Added the steric meshes to deforming, the javascript console is requi…

…red for using the feature.

src/main/java/deformablemesh/SegmentationController.java

@@ -61,6 +61,10 @@ public void setPressure(double d) {
         model.setPressure(d);
     }
 
+    public void setStericNeighborWeight(double d){
+        model.setStericNeighborWeight(d);
+    }
+
     public void setCortexThickness(double d) {
         model.setCortexThickness(d);
     }

src/main/java/deformablemesh/SegmentationModel.java

@@ -1,13 +1,6 @@
 package deformablemesh;
 
-import deformablemesh.externalenergies.ExternalEnergy;
-import deformablemesh.externalenergies.GradientEnergy;
-import deformablemesh.externalenergies.ImageEnergyType;
-import deformablemesh.externalenergies.IntensityEnergy;
-import deformablemesh.externalenergies.PerpendicularGradientEnergy;
-import deformablemesh.externalenergies.PerpendicularIntensityEnergy;
-import deformablemesh.externalenergies.PressureForce;
-import deformablemesh.externalenergies.TriangleAreaDistributor;
+import deformablemesh.externalenergies.*;
 import deformablemesh.geometry.BinaryMomentsOfInertia;
 import deformablemesh.geometry.Box3D;
 import deformablemesh.geometry.DeformableMesh3D;
@@ -61,6 +54,8 @@ public class SegmentationModel {
     double ALPHA = 1.0;
     double BETA = 0.0;
     double pressure = 0.0;
+    double stericNeighborWeight;
+
     private double cortex_thickness = 0.3;
 
     boolean reshape = true;
@@ -351,6 +346,13 @@ public double getPressure() {
         return pressure;
     }
 
+    public void setStericNeighborWeight(double d){
+        stericNeighborWeight = d;
+    }
+
+    public double getStericNeighborWeight(){
+        return stericNeighborWeight;
+    }
     public void saveMeshes(final File f) throws IOException {
         lastSavedFile = null;
         MeshWriter.saveMeshes(f, tracker);
@@ -528,13 +530,33 @@ public void externalEnergies(){
 
         if(normalize!=0){
             selectedMesh.addExternalEnergy(new TriangleAreaDistributor(stack, selectedMesh, normalize));
+        }
 
+        if(stericNeighborWeight!=0){
+            List<ExternalEnergy> segs = generateStericEnergies();
+            for(ExternalEnergy eg: segs){
+                selectedMesh.addExternalEnergy(eg);
+            }
         }
 
         snakeBox.addRingEnergy(stack.CURRENT, selectedMesh);
 
     }
 
+    private List<ExternalEnergy> generateStericEnergies() {
+        List<Track> tracks = tracker.getAllMeshTracks();
+        DeformableMesh3D sel = getSelectedMesh(stack.CURRENT);
+        List<ExternalEnergy> es = new ArrayList<>(tracks.size());
+        for(Track track: tracks){
+            if(!track.containsMesh(sel) && track.containsKey(stack.CURRENT) ){
+
+                es.add(new StericMesh(track.getMesh(stack.CURRENT), stericNeighborWeight));
+
+            }
+        }
+        return es;
+    }
+
     public double getCurveWeight() {
 
         return snakeBox.getCurveWeight();

src/main/java/deformablemesh/externalenergies/StericMesh.java

@@ -4,9 +4,10 @@
 import deformablemesh.geometry.InterceptingMesh3D;
 
 public class StericMesh implements ExternalEnergy{
-    //final InterceptingMesh3D mesh;
+    InterceptingMesh3D mesh;
     final DeformableMesh3D deformableMesh;
     final double weight;
+    boolean staticShape = true;
     public StericMesh(DeformableMesh3D a, double weight){
         //mesh = new InterceptingMesh3D(a);
         deformableMesh = a;
@@ -15,7 +16,9 @@ public StericMesh(DeformableMesh3D a, double weight){
 
     @Override
     public void updateForces(double[] positions, double[] fx, double[] fy, double[] fz) {
-        InterceptingMesh3D mesh = new InterceptingMesh3D(deformableMesh);
+        if(!staticShape || mesh==null) {
+            mesh = new InterceptingMesh3D(deformableMesh);
+        }
         double[] pt = new double[3];
         double[] center = mesh.getCenter();
         for(int i = 0; i<fx.length; i++){

src/main/java/deformablemesh/simulations/TwoDrops.java

@@ -16,29 +16,29 @@
 public class TwoDrops {
     DeformableMesh3D a;
     DeformableMesh3D b;
-    double gravityMagnitude = 0.0;
-    double surfaceFactor = 0.0;
-    double volumeConservation = 1.0;
+    double gravityMagnitude = 0.00001;
+    double surfaceFactor = 0.0002;
+    double volumeConservation = 0.01;
     double steric = 0.0;
-    double sticky = 1.0;
+    double sticky = 0.01;
     List<StickyVertex> links = new ArrayList<>();
     public TwoDrops(){
         Sphere sA = new Sphere(new double[]{-0.1, 0, 0.5}, 0.1);
-        a = new NewtonMesh3D(RayCastMesh.rayCastMesh(sA, sA.getCenter(), 2));
-        //a = RayCastMesh.rayCastMesh(sA, sA.getCenter(), 2);
-        a.GAMMA = 500;
+        //a = new NewtonMesh3D(RayCastMesh.rayCastMesh(sA, sA.getCenter(), 2));
+        a = RayCastMesh.rayCastMesh(sA, sA.getCenter(), 2);
+        a.GAMMA = 1;
         a.ALPHA = 0.01;
         a.BETA = 0.0;
         a.reshape();
         a.setShowSurface(true);
         a.setColor(Color.RED);
         Sphere sB = new Sphere(new double[]{0.1, 0, 0.5}, 0.1);
-        b = new NewtonMesh3D(RayCastMesh.rayCastMesh(sB, sB.getCenter(), 2));
-        //b = RayCastMesh.rayCastMesh(sB, sB.getCenter(), 2);
+        //b = new NewtonMesh3D(RayCastMesh.rayCastMesh(sB, sB.getCenter(), 2));
+        b = RayCastMesh.rayCastMesh(sB, sB.getCenter(), 2);
 
-        b.ALPHA = 0.1;
-        b.BETA = 0.0;
-        b.GAMMA = 500;
+        b.ALPHA = 0.01;
+        b.BETA = 0.001;
+        b.GAMMA = 1;
         b.reshape();
         b.setColor(Color.BLUE);
         b.setShowSurface(true);
@@ -100,10 +100,43 @@ public double getEnergy(double[] pos) {
             b.addExternalEnergy(new StericMesh(a, steric));
         }
 
-        if(sticky != 0) {
-            stickVertexes(a, b);
+
+    }
+
+    Set<Integer> stuckA = new HashSet<>();
+    Set<Integer> stuckB = new HashSet<>();
+    double cutoff = 0.0001;
+    public void stickyCell(DeformableMesh3D sticky, DeformableMesh3D neighbor){
+        int nA = sticky.positions.length/3;
+        int nB = neighbor.positions.length/3;
+
+
+
+        for(int i = 0; i<nA; i++){
+            if(stuckA.contains(i)) continue;
+            for(int j = 0; j<nB; j++){
+                if(stuckB.contains(j)) continue;
+
+                double[] a = sticky.getCoordinates(i);
+                double[] b = neighbor.getCoordinates(j);
+
+                double dx = b[0] - a[0];
+                double dy = b[1] - a[1];
+                double dz = b[2] - a[2];
+
+                if(dx*dx + dy*dy + dz*dz < cutoff){
+                    stuckA.add(i);
+                    stuckB.add(j);
+                    sticky.addExternalEnergy(new StickyVertex(i, neighbor.nodes.get(j), this.sticky));
+                    neighbor.addExternalEnergy(new StickyVertex(j, sticky.nodes.get(i), this.sticky));
+                }
+
+            }
         }
+
+
     }
+
     public void stickVertexes(DeformableMesh3D a, DeformableMesh3D b){
 
         Set<Node3D> possibleA = new HashSet<>();
@@ -198,6 +231,13 @@ public void createDisplay(){
     public void step(){
         a.update();
         b.update();
+        if(sticky!=0){
+            int before = stuckA.size();
+            stickyCell(a,b);
+            if(stuckA.size() > before){
+                System.out.println("stuck!");
+            }
+        }
     }
     public static void main(String[] args){
         TwoDrops sim = new TwoDrops();