checkpoint
[anneal.git] / src / edu / berkeley / qfat / Mesh.java
index 85e838c..7c38672 100644 (file)
@@ -6,49 +6,72 @@ import javax.swing.*;
 import javax.media.opengl.*;
 import javax.media.opengl.glu.*;
 import edu.berkeley.qfat.geom.*;
+import edu.berkeley.qfat.geom.HasBindingGroup;
 import edu.wlu.cs.levy.CG.KDTree;
 import edu.berkeley.qfat.geom.Point;
+import com.infomatiq.jsi.IntProcedure;
 
 public class Mesh implements Iterable<Mesh.T> {
 
     public static final float EPSILON = (float)0.0001;
     public static final Random random = new Random();
 
-    private PointSet<Vert> pointset = new PointSet<Vert>();
-
-    public Iterable<Vert> vertices() { return pointset; }
-
-    public Iterable<E> edges() {
-        return
-            new Iterable<E>() {
-            public Iterator<E> iterator() {
-                // HACK
-                HashSet<E> hse = new HashSet<E>();
-                for(T t : Mesh.this) {
-                    hse.add(t.e1());
-                    hse.add(t.e2());
-                    hse.add(t.e3());
-                    hse.add(t.e1().pair);
-                    hse.add(t.e2().pair);
-                    hse.add(t.e3().pair);
+    private RTree<T>         triangles = new RTree<T>();
+    private PointSet<Vertex> vertices  = new PointSet<Vertex>();
+
+    public boolean option_wireframe    = false;
+    public boolean option_errorNormals = false;
+    public boolean option_selectable   = true;
+
+    public void render(GL gl, Matrix m) {
+        if (option_wireframe) {
+            gl.glDisable(GL.GL_LIGHTING);
+            gl.glBegin(GL.GL_LINES);
+            gl.glColor3f(1, 1, 1);
+            for (T t : this) {
+                m.times(t.e1().p1.goodp).glVertex(gl);
+                m.times(t.e1().p2.goodp).glVertex(gl);
+                m.times(t.e2().p1.goodp).glVertex(gl);
+                m.times(t.e2().p2.goodp).glVertex(gl);
+                m.times(t.e3().p1.goodp).glVertex(gl);
+                m.times(t.e3().p2.goodp).glVertex(gl);
+            }
+            gl.glEnd();
+            gl.glEnable(GL.GL_LIGHTING);
+            return;
+        }
+        for(T t : this) {
+            gl.glColor4f((float)(0.25+(0.05*t.color)),
+                         (float)(0.25+(0.05*t.color)),
+                         (float)(0.75+(0.05*t.color)),
+                         (float)0.3); 
+            t.glTriangle(gl, m);
+        }
+        if (option_errorNormals)
+            for(T t : this)
+                for(Mesh.Vertex p : new Mesh.Vertex[] { t.v1(), t.v2(), t.v3() }) {
+                    if (p.ok) {
+                        gl.glBegin(GL.GL_LINES);
+                        gl.glColor3f(1, 1, 1);
+                        p.p.glVertex(gl);
+                        p.p.plus(p.norm().times((float)p.error()*10)).glVertex(gl);
+                        gl.glEnd();
+                    }
                 }
-                return hse.iterator();
-            } };
     }
 
-    public Iterator<T> iterator() {
-        for(Vert v : pointset)
-            if (v.e != null && v.e.t != null)
-                return new FaceIterator(v);
-        return new FaceIterator();
-    }
+    public boolean immutableVertices;
+    public Mesh    error_against      = null;
+    public double  error              = 0;
+
+    public Mesh(boolean immutableVertices) { this.immutableVertices = immutableVertices; }
 
-    public Mesh score_against = null;
-    public double score = 0;
-    public float score() { return (float)score; }
+    public void makeVerticesImmutable() { this.immutableVertices = true; }
+    public float error() { return (float)error; }
 
-    public int numedges = 0;
-    public float avgedge = 0;
+    public int size() { return vertices.size(); }
+    public Iterable<Vertex> vertices() { return vertices; }
+    public Iterator<T> iterator() { return triangles.iterator(); }
 
     public void rebindPoints() {
         // unbind all points
@@ -63,47 +86,22 @@ public class Mesh implements Iterable<Mesh.T> {
             t.e2().dobind();
             t.e3().dobind();
         }
-    }
-
-    public void unApplyQuadricToNeighborAll() {
-        HashSet<Vert> done = new HashSet<Vert>();
-        for(T t : this)
-            for(Vert p : new Vert[] { t.v1(), t.v2(), t.v3() }) {
-                if (done.contains(p)) continue;
-                done.add(p);
-                p.unApplyQuadricToNeighbor();
-            }
-    }
-    public void recomputeAllFundamentalQuadrics() {
-        HashSet<Vert> done = new HashSet<Vert>();
-        for(T t : this)
-            for(Vert p : new Vert[] { t.v1(), t.v2(), t.v3() }) {
-                if (done.contains(p)) continue;
-                done.add(p);
-                p.recomputeFundamentalQuadric();
-            }
-    }
-    public float applyQuadricToNeighborAll() {
-        int num = 0;
-        double dist = 0;
-        HashSet<Vert> done = new HashSet<Vert>();
-        for(T t : this)
-            for(Vert p : new Vert[] { t.v1(), t.v2(), t.v3() }) {
-                if (done.contains(p)) continue;
-                done.add(p);
-                p.applyQuadricToNeighbor();
-                
-            }
-        return (float)(dist/num);
+        System.out.println("rebound!");
     }
 
     public void transform(Matrix m) {
-        ArrayList<Vert> set = new ArrayList<Vert>();
-        for (Vert v : pointset)
-            set.add(v);
-        for(Vert v : set) v.transform(m);
+        ArrayList<Vertex> set = new ArrayList<Vertex>();
+        for(Vertex v : vertices) set.add(v);
+        for(Vertex v : set) v.transform(m.times(v.p), true, null);
+        for(Vertex v : set) v.goodp = v.p;
     }
 
+    public void rebuild() { /*vertices.rebuild();*/ }
+    public Vec diagonal() { return vertices.diagonal(); }
+    public Point centroid() { return vertices.centroid(); }
+    public Vertex nearest(Point p) { return vertices.nearest(p); }
+
+    /** compute the volume of the mesh */
     public float volume() {
         double total = 0;
         for(T t : this) {
@@ -116,284 +114,447 @@ public class Mesh implements Iterable<Mesh.T> {
         return (float)total;
     }
 
-    public void rebuildPointSet() { pointset.rebuild(); }
-    public Vec diagonal() { return pointset.diagonal(); }
-    public Point centroid() { return pointset.centroid(); }
-    public Vert nearest(Point p) { return pointset.nearest(p); }
 
-    public final class Vert extends HasPoint {
-        public Point p;
+    // Vertexices //////////////////////////////////////////////////////////////////////////////
+
+    /** a vertex in the mesh */
+    public final class Vertex extends HasQuadric implements Visitor {
+        public Point p, goodp;
+        public Point oldp;
         E e;                // some edge *leaving* this point
 
-        /** the nearest vertex in the "score_against" mesh */
-        Vert   nearest_in_other_mesh;
-        /** the number of vertices in the other mesh for which this is the nearest_in_other_mesh */
-        int    quadric_count;
-        /** the total error quadric (contributions from all vertices in other mesh for which this is nearest) */
-        Matrix quadric = Matrix.ZERO;
+        private boolean illegal = false;
 
-        Vert bound_to = this;
-        Matrix binding = new Matrix();
-        float oldscore = 0;
-        boolean quadricStale = false;
+        public boolean visible = false;
 
-        public Matrix errorQuadric() { return quadric; }
         public Point getPoint() { return p; }
-        public float score() { return oldscore; }
+        public float error() { return olderror; }
 
-        private Matrix fundamentalQuadric = null;
-        public Matrix fundamentalQuadric() {
-            if (fundamentalQuadric == null) recomputeFundamentalQuadric();
-            return fundamentalQuadric;
+        private Vertex(Point p) {
+            this.p = p;
+            this.goodp = p;
+            this.oldp = p;
+            if (vertices.get(p) != null) throw new Error();
+            vertices.add(this);
+        }
+
+        public void reinsert() {
+            vertices.remove(this);
+            vertices.add(this);
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) e.t.reinsert();
+        }
+
+        public float olderror = 0;
+        public void setError(float nerror) {
+            error -= olderror;
+            olderror = nerror;
+            error += olderror;
+        }
+
+        /*
+        public Vertex hack(GL gl, Point mouse) {
+            double dist = Double.MAX_VALUE;
+            Vertex cur = null;
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                Vertex v = e.getOther(this);
+                double dist2 = v.getPoint().glProject(gl).distance(mouse);
+                if ((cur==null || dist2 < dist) && v.visible) {
+                    dist = dist2;
+                    cur = v;
+                }
+            }
+            return cur;
         }
+        */
 
-        private Vert(Point p) {
-            this.p = p;
-            if (pointset.get(p) != null) throw new Error();
-            pointset.add(this);
+        public float averageTriangleArea() {
+            int count = 0;
+            float ret = 0;
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                ret += e.t.area();
+                count++;
+            }
+            return ret/count;
+        }
+        public float averageEdgeLength() {
+            int count = 0;
+            float ret = 0;
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                ret += e.length();
+                count++;
+            }
+            return ret/count;
         }
 
-        public void recomputeFundamentalQuadric() {
-            if (!quadricStale && fundamentalQuadric != null) return;
-            quadricStale = false;
-            unApplyQuadricToNeighbor();
+        public Matrix _recomputeFundamentalQuadric() {
             Matrix m = Matrix.ZERO;
-            E e = this.e;
-            do {
-                T t = e.t;
-                m = m.plus(t.norm().fundamentalQuadric(t.centroid()));
-                e = e.pair.next;
-            } while(e != this.e);
-            fundamentalQuadric = m;
-            applyQuadricToNeighbor();
+            int count = 0;
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                m = m.plus(e.t.norm().fundamentalQuadric(e.t.centroid()));
+                count++;
+            }
+            if (count > 0) {
+                m = m.plus(norm().fundamentalQuadric(this.p).times(count));
+                count *= 2;
+            }
+            return m.times(1/(float)count);
         }
 
-        public void unApplyQuadricToNeighbor() {
-            if (nearest_in_other_mesh == null) return;
-            if (fundamentalQuadric == null) return;
-            nearest_in_other_mesh.unComputeError();
-            nearest_in_other_mesh.quadric = nearest_in_other_mesh.quadric.minus(fundamentalQuadric);
-            nearest_in_other_mesh.quadric_count--;
-            if (nearest_in_other_mesh.quadric_count==0)
-                nearest_in_other_mesh.quadric = Matrix.ZERO;
-            nearest_in_other_mesh.computeError();
-            nearest_in_other_mesh = null;
+        public HasQuadric nearest() { return error_against==null ? null : error_against.vertices.nearest(p, this); }
+        public void computeError() {
+            if (error_against==null) return;
+            float nerror =
+                nearest_in_other_mesh != null
+                ? nearest_in_other_mesh.fundamentalQuadric().preAndPostMultiply(p)
+                : nearest().fundamentalQuadric().preAndPostMultiply(p);
+            if (quadric_count != 0)
+                nerror = (nerror + quadric.preAndPostMultiply(p))/(quadric_count+1);
+
+            if (!immutableVertices && quadric_count == 0) {
+                //nerror = Math.max(nerror, 0.4f);
+                //nerror *= 2;
+            }
+            //System.out.println(nerror);
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                double ang = e.dihedralAngle();
+                if (ang > Math.PI) throw new Error();
+                if (ang < -Math.PI) throw new Error();
+                float minangle = (float)(Math.PI * 0.8);
+                //nerror += ((ang / Math.PI)*(ang/Math.PI)) * e.length() * 0.05;
+
+                nerror += (1-e.t.quality())*0.0001;
+                if (ang > minangle) nerror += (ang - minangle);
+
+                //System.out.println(((ang / Math.PI)*(ang/Math.PI)) * 0.000001);
+                /*
+                if (e.t.aspect() < 0.2) {
+                    nerror += (0.2-e.t.aspect()) * 10;
+                }
+                */
+            }
+            if (!immutableVertices) {
+                Vertex n = (Vertex)nearest();
+                float d = norm().dot(n.norm());
+                if (d > 1 || d < -1) throw new Error();
+                if (d >= 0) {
+                    nerror *= (2.0f - d);
+                } else {
+                    nerror += 0.0003 * (2.0f + d);
+                    nerror *= (2.0f + d);
+                }
+            }
+
+            setError(nerror);
         }
 
-        public void applyQuadricToNeighbor() {
-            if (score_against == null) return;
+        public boolean move(Vec vv, boolean ignoreProblems) {
 
-            Vert new_nearest = score_against.nearest(p);
-            if (nearest_in_other_mesh != null && new_nearest == nearest_in_other_mesh) return;
+            boolean good = true;
 
-            if (nearest_in_other_mesh != null) unApplyQuadricToNeighbor();
-            if (nearest_in_other_mesh != null) throw new Error();
+            //     t1' = M * t1
+            //     t2' = t2.getMatrix(t1) * t1'
+            //     t2' = t2.getMatrix(t1) * M * t1
+            //     t1 =     t1.getMatrix(t2) * t2
+            // M * t1 = M * t1.getMatrix(t2) * t2
 
-            nearest_in_other_mesh = new_nearest;
-                
-            // don't attract to vertices that face the other way
-            if (nearest_in_other_mesh.e == null || nearest_in_other_mesh.norm().dot(norm()) < 0) {
-                nearest_in_other_mesh = null;
-            } else {
-                nearest_in_other_mesh.unComputeError();
-                nearest_in_other_mesh.quadric = nearest_in_other_mesh.quadric.plus(fundamentalQuadric());
-                nearest_in_other_mesh.quadric_count++;
-                nearest_in_other_mesh.computeError();
+            if (bindingGroup!=null && this != bindingGroup.getMaster()) {
+                Matrix m2 = getBindingMatrix(bindingGroup.getMaster());
+                Vec v2 = m2.times(vv.plus(getPoint())).minus(m2.times(getPoint()));
+                return ((Vertex)bindingGroup.getMaster()).move(v2, ignoreProblems);
             }
-            reComputeError();
-        }
 
-        public void reComputeError() {
-            unComputeError();
-            computeError();
-        }
-        public void unComputeError() {
-            score -= oldscore;
-            oldscore = 0;
-        }
-        public void computeError() {
-            oldscore = quadric_count == 0 ? 0 : (quadric.preAndPostMultiply(p) / quadric_count);
-            score += oldscore;
+            Point op = this.p;
+            Point pp = vv.plus(getPoint());
+            if (bindingGroup != null) {
+                /*
+                for(int i=0; i<20 ; i++) {
+                    Point p2 = getConstraint().times(pp);
+                    pp = pp.midpoint(p2);
+                    //System.out.println(m.minus(m2));
+                }
+            */
+                    pp = getConstraint().times(pp);
+            }
+            pp = pp.minus(op).norm().times(vv.mag()).plus(op);
+            ok = false;
+            Point pt = pp;
+            for(Vertex v : (Iterable<Vertex>)getBoundPeers()) {
+                Point pt2 = v.getBindingMatrix(this).times(pt);
+                /*
+                if (Math.abs( v.p.minus(pt2).mag() / pt.minus(op).mag() ) > 5)
+                    throw new Error(v.p+" "+pt2+"\n"+op+" "+pt+"\n"+v.getBindingMatrix(this));
+                if (Math.abs( v.p.minus(pt2).mag() / pt.minus(op).mag() ) < 1/5) throw new Error();
+                */
+                good &= v.transform(pt2, ignoreProblems, v.getBindingMatrix(this));
+            }
+
+            if (!good && !ignoreProblems) {
+                for(Vertex v : (Iterable<Vertex>)getBoundPeers()) 
+                    v.transform(v.oldp, true, null);
+            }
+
+            for(Vertex v : (Iterable<Vertex>)getBoundPeers())
+                v.recomputeFundamentalQuadricIfNeighborChanged();
+            for(Vertex v : (Iterable<Vertex>)getBoundPeers())
+                v.reComputeErrorAround();
+            ok = true;
+            return good;
         }
+        public boolean ok = true;
 
         /** does NOT update bound pairs! */
-        public boolean transform(Matrix m) {
+        private boolean transform(Point newp, boolean ignoreProblems, Matrix yes) {
+            this.oldp = this.p;
+            if (immutableVertices) throw new Error();
+
             unApplyQuadricToNeighbor();
-            try {
-                if (pointset.get(this.p)==null) throw new Error();
-                pointset.remove(this);
-                float newx = m.a*p.x + m.b*p.y + m.c*p.z + m.d;
-                float newy = m.e*p.x + m.f*p.y + m.g*p.z + m.h;
-                float newz = m.i*p.x + m.j*p.y + m.k*p.z + m.l;
-                this.p = new Point(newx, newy, newz);
-                pointset.add(this);
-            } catch (Exception e) {
-                throw new RuntimeException(e);
+
+            boolean illegalbefore = illegal;
+            illegal = false;
+            /*
+            if (this.p.minus(newp).mag() > 0.1 && !ignoreProblems) {
+                try {
+                    throw new Exception(""+this.p.minus(newp).mag()+" "+ignoreProblems+" "+yes);
+                } catch(Exception e) {
+                    e.printStackTrace();
+                }
+                illegal = true;
             }
+            */
+
+            this.p = newp;
+            reinsert();
             applyQuadricToNeighbor();
 
-            // should recompute fundamental quadrics of all vertices sharing a face, but we defer...
-            E e = this.e;
-            do {
+            if (!ignoreProblems) {
+                checkLegality();
+            }
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next)
                 e.p2.quadricStale = true;
-                e = e.pair.next;
-            } while(e != this.e);
-
+            return !illegal || (illegalbefore && illegal);
+        } 
 
-            // FIXME: intersection test needed?
-            return true;
+        public void checkLegality() {
+            /*
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next) {
+                if (Math.abs(e.dihedralAngle()) > (Math.PI * 0.9) ||
+                    Math.abs(e.next.dihedralAngle()) > (Math.PI * 0.9)) illegal = true;
+                if (e.t.aspect() < 0.2) illegal = true;
+            }
+            */
+            if (!illegal) triangles.range(oldp, this.p, (Visitor<T>)this);
         }
 
-        public boolean move(Vec v) {
-            Matrix m = new Matrix(v);
-            Vert p = this;
-            boolean good = true;
-            do {
-                good &= p.transform(m);
-                p = p.bound_to;
-            } while (p != this);
-            return good;
+        public void reComputeErrorAround() {
+            reComputeError();
+            if (nearest_in_other_mesh != null)
+                nearest_in_other_mesh.reComputeError();
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next)
+                e.p2.reComputeError();
+        }
+
+        public boolean visit(Object o) {
+            if (o instanceof Vertex)
+                return ((Vertex)o).e != null && ((Vertex)o).norm().dot(Vertex.this.norm()) >= 0;
+            T t = (T)o;
+            if (illegal) return false;
+            for(E e = Vertex.this.e; e!=null; e=e.pair.next==Vertex.this.e?null:e.pair.next) {
+                if (!t.has(e.p1) && !t.has(e.p2) && e.intersects(t)) { illegal = true; }
+                if (e.t != null) {
+                    if (!e.t.has(t.e1().p1) && !e.t.has(t.e1().p2) && t.e1().intersects(e.t)) { illegal = true; }
+                    if (!e.t.has(t.e2().p1) && !e.t.has(t.e2().p2) && t.e2().intersects(e.t)) { illegal = true; }
+                    if (!e.t.has(t.e3().p1) && !e.t.has(t.e3().p2) && t.e3().intersects(e.t)) { illegal = true; }
+                }
+            }
+            return !illegal;
         }
 
+        public E getEdge() { return e; }
         public E getFreeIncident() {
             E ret = getFreeIncident(e, e);
             if (ret != null) return ret;
-            ret = getFreeIncident(e.pair.next, e.pair.next);
-            if (ret == null) throw new Error("unable to find free incident to " + this);
-            return ret;
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next)
+                System.out.println(e + " " + e.t);
+            throw new Error("unable to find free incident to " + this);
         }
 
         public E getFreeIncident(E start, E before) {
-            E e = start;
-            do {
-                if (e.pair.p2 == this && e.pair.t == null && e.pair.next.t == null) return e.pair;
-                e = e.pair.next;
-            } while(e != before);
+            for(E e = start; e!=null; e=e.pair.next==before?null:e.pair.next)
+                if (e.pair.p2 == this && e.pair.t == null && e.pair.next.t == null)
+                    return e.pair;
             return null;
         }
 
         public E getE(Point p2) {
-            Vert v = pointset.get(p2);
+            Vertex v = vertices.get(p2);
             if (v==null) return null;
             return getE(v);
         }
-        public E getE(Vert p2) {
-            E e = this.e;
-            do {
-                if (e==null) return null;
+        public E getE(Vertex p2) {
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next)
                 if (e.p1 == this && e.p2 == p2) return e;
-                e = e.pair.next;
-            } while (e!=this.e);
             return null;
         }
 
+        private void glNormal(GL gl) {
+            Vec norm = norm();
+            gl.glNormal3f(norm.x, norm.y, norm.z);
+        }
         public Vec norm() {
             Vec norm = new Vec(0, 0, 0);
-            E e = this.e;
-            do {
-                if (e.t != null) norm = norm.plus(e.t.norm().times((float)e.prev.angle()));
-                e = e.pair.next;
-            } while(e != this.e);
+            for(E e = this.e; e!=null; e=e.pair.next==this.e?null:e.pair.next)
+                if (e.t != null)
+                    norm = norm.plus(e.t.norm().times((float)e.prev.angle()));
             return norm.norm();
         }
 
-        public boolean isBoundTo(Vert p) {
-            Vert px = p;
-            do {
-                if (px==this) return true;
-                px = px.bound_to;
-            } while(px != p);
-            return false;
-        }
-        public void unbind() { bound_to = this; binding = new Matrix(); }
-        public void bind(Vert p) { bind(p, new Matrix()); }
-        public void bind(Vert p, Matrix binding) {
-            if (isBoundTo(p)) return;
-            Vert temp_bound_to = p.bound_to;
-            Matrix temp_binding = p.binding;
-            p.bound_to = this.bound_to;
-            p.binding = binding.times(this.binding); // FIXME: may have order wrong here
-            this.bound_to = temp_bound_to;
-            this.binding = temp_binding.times(temp_binding); // FIXME: may have order wrong here
-        }
+        public void bindTo(Vertex p) { bindTo(Matrix.ONE, p); }
     }
 
-    public class BindingGroup {
-        private HashSet<E> set = new HashSet<E>();
-        public BindingGroup bind_others;
-        public BindingGroup other() { return bind_others; }
-        public BindingGroup(BindingGroup bind_others) { this.bind_others = bind_others; }
-        public BindingGroup() {
-            this.bind_others = new BindingGroup(this);
-        }
-        public void add(E e) {
-            if (set.contains(e)) return;
-            for (E epeer : e.bind_peers.set) {
-                epeer.bind_peers = this;
-                set.add(epeer);
-            }
-            for (E eother : e.bind_to.set) {
-                eother.bind_to = bind_others;
-                bind_others.add(eother);
-            }
-            /*
-            for(E ex : (!swap ? right : left)) {
-                if (e.prev.isBoundTo(ex.prev)) {
-                    System.out.println("hit!");
-                }
-            }
-            */
-        }
-        public void dobind(E e) {
-            for(E ebound : set) {
-                e.p1.bind(ebound.p2);
-                e.p2.bind(ebound.p1);
-            }
-        }
-        public void shatter(BindingGroup bg1, BindingGroup bg2) {
-            for(E e : set) {
-                e.shatter(e.midpoint(), bg1, bg2, false);
-            }
-        }
-    }
 
     /** [UNIQUE] an edge */
-    public final class E implements Comparable<E> {
+    public final class E extends HasBindingGroup implements Comparable<E> {
 
-        public final Vert p1, p2;
+        public final Vertex p1, p2;
         T t;     // triangle to our "left"
         E prev;  // previous half-edge
         E next;  // next half-edge
         E pair;  // partner half-edge
-        public BindingGroup bind_peers  = new BindingGroup();
-        public BindingGroup bind_to     = bind_peers.other();
         boolean shattered = false;
 
-        public int compareTo(E e) { return e.length() > length() ? 1 : -1; }
-        public void bindEdge(E e) { bind_to.add(e); }
-        public void dobind() { bind_to.dobind(this); }
-
-        public Point shatter() { return shatter(midpoint(), null, null, false); }
-        public Point shatter(Point mid, BindingGroup bg1, BindingGroup bg2, boolean swap) {
-            if (shattered) return mid;
-            shattered = true;
+        public boolean intersects(T t) { return t.intersects(p1.p, p2.p); }
+
+        public Segment getSegment() { return new Segment(p1.getPoint(), p2.getPoint()); }
+
+        public void bindingGroupChanged(edu.berkeley.qfat.geom.BindingGroup newBindingGroup_) {
+
+            edu.berkeley.qfat.geom.BindingGroup<E> newBindingGroup =
+                (edu.berkeley.qfat.geom.BindingGroup<E>)newBindingGroup_;
+            if (newBindingGroup==null) return;
+            if (this==newBindingGroup.getMaster()) return;
+            HashSet<E> nbg = new HashSet<E>();
+            for(E eother : (Iterable<E>)newBindingGroup) nbg.add(eother);
+            for(E eother : nbg) {
+                if (next==null || prev==null) continue;
+                if (eother.next==null || eother.prev==null) continue;
+
+                if (next.isBoundTo(eother.pair.prev.pair) && !prev.isBoundTo(eother.pair.next.pair))
+                    prev.bindTo(next.getBindingMatrix(eother.pair.prev.pair), eother.pair.next.pair);
+                if (!next.isBoundTo(eother.pair.prev.pair) && prev.isBoundTo(eother.pair.next.pair))
+                    next.bindTo(prev.getBindingMatrix(eother.pair.next.pair), eother.pair.prev.pair);
+
+                /*
+                if (next.isBoundTo(eother.prev) && !prev.isBoundTo(eother.next))
+                    prev.bindTo(next.getBindingMatrix(eother.prev), eother.next);
+                if (!next.isBoundTo(eother.prev) && prev.isBoundTo(eother.next))
+                    next.bindTo(prev.getBindingMatrix(eother.next), eother.prev);
+                */
+                if (next.isBoundTo(eother.next) && !prev.isBoundTo(eother.prev))
+                    prev.bindTo(next.getBindingMatrix(eother.next), eother.prev);
+                if (!next.isBoundTo(eother.next) && prev.isBoundTo(eother.prev))
+                    next.bindTo(prev.getBindingMatrix(eother.prev), eother.next);
+            }
 
-            Vert r = next.p2;
-            E next = this.next;
-            E prev = this.prev;
+        }
 
-            if (bg1==null) bg1 = new BindingGroup();
-            if (bg2==null) bg2 = new BindingGroup();
-            bind_peers.shatter(bg1, bg2);
-            bind_to.shatter(bg2.other(), bg1.other());
-            pair.shatter();
-            destroy();
+        public float stretchRatio() {
+            Vertex nearest = error_against.nearest(midpoint());
+            float nearest_distance = midpoint().distance(nearest.p);
+            float other_distance =
+                (p1.p.distance(error_against.nearest(p1.p).p)+
+                 p2.p.distance(error_against.nearest(p2.p).p))/2;
+            return nearest_distance/other_distance;
+        }
+        public float comparator() {
+            return length();
+        }
+        public int compareTo(E e) {
+            return e.comparator() > comparator() ? 1 : -1;
+        }
+        public void bindEdge(E e, Matrix m) {
+            _bindEdge(e, m);
+            pair._bindEdge(e.pair, m);
+        }
+        public void _bindEdge(E e, Matrix m) {
+            e = e.pair;
+            /*
+            //assumes edges are identical length at binding time
+            Vec reflectionPlaneNormal = e.p2.p.minus(e.p1.p).norm();
+            float a = reflectionPlaneNormal.x;
+            float b = reflectionPlaneNormal.y;
+            float c = reflectionPlaneNormal.z;
+            Matrix reflectionMatrix =
+                new Matrix( 1-2*a*a,  -2*a*b,  -2*a*c, 0,
+                            -2*a*b,  1-2*b*b,  -2*b*c, 0,
+                            -2*a*c,   -2*b*c, 1-2*c*c, 0,
+                            0,       0,       0,       1);
+            m = m.times(Matrix.translate(e.midpoint().minus(Point.ORIGIN))
+                        .times(reflectionMatrix)
+                        .times(Matrix.translate(Point.ORIGIN.minus(e.midpoint()))));
+            System.out.println(reflectionPlaneNormal);
+            System.out.println("  " + p1.p + " " + m.times(e.p1.p));
+            System.out.println("  " + p2.p + " " + m.times(e.p2.p));
+            */
+            /*
+            if (m.times(e.p1.p).minus(p1.p).mag() > EPSILON) throw new Error();
+            if (m.times(e.p2.p).minus(p2.p).mag() > EPSILON) throw new Error();
+            */
+            this.bindTo(m, e);
+        }
+        
+        public void dobind() {
+            for(E e : (Iterable<E>)getBoundPeers()) {
+                if (e==this) continue;
+                p1.bindTo(getBindingMatrix(e), e.p1);
+                p2.bindTo(getBindingMatrix(e), e.p2);
+                e.p1.setConstraint(getConstraint());
+                e.p2.setConstraint(getConstraint());
+            }
+        }
 
-            newT(r.p, p1.p, mid, null);
-            newT(r.p, mid, p2.p, null);
-            bg1.add(p1.getE(mid));
-            bg2.add(p2.getE(mid).pair);
-            return mid;
+        public Point shatter() {
+            if (shattered || destroyed) return null;
+            shattered = true;
+            E first = null;
+            E firste = null;
+            E firstx = null;
+            E firstq = null;
+            for(E e : (Iterable<E>)getBoundPeers()) {
+                E enext = e.next;
+                E eprev = e.prev;
+                E pnext = e.pair.next;
+                E pprev = e.pair.prev;
+                Point mid = e.midpoint();
+                Vertex r = e.next.p2;
+                Vertex l = e.pair.next.p2;
+                if (!e.destroyed) {
+                    e.destroy();
+                    e.pair.destroy();
+                    newT(r.p, e.p1.p, mid,    null, 0);
+                    newT(r.p, mid,    e.p2.p, null, 0);
+                    newT(l.p, mid,    e.p1.p, null, 0);
+                    newT(l.p, e.p2.p, mid,    null, 0);
+                }
+            }
+            for(E e : (Iterable<E>)getBoundPeers()) {
+                Point mid = e.midpoint();
+                if (first==null) {
+                    first = e.p1.getE(mid);
+                    firste = e;
+                    firstx = e.pair;
+                    firstq = e.p2.getE(mid).pair;
+                    continue;
+                }
+                e.p1.getE(mid).          bindTo(e.getBindingMatrix(firste), first);
+                e.p1.getE(mid).pair.     bindTo(e.getBindingMatrix(firste), first.pair);
+                e.p2.getE(mid).pair.     bindTo(e.getBindingMatrix(firste), firstq);
+                e.p2.getE(mid).pair.pair.bindTo(e.getBindingMatrix(firste), firstq.pair);
+            }
+            /*
+            first.setConstraint(firste.getConstraint());
+            firstq.setConstraint(firste.getConstraint());
+            */
+            return null;
         }
 
         public boolean destroyed = false;
@@ -401,45 +562,54 @@ public class Mesh implements Iterable<Mesh.T> {
             if (destroyed) return;
             destroyed = true;
             pair.destroyed = true;
+
+            if (t != null) t.destroy();
+            t = null;
+
+            if (pair.t != null) pair.t.destroy();
+            pair.t = null;
+
             if (next.t != null) next.t.destroy();
             if (prev.t != null) prev.t.destroy();
             next.t = null;
             prev.t = null;
+
+            if (pair.next.t != null) pair.next.t.destroy();
+            if (pair.prev.t != null) pair.next.t.destroy();
             pair.next.t = null;
             pair.prev.t = null;
-            this.bind_to = null;
-            pair.bind_to = null;
-            this.bind_peers = null;
-            pair.bind_peers = null;
+
             pair.prev.next = next;
             next.prev = pair.prev;
             prev.next = pair.next;
             pair.next = prev;
             if (p1.e == this) p1.e = prev.next;
             if (pair.p1.e == pair) pair.p1.e = pair.prev.next;
-            avgedge -= this.length();
-            avgedge -= pair.length();
-            numedges--;
-            numedges--;
         }
 
         private void sync() {
             this.prev.next = this;
             this.next.prev = this;
             this.pair.pair = this;
-            bind_peers.add(this);
             if (this.next.p1 != p2) throw new Error();
             if (this.prev.p2 != p1) throw new Error();
             if (this.p1.e == null) this.p1.e = this;
-            if (!added) {
-                added = true;
-                numedges++;
-                avgedge += length();
-            }
+            if (!added) added = true;
         }
         private boolean added = false;
 
-        public T makeT() { return t==null ? (t = new T(this)) : t; }
+        public T makeT(int colorclass) { return t==null ? (t = new T(this, colorclass)) : t; }
+
+        public double dihedralAngle() {
+            Vec v1 = t.norm().times(-1);
+            Vec v2 = pair.t.norm().times(-1);
+            double prod = v1.norm().dot(v2.norm());
+            prod = Math.min(1,prod);
+            prod = Math.max(-1,prod);
+            double ret = Math.acos(prod);
+            if (Double.isNaN(ret)) throw new Error("nan! " + prod);
+            return ret;
+        }
 
         /** angle between this half-edge and the next */
         public double angle() {
@@ -448,10 +618,16 @@ public class Mesh implements Iterable<Mesh.T> {
             return Math.acos(v1.norm().dot(v2.norm()));
         }
 
+        public Vertex getOther(Vertex v) {
+            if (this.p1 == v) return p2;
+            if (this.p2 == v) return p1;
+            throw new Error();
+        }
+
         public void makeAdjacent(E e) {
             if (this.next == e) return;
             if (p2 != e.p1) throw new Error("cannot make adjacent -- no shared vertex");
-            if (t != null || e.t != null) throw new Error("cannot make adjacent -- edges not both free");
+            if (t != null || e.t != null) throw new Error("cannot make adjacent -- edges not both free ");
 
             E freeIncident = p2.getFreeIncident(e, this);
 
@@ -470,10 +646,10 @@ public class Mesh implements Iterable<Mesh.T> {
 
         /** creates an isolated edge out in the middle of space */
         public E(Point p1, Point p2) {
-            if (pointset.get(p1) != null) throw new Error();
-            if (pointset.get(p2) != null) throw new Error();
-            this.p1 = new Vert(p1);
-            this.p2 = new Vert(p2);
+            if (vertices.get(p1) != null) throw new Error();
+            if (vertices.get(p2) != null) throw new Error();
+            this.p1 = new Vertex(p1);
+            this.p2 = new Vertex(p2);
             this.prev = this.next = this.pair = new E(this, this, this);
             this.p1.e = this;
             this.p2.e = this.pair;
@@ -482,9 +658,9 @@ public class Mesh implements Iterable<Mesh.T> {
 
         /** adds a new half-edge from prev.p2 to p2 */
         public E(E prev, Point p) {
-            Vert p2;
-            p2 = pointset.get(p);
-            if (p2 == null) p2 = new Vert(p);
+            Vertex p2;
+            p2 = vertices.get(p);
+            if (p2 == null) p2 = new Vertex(p);
             this.p1 = prev.p2;
             this.p2 = p2;
             this.prev = prev;
@@ -513,84 +689,15 @@ public class Mesh implements Iterable<Mesh.T> {
             sync();
         }
         public Point midpoint() { return new Point((p1.p.x+p2.p.x)/2, (p1.p.y+p2.p.y)/2, (p1.p.z+p2.p.z)/2); }
-        public boolean has(Vert v) { return v==p1 || v==p2; }
+        public boolean has(Vertex v) { return v==p1 || v==p2; }
         public float length() { return p1.p.minus(p2.p).mag(); }
         public String toString() { return p1+"->"+p2; }
 
-        public boolean intersects(T t) {
-            double A0=t.v1().p.x, A1=t.v1().p.y, A2=t.v1().p.z;
-            double B0=t.v2().p.x, B1=t.v2().p.y, B2=t.v2().p.z;
-            double C0=t.v3().p.x, C1=t.v3().p.y, C2=t.v3().p.z;
-            double j0=p1.p.x, j1=p1.p.y, j2=p1.p.z;
-            double k0=p2.p.x, k1=p2.p.y, k2=p2.p.z;
-            double J0, J1, J2;
-            double K0, K1, K2;
-            double i0, i1, i2;
-            double a0, a1, a2;
-            double b0, b1, b2;
-            double c0, c1, c2;
-            double in_det;
-            double R00, R01, R02, R03,
-                R10, R11, R12, R13,
-                R20, R21, R22, R23,
-                R30, R31, R32, R33;
-
-
-            /* a = B - A */
-            a0 = B0 - A0; 
-            a1 = B1 - A1; 
-            a2 = B2 - A2;
-            /* b = C - B */
-            b0 = C0 - A0;
-            b1 = C1 - A1;
-            b2 = C2 - A2;
-            /* c = a &times; b */
-            c0 = a1 * b2 - a2 * b1;
-            c1 = a2 * b0 - a0 * b2;
-            c2 = a0 * b1 - a1 * b0;
-            /* M^(-1) = (1/det(M)) * adj(M) */
-            in_det = 1 / (c0 * c0 + c1 * c1 + c2 * c2);
-            R00 = (b1 * c2 - b2 * c1) * in_det;
-            R01 = (b2 * c0 - b0 * c2) * in_det;
-            R02 = (b0 * c1 - b1 * c0) * in_det;
-            R10 = (c1 * a2 - c2 * a1) * in_det;
-            R11 = (c2 * a0 - c0 * a2) * in_det;
-            R12 = (c0 * a1 - c1 * a0) * in_det;
-            R20 = (c0) * in_det;
-            R21 = (c1) * in_det;
-            R22 = (c2) * in_det;
-  
-            /* O = M^(-1) * A */
-            R03 = -(R00 * A0 + R01 * A1 + R02 * A2);
-            R13 = -(R10 * A0 + R11 * A1 + R12 * A2);
-            R23 = -(R20 * A0 + R21 * A1 + R22 * A2);
-            /* fill in last row of 4x4 matrix */
-            R30 = R31 = R32 = 0;
-            R33 = 1;
-  
-            J2 = R20 * j0 + R21 * j1 + R22 * j2 + R23;
-            K2 = R20 * k0 + R21 * k1 + R22 * k2 + R23;
-            if (J2 * K2 >= 0) return false;
-
-            J0 = R00 * j0 + R01 * j1 + R02 * j2 + R03;
-            K0 = R00 * k0 + R01 * k1 + R02 * k2 + R03;
-            i0 = J0 + J2 * ((K0 - J0) / (J2 - K2));
-            if (i0 < 0 || i0 > 1) return false;
-  
-            J1 = R10 * j0 + R11 * j1 + R12 * j2 + R13;
-            K1 = R10 * k0 + R11 * k1 + R12 * k2 + R13;
-            i1 = J1 + J2 * ((K1 - J1) / (J2 - K2));
-            if (i1 < 0 || i1 > 1 || i0 + i1 > 1) return false;
-
-            return true;            
-        }
     }
 
     public E makeE(Point p1, Point p2) {
-        Vert v1 = pointset.get(p1);
-        Vert v2 = pointset.get(p2);
+        Vertex v1 = vertices.get(p1);
+        Vertex v2 = vertices.get(p2);
         if (v1 != null && v2 != null) {
             E e = v1.getE(v2);
             if (e != null) return e;
@@ -601,7 +708,22 @@ public class Mesh implements Iterable<Mesh.T> {
         if (v2 != null) return new E(v2.getFreeIncident(), p1).pair;
         return new E(p1, p2);
     }
-    public T newT(Point p1, Point p2, Point p3, Vec norm) {
+    public boolean coalesce = false;
+    private static float round(float f) {
+        return Math.round(f*1000)/1000f;
+    }
+    public T newT(Point p1, Point p2, Point p3, Vec norm, int colorclass) {
+        if (coalesce) {
+
+            for(Vertex v : vertices) { if (p1.distance(v.p) < EPSILON) { p1 = v.p; break; } }
+            for(Vertex v : vertices) { if (p2.distance(v.p) < EPSILON) { p2 = v.p; break; } }
+            for(Vertex v : vertices) { if (p3.distance(v.p) < EPSILON) { p3 = v.p; break; } }
+            /*
+            p1 = new Point(round(p1.x), round(p1.y), round(p1.z));
+            p2 = new Point(round(p2.x), round(p2.y), round(p2.z));
+            p3 = new Point(round(p3.x), round(p3.y), round(p3.z));
+            */
+        }
         if (norm != null) {
             Vec norm2 = p3.minus(p1).cross(p2.minus(p1));
             float dot = norm.dot(norm2);
@@ -616,44 +738,24 @@ public class Mesh implements Iterable<Mesh.T> {
             e23.makeAdjacent(e31);
             e31.makeAdjacent(e12);
         }
-        T ret = e12.makeT();
+        T ret = e12.makeT(colorclass);
         if (e12.t == null) throw new Error();
         if (e23.t == null) throw new Error();
         if (e31.t == null) throw new Error();
         return ret;
     }
 
-
-    public class FaceIterator implements Iterator<T> {
-        private HashSet<T> visited = new HashSet<T>();
-        private LinkedList<T> next = new LinkedList<T>();
-        public FaceIterator() { }
-        public FaceIterator(Vert v) { next.addFirst(v.e.t); }
-        public boolean hasNext() { return next.peek()!=null; }
-        public void remove() { throw new Error(); }
-        public T next() {
-            T ret = next.removeFirst();
-            if (ret == null) return null;
-            visited.add(ret);
-            T t1 = ret.e1().pair.t;
-            T t2 = ret.e2().pair.t;
-            T t3 = ret.e3().pair.t;
-            if (t1 != null && !visited.contains(t1)) next.addFirst(t1);
-            if (t2 != null && !visited.contains(t2)) next.addFirst(t2);
-            if (t3 != null && !visited.contains(t3)) next.addFirst(t3);
-            return ret;
-        }
-    }
-
+    private int max_serial = 0;
     /** [UNIQUE] a triangle (face) */
     public final class T extends Triangle {
         public final E e1;
         public final int color;
+        public final int colorclass;
 
-        public void destroy() {
-        }
+        public final int serial = max_serial++;
+        public boolean occluded;
 
-        T(E e1) {
+        T(E e1, int colorclass) {
             this.e1 = e1;
             E e2 = e1.next;
             E e3 = e2.next;
@@ -675,18 +777,47 @@ public class Mesh implements Iterable<Mesh.T> {
                 break;
             }
             this.color = color;
+            this.colorclass = colorclass;
+            triangles.add(this);
         }
         public E e1() { return e1; }
         public E e2() { return e1.next; }
         public E e3() { return e1.prev; }
-        public Vert v1() { return e1.p1; }
-        public Vert v2() { return e1.p2; }
-        public Vert v3() { return e1.next.p2; }
+        public Vertex v1() { return e1.p1; }
+        public Vertex v2() { return e1.p2; }
+        public Vertex v3() { return e1.next.p2; }
         public Point p1() { return e1.p1.p; }
         public Point p2() { return e1.p2.p; }
         public Point p3() { return e1.next.p2.p; }
         public boolean hasE(E e) { return e1==e || e1.next==e || e1.prev==e; }
-        public boolean has(Vert v) { return v1()==v || v2()==v || v3()==v; }
-    }
+        public boolean has(Vertex v) { return v1()==v || v2()==v || v3()==v; }
+
+        public void removeFromRTree() { triangles.remove(this); }
+        public void addToRTree() { triangles.insert(this); }
+        public void destroy() { triangles.remove(this); }
+        public void reinsert() { triangles.remove(this); triangles.add(this); }
+
+        public boolean shouldBeDrawn() {
 
+            if (e1().bindingGroupSize() <= 1) return false;
+            if (e2().bindingGroupSize() <= 1) return false;
+            if (e3().bindingGroupSize() <= 1) return false;
+
+            return true;
+        }
+
+        public void glTriangle(GL gl, Matrix m) {
+            gl.glPushName(serial);
+            gl.glBegin(GL.GL_TRIANGLES);
+            glVertices(gl, m);
+            gl.glEnd();
+            gl.glPopName();
+        }
+
+        /** issue gl.glVertex() for each of the triangle's points */
+        public void glVertices(GL gl, Matrix m) {
+            if (!shouldBeDrawn()) return;
+            super.glVertices(gl, m);
+        }
+    }
 }