Merge branch 'fix'

.gitignore

-build/
-config/
-dist/
-nbproject/
-dist/
-build.xml
-catalog.xml
-manifest.mf
\ No newline at end of file
+/build/
+/config/
+/dist/
+/nbproject/
+/dist/
+/build.xml
+/catalog.xml
+/manifest.mf
+/amc59.4/
+/src.rar
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff:
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/dictionaries
+
+# Sensitive or high-churn files:
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.xml
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+
+# Gradle:
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Mongo Explorer plugin:
+.idea/**/mongoSettings.xml
+
+## File-based project format:
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
\ No newline at end of file

reproduce/Output-S+SSPR-F4a.csv

+_MMC,302.0

reproduce/skeleton.asf

+# AST/ASF file generated using VICON BodyLanguage
+# -----------------------------------------------
+:version 1.10
+:name VICON
+:units
+  mass 1.0
+  length 0.45
+  angle deg
+:documentation
+   .ast/.asf automatically generated from VICON data using
+   VICON BodyBuilder and BodyLanguage model FoxedUp or BRILLIANT.MOD
+:root
+   order TX TY TZ RX RY RZ
+   axis XYZ
+   position 0 0 0  
+   orientation 0 0 0 
+:bonedata
+  begin
+     id 1 
+     name lhipjoint
+     direction 0.566809 -0.746272 0.349008 
+     length 2.486467 
+     axis 0 0 0  XYZ
+  end
+  begin
+     id 2 
+     name lfemur
+     direction 0.34202 -0.939693 0  
+     length 7.0298533
+     axis 0 0 20  XYZ
+    dof rx ry rz
+    limits (-160.0 20.0)
+           (-70.0 70.0)
+           (-60.0 70.0)
+  end
+  begin
+     id 3 
+     name ltibia
+     direction 0.34202 -0.939693 0   
+     length 7.5665565   
+     axis 0 0 20   XYZ
+    dof rx
+    limits (-10.0 170.0)
+  end
+  begin
+     id 4 
+     name lfoot
+     direction 0.0665746 -0.182912 0.980873   
+     length 2.0319207   
+     axis -90 7.62852e-016 20   XYZ
+    dof rx rz
+    limits (-45.0 90.0)
+           (-70.0 20.0)
+  end
+  begin
+     id 5 
+     name ltoes
+     direction 1.53601e-011 -4.22058e-011 1   
+     length 1.0248597   
+     axis -90 7.62852e-016 20   XYZ
+    dof rx
+    limits (-90.0 20.0)
+  end
+  begin
+     id 6 
+     name rhipjoint
+     direction -0.550236 -0.756381 0.353735   
+     length 2.4588327  
+     axis 0 0 0  XYZ 
+  end
+  begin
+     id 7 
+     name rfemur
+     direction -0.34202 -0.939693 0   
+     length 7.092786   
+     axis 0 0 -20   XYZ
+    dof rx ry rz
+    limits (-160.0 20.0)
+           (-70.0 70.0)
+           (-70.0 60.0)
+  end
+  begin
+     id 8 
+     name rtibia
+     direction -0.34202 -0.939693 0   
+     length 7.521779   
+     axis 0 0 -20   XYZ
+    dof rx
+    limits (-10.0 170.0)
+  end
+  begin
+     id 9 
+     name rfoot
+     direction -0.0683029 -0.187661 0.979856   
+     length 2.0840635  
+     axis -90 -7.62852e-016 -20   XYZ
+    dof rx rz
+    limits (-45.0 90.0)
+           (-20.0 70.0)
+  end
+  begin
+     id 10 
+     name rtoes
+     direction -1.53528e-011 -4.21968e-011 1   
+     length 1.0457201   
+     axis -90 -7.62852e-016 -20   XYZ
+    dof rx
+    limits (-90.0 20.0)
+  end
+  begin
+     id 11 
+     name lowerback
+     direction 0.013823 0.995423 -0.0945635   
+     length 2.0337632   
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 12 
+     name upperback
+     direction 0.0276657 0.9994 -0.020853   
+     length 2.0335853   
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 13 
+     name thorax
+     direction 0.019782 0.999531 0.0233827   
+     length 2.052965   
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 14 
+     name lowerneck
+     direction -0.0308541 0.994709 0.0979874   
+     length 1.7053784  
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 15 
+     name upperneck
+     direction 0.0588398 0.995804 -0.0700903   
+     length 1.7072247   
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 16
+     name head
+     direction 0.0209966 0.999159 -0.0352225  
+     length 1.7143868  
+     axis 0 0 0   XYZ
+    dof rx ry rz
+    limits (-20.0 45.0)
+           (-30.0 30.0)
+           (-30.0 30.0)
+  end
+  begin
+     id 17 
+     name lclavicle
+     direction 0.938182 0.335073 -0.0868338  
+     length 3.4613798  
+     axis 0 0 0   XYZ
+    dof ry rz
+    limits (-20.0 10.0)
+           (0.0 20.0)
+  end
+  begin
+     id 18 
+     name lhumerus
+     direction 1 -4.48971e-011 -1.26313e-017   
+     length 5.0736656  
+     axis 180 -30 -90   XYZ
+    dof rx ry rz
+    limits (-60.0 90.0)
+           (-90.0 90.0)
+           (-90.0 90.0)
+  end
+  begin
+     id 19
+     name lradius
+     direction 1 -4.48948e-011 -5.89033e-027   
+     length 3.306365   
+     axis 180 -30 -90   XYZ
+    dof rx
+    limits (-10.0 170.0)
+  end
+  begin
+     id 20
+     name lwrist
+     direction 1 -4.48977e-011 -1.48983e-026   
+     length 1.653182   
+     axis 9.0955e-015 90 90   XYZ
+    dof ry
+    limits (-180.0 0.0)
+  end
+  begin
+     id 21 
+     name lhand
+     direction 1 -4.49046e-011 -2.98066e-026   
+     length 0.6464882   
+     axis 1.90115e-014 90 90   XYZ
+    dof rx rz
+    limits (-90.0 90.0)
+           (-45.0 45.0)
+  end
+  begin
+     id 22 
+     name lfingers
+     direction 1 -4.48907e-011 -5.95731e-026   
+     length 0.52121544   
+     axis 3.80223e-014 90 90   XYZ
+    dof rx
+    limits (0.0 90.0)
+  end
+  begin
+     id 23
+     name lthumb
+     direction 0.707107 -6.34963e-011 0.707107   
+     length 0.748365   
+     axis -90 45 -3.84942e-014   XYZ
+    dof rx rz
+    limits (-45.0 45.0)
+           (-45.0 45.0)
+  end
+  begin
+     id 24 
+     name rclavicle
+     direction -0.909637 0.398485 -0.11735   
+     length 3.431019  
+     axis 0 0 0   XYZ 
+    dof ry rz
+    limits (-10.0 20.0)
+           (-20.0 0.0)
+  end
+  begin
+     id 25 
+     name rhumerus
+     direction -1 -4.48978e-011 -1.09333e-027  
+     length 5.1241627  
+     axis 180 30 90   XYZ
+    dof rx ry rz
+    limits (-90.0 60.0)
+           (-90.0 90.0)
+           (-90.0 90.0)
+  end
+  begin
+     id 26 
+     name rradius
+     direction -1 -4.48953e-011 -7.61841e-027   
+     length 3.3258677  
+     axis 180 30 90   XYZ
+    dof rx
+    limits (-10.0 170.0)
+  end
+  begin
+     id 27 
+     name rwrist
+     direction -1 -4.48977e-011 -1.48983e-026   
+     length 1.6629333   
+     axis 9.0955e-015 -90 -90   XYZ
+    dof ry
+    limits (-180.0 0.0)
+  end
+  begin
+     id 28
+     name rhand
+     direction -1 -4.49027e-011 -2.98038e-026   
+     length 0.6713095   
+     axis 1.90115e-014 -90 -90   XYZ
+    dof rx rz
+    limits (-90.0 90.0)
+           (-45.0 45.0)
+  end
+  begin
+     id 29
+     name rfingers
+     direction -1 -4.48838e-011 -5.95531e-026   
+     length 0.54123974   
+     axis 3.80223e-014 -90 -90   XYZ
+    dof rx
+    limits (0.0 90.0)
+  end
+  begin
+     id 30
+     name rthumb
+     direction -0.707107 -6.34937e-011 0.707107   
+     length 0.7770802   
+     axis -90 -45 3.84942e-014   XYZ
+    dof rx rz
+    limits (-45.0 45.0)
+           (-45.0 45.0)
+  end
+:hierarchy
+  begin
+    root lhipjoint rhipjoint lowerback
+    lhipjoint lfemur
+    lfemur ltibia
+    ltibia lfoot
+    lfoot ltoes
+    rhipjoint rfemur
+    rfemur rtibia
+    rtibia rfoot
+    rfoot rtoes
+    lowerback upperback
+    upperback thorax
+    thorax lowerneck lclavicle rclavicle
+    lowerneck upperneck
+    upperneck head
+    lclavicle lhumerus
+    lhumerus lradius
+    lradius lwrist
+    lwrist lhand lthumb
+    lhand lfingers
+    rclavicle rhumerus
+    rhumerus rradius
+    rradius rwrist
+    rwrist rhand rthumb
+    rhand rfingers
+  end

src/algorithms/Classifier.java

 package algorithms;
 
-import Jama.Matrix;
 import java.io.Serializable;
-import java.util.List;
-import objects.DistanceMatrix;
 import objects.Template;
 
 public abstract class Classifier implements Serializable {
-
-    private DistanceTemplates distanceTemplates;
-    private DistanceMatrix distanceMatrix;
-    private Matrix transformationMatrix;
-
-    public Classifier() {
-    }
-
-    public DistanceTemplates getDistanceTemplates() {
-        return distanceTemplates;
+    
+    private Decision decision;
+    
+    public Decision getDecision() {
+        return decision;
     }
 
-    public void setDistanceTemplates(DistanceTemplates distanceTemplates) {
-        this.distanceTemplates = distanceTemplates;
+    public void setDecision(Decision decision) {
+        this.decision = decision;
     }
 
-    public DistanceMatrix getDistanceMatrix() {
-        return distanceMatrix;
-    }
-
-    public void setDistanceMatrix(DistanceMatrix distanceMatrix) {
-        this.distanceMatrix = distanceMatrix;
-    }
-
-    public Matrix getTransformationMatrix() {
-        return transformationMatrix;
-    }
-
-    public void setTransformationMatrix(Matrix transformationMatrix) {
-        this.transformationMatrix = transformationMatrix;
-    }
-
-    public abstract int classify(Template templateQuery, List<Template> templatesGallery);
-
-    public double getDistance(Template template1, Template template2) {
-        return distanceMatrix == null ? distanceTemplates.getDistance(template1, template2) : distanceMatrix.getDistance(template1, template2);
+    public String classify(Template template){
+        return decision.decide(template);
     }
 }

src/algorithms/Classifier1NN.java

-package algorithms;
-
-import java.util.List;
-import objects.Template;
-
-public class Classifier1NN extends Classifier {
-
-    @Override
-    public int classify(Template templateQuery, List<Template> templatesGallery) {
-        Template closestTemplate = new Template(0, "", null);
-        double minDistance = Double.MAX_VALUE;
-        for (Template template : templatesGallery) {
-            double distance = getDistance(template, templateQuery);
-            if (minDistance > distance) {
-                minDistance = distance;
-                closestTemplate = template;
-            }
-        }
-        return closestTemplate.getSubject();
-    }
-}

src/algorithms/Classifier1NNDTWKrzeszowski.java

+package algorithms;
+
+public class Classifier1NNDTWKrzeszowski extends Classifier {
+
+    public Classifier1NNDTWKrzeszowski() {
+        DecisionKNN decision = new DecisionKNN();
+        decision.setK(1);
+        DistanceTemplatesDTW distanceTemplates = new DistanceTemplatesDTW();
+        distanceTemplates.setDistancePoses(new DistancePosesKrzeszowski());
+        decision.setDistanceTemplates(distanceTemplates);
+        setDecision(decision);
+    }
+
+    public final class DistancePosesKrzeszowski extends DistancePoses {
+
+        @Override
+        public double getDistance(double[] pose1, double[] pose2) {
+            double w1 = 57.3;
+            double w2 = 1.7;
+            int length = pose1.length;
+            if (pose2.length != length) {
+                System.out.println("wrong dimensions");
+            }
+            double rho = 0;
+            int d = 0;
+            while (d < length - 2) {
+                double sumAngles = 0;
+                for (int i = 0; i < 3; i++) {
+                    sumAngles += Math.pow(180 - Math.abs(Math.abs(pose1[d + i] - pose2[d + i]) - 180), 2);
+                    d++;
+                }
+                rho += Math.sqrt(sumAngles);
+            }
+            double heightAndAnkleDistanceDifference = 0;
+            while (d < length) {
+                heightAndAnkleDistanceDifference += Math.abs(pose1[d] - pose2[d]);
+                d++;
+            }
+            return w1 * rho + w2 * heightAndAnkleDistanceDifference;
+        }
+    }
+}

src/algorithms/Classifier1NNDTWL1.java

+package algorithms;
+
+public class Classifier1NNDTWL1 extends Classifier {
+
+    public Classifier1NNDTWL1() {
+        DecisionKNN decision = new DecisionKNN();
+        decision.setK(1);
+        DistanceTemplatesDTW distanceTemplates = new DistanceTemplatesDTW();
+        distanceTemplates.setDistancePoses(new DistancePosesL1());
+        decision.setDistanceTemplates(distanceTemplates);
+        setDecision(decision);
+    }
+}

src/algorithms/Classifier1NNDTWL2.java

+package algorithms;
+
+public class Classifier1NNDTWL2 extends Classifier {
+
+    public Classifier1NNDTWL2() {
+        DecisionKNN decision = new DecisionKNN();
+        decision.setK(1);
+        DistanceTemplatesDTW distanceTemplates = new DistanceTemplatesDTW();
+        distanceTemplates.setDistancePoses(new DistancePosesL2());
+        decision.setDistanceTemplates(distanceTemplates);
+        setDecision(decision);
+    }
+}

src/methods/MethodKumar.java → src/algorithms/Classifier1NNKumar.java

-package methods;
+package algorithms;
 
 import Jama.EigenvalueDecomposition;
 import Jama.Matrix;
-import algorithms.Classifier1NN;
-import algorithms.DistanceTemplates;
-import executor.Executor;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import objects.Feature;
-import objects.Motion;
-import objects.Parameter;
 import objects.Template;
 
-public class MethodKumar extends Method {
+public class Classifier1NNKumar extends Classifier {
 
-    private static final int length = 150; //?
-
-    public MethodKumar() {
-    }
-
-    @Override
-    public Motion loadMotion(File fileAMC) throws IOException {
-        return Executor.loadMotionJointCoordinates(fileAMC);
-    }
-
-    @Override
-    public void learnClassifier(List<Motion> motionsLearning) {
-        Classifier1NN classifier = new Classifier1NN();
-        DistanceTemplatesKumar distanceTemplates = new DistanceTemplatesKumar();
-        distanceTemplates.setMeanMatrix(getMeanMatrix(extractTemplates(motionsLearning)));
-        classifier.setDistanceTemplates(distanceTemplates);
-        setClassifier(classifier);
-    }
-
-    @Override
-    public List<Feature> extractFeatures(Motion motion) {
-        motion.adjust(length);
-        double[][] data = getVectorJointCoordinates(motion).getArray();
-        double[] vector = new double[data.length];
-        for (int i = 0; i < data.length; i++) {
-            vector[i] = data[i][0];
-        }
-        Matrix matrix = new Matrix(vector, getAxes().length * length);
-        List<Feature> features = new ArrayList();
-        for (int r = 0; r < matrix.getRowDimension(); r++) {
-            Parameter[] parameters = new Parameter[matrix.getColumnDimension()];
-            for (int c = 0; c < matrix.getColumnDimension(); c++) {
-                parameters[c] = new Parameter(String.valueOf(c), matrix.get(r, c));
-            }
-            features.add(new Feature(parameters));
-        }
-        return features;
+    public Classifier1NNKumar() {
+        DecisionKNN decision = new DecisionKNN();
+        decision.setK(1);
+        decision.setDistanceTemplates(new DistanceTemplatesKumar());
+        setDecision(decision);
     }
 
     public final class DistanceTemplatesKumar extends DistanceTemplates {
 
-        Matrix meanMatrix;
-
         public DistanceTemplatesKumar() {
         }