Resolve "Accelerate N:N"

Comparison/src/main/java/cz/fidentis/analyst/face/HumanFace.java

@@ -25,9 +25,6 @@ import java.util.List;
 import java.util.ArrayList;
 import java.util.Objects;
 import javax.imageio.ImageIO;
-//import org.nustaq.serialization.FSTConfiguration;
-//import org.nustaq.serialization.FSTObjectInput;
-//import org.nustaq.serialization.FSTObjectOutput;
 
 /**
  * This class encapsulates data for a 3D scan of a single human face.
@@ -47,7 +44,11 @@ public class HumanFace implements Serializable {
     
     private MeshModel meshModel;
     
-    private KdTree kdTree;
+    /**
+     * {@code KdTree} is marked as transient because the Kryo library is not able
+     * to handle the reference of {@code KdNode} to {@code MeshModel}s.
+     */
+    private transient KdTree kdTree; 
 
     private Plane symmetryPlane;
     

Comparison/src/main/java/cz/fidentis/analyst/face/HumanFaceFactory.java

@@ -5,8 +5,6 @@ import com.esotericsoftware.kryo.io.Input;
 import com.esotericsoftware.kryo.io.Output;
 import com.esotericsoftware.kryo.util.DefaultInstantiatorStrategy;
 import cz.fidentis.analyst.Logger;
-import cz.fidentis.analyst.kdtree.KdNode;
-import cz.fidentis.analyst.kdtree.KdTree;
 import cz.fidentis.analyst.mesh.core.CornerTable;
 import cz.fidentis.analyst.mesh.core.CornerTableRow;
 import cz.fidentis.analyst.mesh.core.MeshFacetImpl;
@@ -121,8 +119,6 @@ public class HumanFaceFactory {
                 HumanFaceFactory.kryo.register(CornerTableRow.class);
                 HumanFaceFactory.kryo.register(BBox.class);
                 HumanFaceFactory.kryo.register(Plane.class);
-                HumanFaceFactory.kryo.register(KdTree.class);
-                HumanFaceFactory.kryo.register(KdNode.class);
                 HumanFaceFactory.kryo.register(Point3d.class);
                 HumanFaceFactory.kryo.register(Vector3d.class);
                 HumanFaceFactory.kryo.register(ArrayList.class);

Comparison/src/main/java/cz/fidentis/analyst/visitors/kdtree/AvgFaceConstructor.java

@@ -6,13 +6,15 @@ import cz.fidentis.analyst.mesh.core.MeshFacet;
 import cz.fidentis.analyst.mesh.core.MeshFacetImpl;
 import cz.fidentis.analyst.mesh.core.MeshModel;
 import cz.fidentis.analyst.visitors.mesh.HausdorffDistance;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
@@ -63,9 +65,13 @@ public class AvgFaceConstructor extends KdTreeVisitor {
         }
         
         // fill vertTarns with empty list for each facet
-        templateFacets.parallelStream().forEach(
-                f -> this.transformations.put(f, new ArrayList<>(f.getVertices().size()))
-        );
+        templateFacets.parallelStream().forEach(f -> {
+                //transformations.put(f, new ArrayList<>(f.getVertices().size()));
+                transformations.put(f, Stream.generate(Vector3d::new)
+                        .limit(f.getVertices().size())
+                        .collect(Collectors.toList())
+                );
+        });
     }
     
     /**
@@ -90,24 +96,20 @@ public class AvgFaceConstructor extends KdTreeVisitor {
                 HausdorffDistance.Strategy.POINT_TO_POINT, 
                 false, // relative distance
                 true,  // parallel computation
-                false  // auto cut
+                false  // auto crop
         );
         transformations.keySet().forEach(f -> hDist.visitMeshFacet(f)); 
         
         // compute shifts of my vertices
         for (MeshFacet myFacet: transformations.keySet()) {
             List<Point3d> closestPoints = hDist.getNearestPoints().get(myFacet);
-            for (int i = 0; i < myFacet.getNumberOfVertices(); i++) {
-                //Vector3d moveDir = new Vector3d(myFacet.getVertex(i).getPosition());
-                //moveDir.sub(closestPoints.get(i));
+            
+            // shift vertices concurrently
+            IntStream.range(0, closestPoints.size()).parallel().forEach(i -> {
                 Vector3d moveDir = new Vector3d(closestPoints.get(i));
                 moveDir.sub(myFacet.getVertex(i).getPosition());
-                if (transformations.get(myFacet).size() < myFacet.getNumberOfVertices()) { // First inspected facet
-                    transformations.get(myFacet).add(moveDir);
-                } else {
-                    transformations.get(myFacet).get(i).add(moveDir);
-                }
-            }
+                transformations.get(myFacet).get(i).add(moveDir);
+            });
         }
     }
     
@@ -120,11 +122,11 @@ public class AvgFaceConstructor extends KdTreeVisitor {
             avgMeshModel = new MeshModel();
             for (MeshFacet f: transformations.keySet()) { // clone all facets of the template face
                 MeshFacet newFacet = new MeshFacetImpl(f);
-                for (int i = 0; i < newFacet.getNumberOfVertices(); i++ ) { // move all vertices
+                IntStream.range(0, newFacet.getNumberOfVertices()).parallel().forEach(i -> {
                     Vector3d tr = new Vector3d(transformations.get(f).get(i));
                     tr.scale(1.0/numInspectedFacets);
                     newFacet.getVertex(i).getPosition().add(tr);
-                }
+                });
                 avgMeshModel.addFacet(newFacet);
             }
         }

GUI/src/main/java/cz/fidentis/analyst/batch/ApproxHausdorffDistTask.java

@@ -31,7 +31,7 @@ import java.util.stream.DoubleStream;
 public class ApproxHausdorffDistTask extends SimilarityTask {
     
     private final Stopwatch totalTime = new Stopwatch("Total computation time:\t\t");
-    private final Stopwatch hdComputationTime = new Stopwatch("Hausdorff distance preparation time:\t");
+    private final Stopwatch hdComputationTime = new Stopwatch("Hausdorff distance computation time:\t");
     private final Stopwatch loadTime = new Stopwatch("Disk access time:\t\t");
     private final Stopwatch kdTreeConstructionTime = new Stopwatch("KD trees construction time:\t\t");
     private final Stopwatch finalHdComputationTime = new Stopwatch("Hausdorff distance finalization time:\t");
@@ -103,7 +103,9 @@ public class ApproxHausdorffDistTask extends SimilarityTask {
                         .flatMap(List::stream).collect(Collectors.toList())); 
                 hdComputationTime.stop();
 
-                face.removeKdTree(); // k-d tree construction is fast, and the memory is more valuable
+                // Memory is more valuable. And it's probable that we will not need
+                // k-d trees anymore. If yes, then they are quicly re-computed.
+                face.removeKdTree(); 
             } else {
                 distCache.add(DoubleStream.generate(() -> 0.0d)
                         .limit(templateFace.getMeshModel().getNumVertices())
@@ -133,8 +135,8 @@ public class ApproxHausdorffDistTask extends SimilarityTask {
     
     protected void printTimeStats() {
         Logger.print(hdComputationTime.toString());
-        Logger.print(loadTime.toString());
         Logger.print(finalHdComputationTime.toString());
+        Logger.print(loadTime.toString());
         Logger.print(kdTreeConstructionTime.toString());
         Logger.print(totalTime.toString());
     }

GUI/src/main/java/cz/fidentis/analyst/batch/IcpTask.java

@@ -128,7 +128,7 @@ public class IcpTask extends SwingWorker<MeshModel, HumanFace> {
                 
                 if (computeAvgFace) { // AVG template face
                     kdTreeConstructionTime.start();
-                    face.computeKdTree(computeICP); // if transformed by ICP, force rk-d tree e-computation
+                    face.computeKdTree(computeICP); // if transformed by ICP, force k-d tree re-computation
                     kdTreeConstructionTime.stop();
                 
                     avgFaceComputationTime.start();
@@ -139,7 +139,7 @@ public class IcpTask extends SwingWorker<MeshModel, HumanFace> {
                     avgFaceComputationTime.stop();
                 }
                 
-                face.removeKdTree(); // k-d tree construction is fast, and a free memory is more required
+                //face.removeKdTree(); // preserve k-d tree for the similarity computation phase
                 publish(face);       // update progress bar and possibly render the transformed face
             }
 

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

@@ -189,8 +189,8 @@ public class RegistrationAction extends ControlPanelAction implements HumanFaceL
     protected void applyProcrustes() {
         JOptionPane.showMessageDialog(
                 controlPanel,
-                "This method is not finished yet",
-                "Neither feature points nor symmetry planes are transformed properly",
+                "This method is not finished yet (neither feature points nor symmetry planes are transformed properly)",
+                "Warning",
                 JOptionPane.INFORMATION_MESSAGE);
         
         Logger out = Logger.measureTime();

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

@@ -88,6 +88,9 @@ public class RegistrationPanel extends ControlPanel {
         jButtonInfo1.addActionListener((ActionEvent e) -> { 
             showAutoAlignmentInfo();
         });
+        
+        jFormattedTextField1.setValue(Double.valueOf(0.3));
+        jFormattedTextField2.setValue(Integer.valueOf(50));
     }
     
     /**
@@ -166,7 +169,7 @@ public class RegistrationPanel extends ControlPanel {
     }
     
     public double getMinIcpErrorParam() {
-        return ((Number) jFormattedTextField2.getValue()).doubleValue();
+        return ((Number) jFormattedTextField1.getValue()).doubleValue();
     }
     
     /**

MeshModel/src/main/java/cz/fidentis/analyst/kdtree/KdNode.java

 package cz.fidentis.analyst.kdtree;
 
 import cz.fidentis.analyst.mesh.core.MeshFacet;
-import java.io.Serializable;
 
 import java.util.Collections;
 import java.util.HashMap;
@@ -15,7 +14,7 @@ import javax.vecmath.Point3d;
  *
  * @author Maria Kocurekova
  */
-public class KdNode implements Serializable {
+public class KdNode /* implements Serializable */ {
     
     /**
      * Current depth in the kd-tree
@@ -37,7 +36,6 @@ public class KdNode implements Serializable {
      */
     private KdNode lesser = null;
     private KdNode greater = null;
-    private KdNode parent;
 
     /**
      * Constructor of KdNode
@@ -61,7 +59,6 @@ public class KdNode implements Serializable {
         }
         this.facets.putIfAbsent(facet, index);
         this.depth = depth;
-        this.parent = parent;
         this.location = new Point3d(facet.getVertex(index).getPosition());
     }
     
@@ -92,7 +89,6 @@ public class KdNode implements Serializable {
             this.facets.putIfAbsent(facets.get(i), indices.get(i));
         }
         this.depth = depth;
-        this.parent = parent;
         this.location = new Point3d(facets.get(0).getVertex(indices.get(0)).getPosition());
     }
 
@@ -138,15 +134,6 @@ public class KdNode implements Serializable {
         return greater;
     }
 
-    /**
-     * Tree traversal - go to the parent node.
-     * 
-     * @return parent of this node, null if current node is root
-     */
-    public KdNode getParent() {
-        return parent;
-    }
-
     /**
      * Set lesser node.
      *
@@ -179,17 +166,6 @@ public class KdNode implements Serializable {
         return Collections.unmodifiableMap(facets);
     }
 
-    /**
-     * Set parent node.
-     *
-     * @param parent Node to be set as parent
-     * @return current node
-     */
-    public KdNode setParent(KdNode parent) {
-        this.parent = parent;
-        return this;
-    }
-    
     @Override
     public String toString() {
         String ret = "";

MeshModel/src/main/java/cz/fidentis/analyst/mesh/io/MeshObjLoader.java

@@ -34,7 +34,8 @@ import javax.vecmath.Point3d;
 /**
  * Utility class for loading human face from OBJ data format.
  * Expects only one human face in one file stored as one object.
- * @author Marek Bařinka
+ * 
+ * @author Marek Barinka
  */
 public class MeshObjLoader {
 
@@ -71,7 +72,7 @@ public class MeshObjLoader {
     /**
      * Parse OBJObject into MeshModel
      * @param model Model is needed in future. It's holding data pools
-     * @param object Object to parse. It corespond to our MeshModel
+     * @param object Object to parse. It corresponds to our MeshModel
      * @return Returns complete model
      * @throws IOException Data are corrupted
      */
@@ -96,7 +97,7 @@ public class MeshObjLoader {
         MeshFacet meshFacet = new MeshFacetImpl();
         Map<MeshPoint, Integer> vertices = new HashMap<>();
         Map<Edge, Integer> edges = new HashMap<>();
-
+        
         for (OBJFace face : mesh.getFaces()) {
             processFace(model, face, meshFacet, vertices, edges);
         }
@@ -191,7 +192,8 @@ public class MeshObjLoader {
 
     /**
      * Helper class for finding opposite corners
-     * @author Marek Bařinka
+     * 
+     * @author Marek Barinka
      */
     private static class Edge {