[#38] documentation: adding java docs

Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java

@@ -2,16 +2,11 @@ package cz.fidentis.analyst.procrustes;
 
 import cz.fidentis.analyst.face.HumanFace;
 import cz.fidentis.analyst.feature.FeaturePoint;
-import cz.fidentis.analyst.icp.IcpTransformation;
 import cz.fidentis.analyst.mesh.core.MeshPoint;
 import cz.fidentis.analyst.procrustes.exceptions.ProcrustesAnalysisException;
 import cz.fidentis.analyst.procrustes.utils.ProcrustesAnalysisUtils;
-import org.ejml.data.Matrix;
 import org.ejml.simple.SimpleMatrix;
 import org.ejml.simple.SimpleSVD;
-
-import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import javax.vecmath.Point3d;
 

Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisComparison.java

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package cz.fidentis.analyst.procrustes;
 
 import cz.fidentis.analyst.face.HumanFace;
 import cz.fidentis.analyst.face.HumanFaceFactory;
 import cz.fidentis.analyst.feature.FeaturePoint;
-import cz.fidentis.analyst.feature.services.FeaturePointCsvLoader;
-import cz.fidentis.analyst.feature.services.FeaturePointExportService;
 import cz.fidentis.analyst.feature.services.FeaturePointImportService;
 import cz.fidentis.analyst.feature.utils.FileResourcesUtils;
-import cz.fidentis.analyst.mesh.core.MeshModel;
-import cz.fidentis.analyst.mesh.io.MeshObjLoader;
 
-import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.net.URISyntaxException;
-import java.net.URL;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
 
 /**
+ * Class used for testing procrustes analysis and converting feature point file formats.
  *
  * @author Jakub Kolman
  */
@@ -51,9 +38,12 @@ public class ProcrustesAnalysisComparison {
     private static final Path OLD_HEAD_02_PATH = Paths.get(
             "cz", "fidentis", "comparison", "procrustesAnalysis", "faces", "3points_head02_ECA.obj");
 
-
-
-
+    /**
+     * main class used to
+     * @param args
+     * @throws IOException
+     * @throws URISyntaxException
+     */
     public static void main(String[] args) throws IOException, URISyntaxException {
 
         FileResourcesUtils fru = new FileResourcesUtils();

Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisFaceModel.java

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package cz.fidentis.analyst.procrustes;
 
 import cz.fidentis.analyst.face.HumanFace;
@@ -10,7 +5,6 @@ import cz.fidentis.analyst.feature.FeaturePoint;
 import cz.fidentis.analyst.mesh.core.MeshModel;
 import cz.fidentis.analyst.mesh.core.MeshPoint;
 import cz.fidentis.analyst.procrustes.utils.ProcrustesAnalysisUtils;
-import org.ejml.simple.SimpleMatrix;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -29,6 +23,11 @@ public class ProcrustesAnalysisFaceModel {
     private MeshModel meshModel;
     private final HashMap<Integer, Integer> featurePointTypeCorrespondence;
 
+    /**
+     * constructor creating inner attributes used in procrustes analysis from face
+     *
+     * @param face
+     */
     public ProcrustesAnalysisFaceModel(HumanFace face) {
         this.humanFace = face;
         // getFeaturePoints() returns unmodifiable List. To sort it we need to make copy first

Comparison/src/main/java/cz/fidentis/analyst/procrustes/utils/ProcrustesAnalysisUtils.java

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package cz.fidentis.analyst.procrustes.utils;
 
 import cz.fidentis.analyst.feature.FeaturePoint;
 import cz.fidentis.analyst.feature.api.IPosition;
-import cz.fidentis.analyst.feature.provider.FeaturePointTypeProvider;
-import cz.fidentis.analyst.mesh.core.MeshPoint;
 import cz.fidentis.analyst.procrustes.ProcrustesAnalysisFaceModel;
 import org.ejml.simple.SimpleMatrix;
-
 import javax.vecmath.Point3d;
-import javax.vecmath.Vector3f;
-import java.util.*;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+
 
 /**
  * @author Jakub Kolman

GUI/pom.xml

@@ -137,13 +137,7 @@
             <artifactId>AbsoluteLayout</artifactId>
             <version>RELEASE123</version>
         </dependency>
-        
-                <!-- http://ejml.org/wiki/index.php?title=Main_Page -->
-        <dependency>
-            <groupId>org.ejml</groupId>
-            <artifactId>ejml-all</artifactId>
-            <version>0.41</version>
-        </dependency>
+
     </dependencies>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

GUI/src/main/java/cz/fidentis/analyst/registration/RegistrationAction.java

@@ -14,7 +14,6 @@ import cz.fidentis.analyst.mesh.core.MeshFacet;
 import cz.fidentis.analyst.mesh.core.MeshPoint;
 import cz.fidentis.analyst.procrustes.ProcrustesAnalysis;
 import cz.fidentis.analyst.visitors.mesh.HausdorffDistance;
-import org.ejml.simple.SimpleMatrix;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -30,13 +29,13 @@ import javax.vecmath.Vector3d;
 
 /**
  * Action listener for the curvature computation.
- * 
+ *
  * @author Richard Pajersky
  * @author Radek Oslejsek
  * @author Daniel Schramm
  */
 public class RegistrationAction extends ControlPanelAction {
-    
+
     /*
      * Attributes handling the state
      */
@@ -48,24 +47,24 @@ public class RegistrationAction extends ControlPanelAction {
     private String strategy = RegistrationPanel.STRATEGY_POINT_TO_POINT;
     private boolean relativeDist = false;
     private boolean heatmapRender = false;
-    
+
     /*
      * Coloring threshold and statistical values of feature point distances:
      */
     private double fpThreshold = 5.0;
 
     private final RegistrationPanel controlPanel;
-    
+
     /**
      * Constructor.
-     * 
+     *
      * @param canvas OpenGL canvas
      * @param topControlPanel Top component for placing control panels
      */
     public RegistrationAction(Canvas canvas, JTabbedPane topControlPanel) {
         super(canvas, topControlPanel);
         this.controlPanel = new RegistrationPanel(this);
-        
+
         // Place control panel to the topControlPanel
         topControlPanel.addTab(controlPanel.getName(), controlPanel.getIcon(), controlPanel);
         topControlPanel.addChangeListener(e -> {
@@ -81,14 +80,13 @@ public class RegistrationAction extends ControlPanelAction {
         topControlPanel.setSelectedComponent(controlPanel); // Focus registration panel
         calculateHausdorffDistance();
     }
-    
+
     @Override
     public void actionPerformed(ActionEvent ae) {
         double value;
         String action = ae.getActionCommand();
-        
+
 //        OutputWindow.print(ae.getActionCommand());
-        
         switch (action) {
             case RegistrationPanel.ACTION_COMMAND_APPLY_ICP:
                 applyICP();
@@ -98,7 +96,7 @@ public class RegistrationAction extends ControlPanelAction {
                 setHeatmap();
                 break;
             case RegistrationPanel.ACTION_COMMAND_SHIFT_X:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getTranslation().x = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getTranslation().x = value;
@@ -107,7 +105,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_SHIFT_Y:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getTranslation().y = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getTranslation().y = value;
@@ -116,7 +114,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_SHIFT_Z:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getTranslation().z = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getTranslation().z = value;
@@ -125,7 +123,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ROTATE_X:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getRotation().x = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getRotation().x = value;
@@ -134,7 +132,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ROTATE_Y:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getRotation().y = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getRotation().y = value;
@@ -143,7 +141,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ROTATE_Z:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getRotation().z = value;
                 if (getSecondaryFeaturePoints() != null) {
                     getSecondaryFeaturePoints().getRotation().z = value;
@@ -152,7 +150,7 @@ public class RegistrationAction extends ControlPanelAction {
                 //calculateHausdorffDistance();
                 break;
             case RegistrationPanel.ACTION_COMMAND_SCALE:
-                value = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                value = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 getSecondaryDrawableFace().getScale().x = value;
                 getSecondaryDrawableFace().getScale().y = value;
                 getSecondaryDrawableFace().getScale().z = value;
@@ -212,20 +210,20 @@ public class RegistrationAction extends ControlPanelAction {
                 setTransparency(transparency);
                 break;
             case RegistrationPanel.ACTION_COMMAND_FP_CLOSENESS_THRESHOLD:
-                fpThreshold = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                fpThreshold = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 calculateFeaturePoints();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ICP_SCALE:
                 this.scale = ((JCheckBox) ae.getSource()).isSelected();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ICP_MAX_ITERATIONS:
-                maxIterations = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).intValue();
+                maxIterations = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).intValue();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ICP_ERROR:
-                error = ((Number)(((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
+                error = ((Number) (((JFormattedTextField) ae.getSource()).getValue())).doubleValue();
                 break;
             case RegistrationPanel.ACTION_COMMAND_ICP_UNDERSAMPLING:
-                String item = (String)((JComboBox) ae.getSource()).getSelectedItem();
+                String item = (String) ((JComboBox) ae.getSource()).getSelectedItem();
                 switch (item) {
                     case "None":
                         this.undersampling = new NoUndersampling();
@@ -259,14 +257,15 @@ public class RegistrationAction extends ControlPanelAction {
                 initiateProcrustesAnalysis();
                 break;
             default:
-                // to nothing
+            // to nothing
         }
-        
+
         renderScene();
     }
-    
+
     protected void initiateProcrustesAnalysis() {
-        OutputWindow.print("Procrustes Analysis");
+        Logger.print("Procrustes Analysis");
+        Logger out = Logger.measureTime();
 
         HumanFace primaryFace = getScene().getHumanFace(0);
         HumanFace secondaryFace = getScene().getHumanFace(1);
@@ -275,15 +274,24 @@ public class RegistrationAction extends ControlPanelAction {
         procrustesAnalysisInit.analyze();
         calculateFeaturePoints();
         calculateHausdorffDistance();
+
+        out.printDuration("Computation of Procrustes for models with "
+                + getPrimaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
+                + "/"
+                + getSecondaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
+                + " vertices and "
+                + getPrimaryDrawableFace().getHumanFace().getFeaturePoints().size()
+                + "feature points"
+        );
     }
-    
+
     protected void applyICP() {
         Logger out = Logger.measureTime();
-        
+
         IcpTransformer visitor = new IcpTransformer(getPrimaryDrawableFace().getModel(), maxIterations, scale, error, undersampling);
         getSecondaryDrawableFace().getModel().compute(visitor); // NOTE: the secondary face is physically transformed
-        for (List<IcpTransformation> trList: visitor.getTransformations().values()) {
-            for (IcpTransformation tr: trList) {
+        for (List<IcpTransformation> trList : visitor.getTransformations().values()) {
+            for (IcpTransformation tr : trList) {
                 for (int i = 0; i < getSecondaryFeaturePoints().getFeaturePoints().size(); i++) {
                     FeaturePoint fp = getSecondaryFeaturePoints().getFeaturePoints().get(i);
                     Point3d trPoint = tr.transformPoint(fp.getPosition(), scale);
@@ -291,18 +299,20 @@ public class RegistrationAction extends ControlPanelAction {
                 }
             }
         }
-        
-        out.printDuration("Computation of ICP for models with " 
+
+        out.printDuration("Computation of ICP for models with "
                 + getPrimaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                 + "/"
                 + getSecondaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                 + " vertices"
         );
     }
-    
+
     /**
-     * Sets the transparency of {@link #getPrimaryDrawableFace} or {@link #getSecondaryDrawableFace()}
-     * based on the inputted value and {@link @TRANSPARENCY_RANGE}
+     * Sets the transparency of {@link #getPrimaryDrawableFace} or
+     * {@link #getSecondaryDrawableFace()} based on the inputted value and
+     * {@link @TRANSPARENCY_RANGE}
+     *
      * @param value Value
      */
     private void setTransparency(int value) {
@@ -319,25 +329,24 @@ public class RegistrationAction extends ControlPanelAction {
             getSecondaryDrawableFace().setTransparency((2 * RegistrationPanel.TRANSPARENCY_RANGE - value) / 10f);
         }
     }
-    
+
     /**
-     * Calculates feature points which are too far away
-     * and changes their color to green
-     * otherwise set color to default
+     * Calculates feature points which are too far away and changes their color
+     * to green otherwise set color to default
      */
     private void calculateFeaturePoints() {
         Logger.print("Calculation of feature points");
-        
+
         if (getPrimaryDrawableFace() == null) { // scene not yet initiated
             return;
         }
-        
-        if (getPrimaryFeaturePoints() == null || 
-                getSecondaryFeaturePoints() == null ||
-                getPrimaryFeaturePoints().getFeaturePoints().size() != getSecondaryFeaturePoints().getFeaturePoints().size()) {
+
+        if (getPrimaryFeaturePoints() == null
+                || getSecondaryFeaturePoints() == null
+                || getPrimaryFeaturePoints().getFeaturePoints().size() != getSecondaryFeaturePoints().getFeaturePoints().size()) {
             return;
         }
-         
+
         double fpMaxDist = Double.NEGATIVE_INFINITY;
         double fpMinDist = Double.POSITIVE_INFINITY;
         double distSum = 0.0;
@@ -347,9 +356,9 @@ public class RegistrationAction extends ControlPanelAction {
             Point3d transformed = new Point3d(secondary.getX(), secondary.getY(), secondary.getZ());
             transformPoint(transformed);
             double distance = Math.sqrt(
-                Math.pow(transformed.x - primary.getX(), 2) + 
-                Math.pow(transformed.y - primary.getY(), 2) + 
-                Math.pow(transformed.z - primary.getZ(), 2));
+                    Math.pow(transformed.x - primary.getX(), 2)
+                    + Math.pow(transformed.y - primary.getY(), 2)
+                    + Math.pow(transformed.z - primary.getZ(), 2));
             if (distance > fpThreshold) {
                 getPrimaryFeaturePoints().resetColorToDefault(i);
                 getSecondaryFeaturePoints().resetColorToDefault(i);
@@ -364,27 +373,27 @@ public class RegistrationAction extends ControlPanelAction {
         double fpAvgDist = distSum / getPrimaryFeaturePoints().getFeaturePoints().size();
         this.controlPanel.updateFPStats(fpAvgDist, fpMaxDist, fpMinDist);
     }
-    
+
     private void calculateHausdorffDistance() {
         Logger out = Logger.measureTime();
-        
+
         HumanFace primFace = getScene().getHumanFace(0);
         primFace.computeKdTree(false);
         HausdorffDistance hd = new HausdorffDistance(primFace.getKdTree(), HausdorffDistance.Strategy.POINT_TO_POINT_DISTANCE_ONLY, false, true);
         getScene().getHumanFace(1).getMeshModel().compute(hd);
-        
-        out.printDuration("Computation of Hausdorff distance for models with " 
+
+        out.printDuration("Computation of Hausdorff distance for models with "
                 + getPrimaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                 + "/"
                 + getSecondaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                 + " vertices"
         );
-        
+
         double min = Double.POSITIVE_INFINITY;
         double max = Double.NEGATIVE_INFINITY;
         double sum = 0;
-        int    count = 0;
-        for (List<Double> distList: hd.getDistances().values()) {
+        int count = 0;
+        for (List<Double> distList : hd.getDistances().values()) {
             for (double dist : distList) {
                 min = Math.min(min, dist);
                 max = Math.max(max, dist);
@@ -392,14 +401,14 @@ public class RegistrationAction extends ControlPanelAction {
                 count++;
             }
         }
-        
-        this.controlPanel.updateHDStats(sum/count, max, min);
+
+        this.controlPanel.updateHDStats(sum / count, max, min);
     }
 
     /**
-     * Applies carried out transformations
-     * first on {@link #getSecondaryDrawableFace}
-     * and then on {@link #getSecondaryDrawableFace} feature points
+     * Applies carried out transformations first on
+     * {@link #getSecondaryDrawableFace} and then on
+     * {@link #getSecondaryDrawableFace} feature points
      */
     private void transformFace() {
         for (MeshFacet transformedFacet : getSecondaryDrawableFace().getFacets()) {
@@ -415,10 +424,11 @@ public class RegistrationAction extends ControlPanelAction {
             getSecondaryFeaturePoints().getFeaturePoints().set(i, point);
         }
     }
-    
+
     /**
-     * Transforms point based on transformation info from {@link #getSecondaryDrawableFace}
-     * 
+     * Transforms point based on transformation info from
+     * {@link #getSecondaryDrawableFace}
+     *
      * @param point Point to transform
      */
     private void transformPoint(Point3d point) {
@@ -472,7 +482,7 @@ public class RegistrationAction extends ControlPanelAction {
         point.y *= 1 + getSecondaryDrawableFace().getScale().y;
         point.z *= 1 + getSecondaryDrawableFace().getScale().z;
     }
-    
+
     protected void setHeatmap() {
         HausdorffDistance.Strategy useStrategy;
         switch (strategy) {
@@ -485,22 +495,22 @@ public class RegistrationAction extends ControlPanelAction {
             default:
                 throw new UnsupportedOperationException(strategy);
         }
-        
-        if (hdVisitor == null) { 
+
+        if (hdVisitor == null) {
             Logger out = Logger.measureTime();
-            
+
             this.hdVisitor = new HausdorffDistance(getPrimaryDrawableFace().getModel(), useStrategy, relativeDist, true);
             getSecondaryDrawableFace().getModel().compute(hdVisitor);
-            
-            out.printDuration("Computation of Hausdorff distance for models with " 
+
+            out.printDuration("Computation of Hausdorff distance for models with "
                     + getPrimaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                     + "/"
                     + getSecondaryDrawableFace().getHumanFace().getMeshModel().getNumVertices()
                     + " vertices"
             );
         }
-        
+
         getSecondaryDrawableFace().setHeatMap(hdVisitor.getDistances());
     }
-    
+
 }

MeshModel/src/main/java/cz/fidentis/analyst/feature/api/IPosition.java

@@ -13,6 +13,12 @@ import javax.vecmath.Point3d;
  * @author Jakub Kolman
  */
 public interface IPosition {
+
+    /**
+     * get position of Point3d object
+     *
+     * @return position of Point3d object
+     */
     Point3d getPosition();
 
     default double getX() {