i++) {
+            centroids.add(templatesGallery.get(seeds.get(i)));
+        }
+        List<List<Template>> clusters = new ArrayList();
+        boolean done = false;
+        while (!done) {//CHANGE
+            done = true;
+            clusters = new ArrayList();
+            for (int i = 0; i < k; i++) {
+                clusters.add(new ArrayList());
+            }
+            for (Template template : templatesGallery) {
+                double minDistance = Double.MAX_VALUE;
+                int closestCentroidIndex = 0;
+                for (int i = 0; i < k; i++) {
+                    double distance = getDistance(template, centroids.get(i));
+                    if (minDistance > distance) {
+                        minDistance = distance;
+                        closestCentroidIndex = i;
+                    }
+                }
+                clusters.get(closestCentroidIndex).add(template);
+            }
+            for (int i = 0; i < k; i++) {
+                Template centroidOld = centroids.get(i);
+                Template centroidNew = getCentroid(clusters.get(i));
+                centroids.set(i, centroidNew);
+                if(!centroidOld.equals(centroidNew)){
+                    done = false;
+                }
+            }
+        }
+        return clusters;
+    }
+}

src/algorithms/Decision.java

-package algorithms;
-
-import java.util.List;
-import objects.Template;
-
-public abstract class Decision extends Retriever {
-
-    private List gallery;
-
-    public Decision() {
-    }
-
-    public List getGallery() {
-        return gallery;
-    }
-
-    public void setGallery(List gallery) {
-        this.gallery = gallery;
-    }
-    
-    public abstract String getDescription();
-
-    public abstract void importGallery(List<Template> templatesGallery);
-
-    public abstract String decide(Template template);
-}
+package algorithms;
+
+import java.util.List;
+import objects.Template;
+
+public abstract class Decision extends Retriever {
+
+    private List gallery;
+
+    public List getGallery() {
+        return gallery;
+    }
+
+    public void setGallery(List gallery) {
+        this.gallery = gallery;
+    }
+
+    public abstract String getDescription();
+    
+    public abstract void importGallery(List<Template> templatesGallery);
+
+    public abstract String decide(Template template);
+}

src/algorithms/DecisionRandom.java

-package algorithms;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Random;
-import objects.Template;
-
-public class DecisionRandom extends Decision {
-
-    @Override
-    public String getDescription() {
-        return "random";
-    }
-    
-    @Override
-    public void importGallery(List<Template> templatesGallery) {
-        List<String> gallery = new ArrayList();
-        for (Template template : templatesGallery) {
-            gallery.add(template.getSubject());
-        }
-        setGallery(gallery);
-    }
-
-    @Override
-    public String decide(Template templateProbe) {
-        List<String> gallery = getGallery();
-        return gallery.get(new Random().nextInt(gallery.size()));
-    }
-}
+package algorithms;
+
+import java.util.List;
+import java.util.Random;
+import objects.Template;
+
+public class DecisionRandom extends Decision {
+
+    @Override
+    public String getDescription() {
+        return "random";
+    }
+
+    @Override
+    public void importGallery(List<Template> templatesGallery) {
+        setGallery(templatesGallery);
+    }
+
+    @Override
+    public String decide(Template templateProbe) {
+        List<Template> gallery = getGallery();
+        return gallery.get(new Random().nextInt(gallery.size())).getSubject();
+    }
+}

src/algorithms/DecisionSVM.java

-package algorithms;
-
-import java.util.List;
-import libsvm.svm;
-import libsvm.svm_model;
-import libsvm.svm_node;
-import libsvm.svm_parameter;
-import libsvm.svm_problem;
-import objects.Template;
-
-public class DecisionSVM extends Decision {
-    
-    @Override
-    public String getDescription() {
-        return "SVM";
-    }
-    
-    @Override
-    public void importGallery(List<Template> templatesGallery) {
-        setGallery(templatesGallery);
-    }
-
-    @Override
-    public String decide(Template templateProbe) {
-        svm svm = new svm();
-        svm_model svm_model = new svm_model();
-        svm_problem svm_problem = new svm_problem();
-        
-        return "";
-    }
-    
-    double[][] train = new double[1000][]; 
-    double[][] test = new double[10][];
-
-    private svm_model svmTrain() {
-        svm_problem prob = new svm_problem();
-        int dataCount = train.length;
-        prob.y = new double[dataCount];
-        prob.l = dataCount;
-        prob.x = new svm_node[dataCount][];
-
-        for (int i = 0; i < dataCount; i++) {
-            double[] features = train[i];
-            prob.x[i] = new svm_node[features.length - 1];
-            for (int j = 1; j < features.length; j++) {
-                svm_node node = new svm_node();
-                node.index = j;
-                node.value = features[j];
-                prob.x[i][j - 1] = node;
-            }
-            prob.y[i] = features[0];
-        }
-
-        svm_parameter param = new svm_parameter();
-        param.probability = 1;
-        param.gamma = 0.5;
-        param.nu = 0.5;
-        param.C = 1;
-        param.svm_type = svm_parameter.C_SVC;
-        param.kernel_type = svm_parameter.LINEAR;
-        param.cache_size = 20000;
-        param.eps = 0.001;
-
-        svm_model model = svm.svm_train(prob, param);
-
-        return model;
-    }
-}

src/algorithms/DistanceTemplates.java

-package algorithms;
-
-import Jama.Matrix;
-import java.io.Serializable;
-import objects.Template;
-
-public abstract class DistanceTemplates implements Serializable {
-
-    private Matrix distanceTemplatesMatrix;
-
-    public DistanceTemplates() {
-    }
-
-    public Matrix getDistanceTemplatesMatrix() {
-        return distanceTemplatesMatrix;
-    }
-    
-    public void setDistanceTemplatesMatrix(Matrix distanceTemplatesMatrix) {
-        this.distanceTemplatesMatrix = distanceTemplatesMatrix;
-    }
-    
-    public abstract String getDescription();
-
+package algorithms;
+
+import java.io.Serializable;
+import objects.Template;
+
+public abstract class DistanceTemplates implements Serializable {
+    
+    public abstract String getDescription();
+
+    public abstract double getDistance(Template template1, Template template2);
+}