X-Git-Url: http://git.megacz.com/?p=anneal.git;a=blobdiff_plain;f=src%2Fedu%2Fberkeley%2Fqfat%2FMain.java;h=82944767eeab1a8e60a7b52f47147e1c11d7f382;hp=b774066000443e5e9cb28c6922b12f1e56006e14;hb=85a39fe7780fd06019b267db6b2854af1a840d0f;hpb=b6875b8bd79c804e15eb75bc64044ca2c770b07d

diff --git a/src/edu/berkeley/qfat/Main.java b/src/edu/berkeley/qfat/Main.java
index b774066..8294476 100644
--- a/src/edu/berkeley/qfat/Main.java
+++ b/src/edu/berkeley/qfat/Main.java
@@ -1,465 +1,1224 @@
 package edu.berkeley.qfat;
 import java.awt.*;
+import java.io.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.media.opengl.*;
 import javax.media.opengl.glu.*;
 import java.util.*;
+import edu.berkeley.qfat.bind.*;
 import edu.berkeley.qfat.geom.*;
+import edu.berkeley.qfat.stl.*;
+import edu.berkeley.qfat.voxel.*;
 import edu.berkeley.qfat.geom.Point;
+import edu.berkeley.qfat.geom.Polygon;
 
-// FIXME: recenter goal to have centroid coincident with tile
-// FIXME: re-orient goal (how?)
-//        fish case: ensure that spinal axis of fish is the x-axis of the tile
+/*
 
-public class Main implements GLEventListener, MouseListener, MouseMotionListener, KeyListener, MouseWheelListener {
-    
-    boolean alt = false;
-    boolean shift = false;
-    boolean control = false;
+Todo
+- review catmull-clark; move vertex points?
+- re-anneal fish
 
-    public void mouseWheelMoved(MouseWheelEvent e) {
-        tz -= e.getWheelRotation();
-    }
+- show constraints (?)
+- show in red if user tries to move a point to an illegal location
+
+- eliminate use of bindinggroupschanged()
+
+- post qfat on my software page
+
+
+With Sequin
+- constraints admit intersections (lattice)
+- constraints may be transformed linearly
+
+Log console
+  - blend-shaded overlay?  slick.
+
+face/vertex count
+rendering FPS
+ability to not draw edges between faces
+
+
+three circumcircles showing crystal ball -- these don't get scaled
+axes?
+
+drawing modes:
+  - bounding box
+  - vertices
+  - edges
+  - visible-edges
+  - flat with or without edges
+  - shaded with or without edges
+  * contrasting-faces
+
+
+quadric decimation?
+
+show normals
+show bounding box
+show axes (big+fat)
+ */
+
+// TO DO:
+//
+// - Ability to snap three views to orthgonal
+// - SLIDE UI
+//     - left button -> crystal ball
+//     - translate
+//     - rightbutton/mousewheel zoom
+// - v+click to select vertex
+// - show: constraints, bindings, faces
+//
+// Editing:
+//  - fracture edge, face
+//  - change aspect ratio
+//  - translate, rotate goal mesh
+//  - ability to select a point, rotate the model, then move the point
+//  - when moving a vertex in one window, show that window's axes in all other windows
+//
+
+/*
+  blender keys
+  - middle mouse = option+click
+  - right mouse = command+click
+
+  3,7,1 = view along axes (control for opp direction)
+  4, 8, 7, 2 = rotate in discrete increments (+control to translate)
+  middle trag: rotate space
+  shift+middle drag: translate space
+  wheel: zoom
+  home: home view: take current angle, zoom to whole scnee
+  5 = ortho vs non-ortho
+*/
+
+/*
+Meshlab Notes:
+Log console
+  - blend-shaded overlay?  slick.
+
+face/vertex count
+rendering FPS
+ability to not draw edges between faces
+
+
+three circumcircles showing crystal ball -- these don't get scaled
+axes?
+
+drawing modes:
+  - bounding box
+  - vertices
+  - edges
+  - visible-edges
+  - flat with or without edges
+  - shaded with or without edges
+  * contrasting-faces
 
-    public void keyTyped(KeyEvent e)  { }
-    public void keyPressed(KeyEvent e)  {
-        switch(e.getKeyCode()) {
-            case KeyEvent.VK_CONTROL: control = true; break;
-            case KeyEvent.VK_ALT: alt = true; break;
-            case KeyEvent.VK_SHIFT: shift = true; break;
+
+quadric decimation?
+
+show normals
+show bounding box
+show axes (big+fat)
+ */
+
+public class Main extends InteractiveMeshViewer {
+
+    public static int verts = 1;
+
+    public static final Random random = new Random();
+    
+    /** magnification factor */
+    private static final float MAG = 1;
+    public static final float MATCHING_EPSILON = 0.001f;
+
+    private static boolean small(float f) { return Math.abs(f) < 0.001; }
+    public void generateTile(Matrix[] matrices, Mesh mesh) {
+        mesh.coalesce = true;
+        HashSet<HalfSpace> halfSpaces = new HashSet<HalfSpace>();
+        HashSet<Polygon> polygons = new HashSet<Polygon>();
+        for(Matrix m : matrices) {
+                Vec v = m.getTranslationalComponent();
+                if (v.mag() < 0.0001) continue;
+                v = v.times(-1);
+                v = v.times(0.5f);
+                Point p = Point.ZERO.plus(v);
+                v = v.times(-1);
+                
+                //System.out.println(v);
+                HalfSpace hs = new HalfSpace(p, v.norm());
+                halfSpaces.add(hs);
+                polygons.add(new Polygon(hs));
         }
-    }
-    public void keyReleased(KeyEvent e) {
-        switch(e.getKeyCode()) {
-            case KeyEvent.VK_CONTROL: control = false; break;
-            case KeyEvent.VK_ALT: alt = false; break;
-            case KeyEvent.VK_SHIFT: shift = false; break;
+        for(Polygon p : polygons) {
+            System.out.println(p.plane.norm() + " " + p.plane.d);
+            for(HalfSpace hs : halfSpaces) {
+                if (p.plane==hs) continue;
+                p = p.intersect(hs);
+            }
+            p.tesselate(mesh);
         }
     }
 
-    public void mouseClicked(MouseEvent e) { }
-    public void mouseEntered(MouseEvent e) { }
-    public void mouseExited(MouseEvent e) { }
-    public void mousePressed(MouseEvent e) { }
-    public void mouseReleased(MouseEvent e) { }
-
-    int mousex;
-    int mousey;
-    public void mouseMoved(MouseEvent e) {
-        mousex = e.getX();
-        mousey = e.getY();
+    private void quad(Mesh mesh, Matrix m, Point p1_, Point p2_, Point p3_, Point p4_) {
+        Point p1 = m.times(p1_);
+        Point p2 = m.times(p2_);
+        Point p3 = m.times(p3_);
+        Point p4 = m.times(p4_);
+        Point c  = new Point((p1.x+p2.x+p3.x+p4.x)/4,
+                             (p1.y+p2.y+p3.y+p4.y)/4,
+                             (p1.z+p2.z+p3.z+p4.z)/4);
+        mesh.newT(p1, p2, c, null, 0);
+        mesh.newT(p2, p3, c, null, 0);
+        mesh.newT(p3, p4, c, null, 0);
+        mesh.newT(p4, p1, c, null, 0);
     }
 
-    float tx = 0;
-    float ty = 0;
-    float tz = 0;
-    float anglex = 0;
-    float angley = 0;
-    public void mouseDragged(MouseEvent e) {
-        if (shift) {
-            tx += (mousex - e.getX())/(float)20;
-            ty += (mousey - e.getY())/(float)20;
-        } else {
-            anglex -= mousex - e.getX();
-            angley += mousey - e.getY();
+    public void loadGoal(String file) {
+        try {
+            StlFile stlf = new StlFile();
+            InputStream res = this.getClass().getClassLoader().getResourceAsStream(file);
+            stlf.readBinaryFile(file, res);
+            setGoal(new Mesh(false));
+            for(int i=0; i<stlf.coordArray.length; i+=3) {
+                Point p0 = new Point(stlf.coordArray[i+0].x * MAG, stlf.coordArray[i+0].y * MAG, stlf.coordArray[i+0].z * MAG);
+                Point p1 = new Point(stlf.coordArray[i+1].x * MAG, stlf.coordArray[i+1].y * MAG, stlf.coordArray[i+1].z * MAG);
+                Point p2 = new Point(stlf.coordArray[i+2].x * MAG, stlf.coordArray[i+2].y * MAG, stlf.coordArray[i+2].z * MAG);
+                Vec n    = new Vec(stlf.normArray[i/3].x * MAG, stlf.normArray[i/3].y  * MAG, stlf.normArray[i/3].z * MAG);
+                Mesh.T t  = goal.newT(p0, p1, p2, n, 0);
+            }
+            float goal_width  = goal.diagonal().dot(new Vec(1, 0, 0));
+            float goal_height = goal.diagonal().dot(new Vec(0, 1, 0));
+            float goal_depth  = goal.diagonal().dot(new Vec(0, 0, 1));
+            
+        } catch (Exception e) { throw new RuntimeException(e);}
+    }
+    public void fixupGoal() { fixupGoal(true, true); }
+    public void fixupGoal(boolean recenter, boolean lock) {
+        // translate to match centroid
+        if (recenter)
+            goal.transform(Matrix.translate(tile.centroid().minus(goal.centroid())));
+        if (lock) {
+            goal.makeVerticesImmutable();
+            tile.error_against = goal;
+            goal.error_against = tile;
         }
-        mousex = e.getX();
-        mousey = e.getY();
     }
 
-    private Mesh tile = new Mesh();
-    private Mesh goal = new Mesh();
+    public Main(JFrame f) { super(f); }
 
-    /** magnification factor */
-    private static final float MAG = 1;
+    public synchronized void fixupTile() { 
+        for(Matrix m1 : transforms) {
+            for(Matrix m2 : transforms) {
+                if (m1==m2) continue;
+                for(Mesh.T t1 : tile) {
+                    for(Mesh.T t2 : tile) {
+
+                        Matrix m = m1.inverse().times(m2);
+                        Point t1v1 = m.times(t1.v1().p);
+                        Point t1v2 = m.times(t1.v2().p);
+                        Point t1v3 = m.times(t1.v3().p);
 
-    Matrix[] translations;
-    Mesh.Vert[] points;
+                        if (t1v1.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v2.distance(t2.v3().p) < MATCHING_EPSILON &&
+                            t1v3.distance(t2.v2().p) < MATCHING_EPSILON) {
+                            t2.e3().bindEdge(t1.e1().pair, m);
+                            t2.e2().bindEdge(t1.e2().pair, m);
+                            t2.e1().bindEdge(t1.e3().pair, m);
+                        }
+                        if (t1v2.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v3.distance(t2.v3().p) < MATCHING_EPSILON &&
+                            t1v1.distance(t2.v2().p) < MATCHING_EPSILON) {
+                            t2.e3().bindEdge(t1.e2().pair, m);
+                            t2.e2().bindEdge(t1.e3().pair, m);
+                            t2.e1().bindEdge(t1.e1().pair, m);
+                        }
+                        if (t1v3.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v1.distance(t2.v3().p) < MATCHING_EPSILON &&
+                            t1v2.distance(t2.v2().p) < MATCHING_EPSILON) {
+                            t2.e3().bindEdge(t1.e3().pair, m);
+                            t2.e2().bindEdge(t1.e1().pair, m);
+                            t2.e1().bindEdge(t1.e2().pair, m);
+                        }
 
-    public Main(StlFile stlf) {
+                        if (t1v1.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v2.distance(t2.v2().p) < MATCHING_EPSILON &&
+                            t1v3.distance(t2.v3().p) < MATCHING_EPSILON) {
+                            t2.e1().bindEdge(t1.e1(), m);
+                            t2.e2().bindEdge(t1.e2(), m);
+                            t2.e3().bindEdge(t1.e3(), m);
+                        }
+                        if (t1v2.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v3.distance(t2.v2().p) < MATCHING_EPSILON &&
+                            t1v1.distance(t2.v3().p) < MATCHING_EPSILON) {
+                            t2.e2().bindEdge(t1.e1(), m);
+                            t2.e3().bindEdge(t1.e2(), m);
+                            t2.e1().bindEdge(t1.e3(), m);
+                        }
+                        if (t1v3.distance(t2.v1().p) < MATCHING_EPSILON &&
+                            t1v1.distance(t2.v2().p) < MATCHING_EPSILON &&
+                            t1v2.distance(t2.v3().p) < MATCHING_EPSILON) {
+                            t2.e3().bindEdge(t1.e1(), m);
+                            t2.e1().bindEdge(t1.e2(), m);
+                            t2.e2().bindEdge(t1.e3(), m);
+                        }
 
-        for(int i=0; i<stlf.coordArray.length; i+=3) {
-            Point p0 = new Point(stlf.coordArray[i+0].x * MAG, stlf.coordArray[i+0].y * MAG, stlf.coordArray[i+0].z * MAG);
-            Point p1 = new Point(stlf.coordArray[i+1].x * MAG, stlf.coordArray[i+1].y * MAG, stlf.coordArray[i+1].z * MAG);
-            Point p2 = new Point(stlf.coordArray[i+2].x * MAG, stlf.coordArray[i+2].y * MAG, stlf.coordArray[i+2].z * MAG);
-            Vec n  = new Vec(stlf.normArray[i/3].x * MAG, stlf.normArray[i/3].y  * MAG, stlf.normArray[i/3].z * MAG);
-            Mesh.T t  = goal.newT(p0, p1, p2, n);
+                    }
+                }
+            }
         }
+        tile.rebindPoints();
+        System.out.println("tile volume: " + tile.volume());
+        System.out.println("goal volume: " + goal.volume());
+        tile.error_against = goal;
+        goal.error_against = tile;
+        fixupGoal();
+    }
 
-        // rotate to align major axis -- this probably needs to be done by a human.
-        goal.transform(new Matrix(new Vec(0, 0, 1), (float)(Math.PI/2)));
 
+    public class MyMenuItem extends JMenuItem implements ActionListener {
+        public MyMenuItem(String s) {
+            super(s);
+            this.addActionListener(this);
+        }
+        public void actionPerformed(ActionEvent event) {
+            synchronized(Main.this) {
+                    hit();
+            }
+        }
+        public void hit() {}
+    }
 
-        float goal_width  = goal.diagonal().dot(new Vec(1, 0, 0));
-        float goal_height = goal.diagonal().dot(new Vec(0, 1, 0));
-        float goal_depth  = goal.diagonal().dot(new Vec(0, 0, 1));
+    public void marchingCubes() {
+        Mesh mesh = new Mesh(false);
+        mesh.coalesce = true;
+        MarchingCubes.march(new VoxelData() {
+                float radius = 1.0f;
+                public float getMaxX()        { return  1.0f; }
+                public float getMinX()        { return -1.0f; }
+                public int   getNumSamplesX() { return   10; }
+                public float getMaxY()        { return  1.0f; }
+                public float getMinY()        { return -1.0f; }
+                public int   getNumSamplesY() { return   10; }
+                public float getMaxZ()        { return  1.0f; }
+                public float getMinZ()        { return -1.0f; }
+                public int   getNumSamplesZ() { return   10; }
+                public float getSample(Point p) {
+                    double x = p.x;
+                    double y = p.y;
+                    double z = p.z;
+                    return (float)(radius-Math.sqrt(x*x+y*y+z*z));
+                }
+            },
+            mesh);
+        setTile(mesh);
+        //fixupTile();
+    }
 
-        float width  = (float)0.6;
-        float height = (float)0.08;
-        float depth  = (float)0.3;
-        translations = new Matrix[] {
+    public void marchingCubes2() {
+        try {
 
-            new Matrix(new Vec(-(width/2),  height,    0)),
-            new Matrix(new Vec( (width/2),  height,    0)),
-            new Matrix(new Vec(-(width/2), -height,    0)),
-            new Matrix(new Vec( (width/2), -height,    0)),
-            new Matrix(new Vec(-(width/2),       0,  depth)),
-            new Matrix(new Vec( (width/2),       0,  depth)),
-            new Matrix(new Vec(-(width/2),       0, -depth)),
-            new Matrix(new Vec( (width/2),       0, -depth)),
+            final float[][][] samples = new float[256][256][124];
+            double total = 0;
+            int count = 0;
+            for(int i=1; i<=124; i++) {
+                String ix = ""+i;
+                while(ix.length() < 3) ix = "0"+ix;
+                FileInputStream fis = new FileInputStream("/Users/megacz/Desktop/projects/mri brain images/spgr/I."+ix);
+                DataInputStream dis = new DataInputStream(new BufferedInputStream(fis));
+                dis.skip(7904);
+                for(int x=0; x<256; x++)
+                    for(int y=0; y<256; y++) {
+                        short s = dis.readShort();
+                        samples[x][y][i-1] = (float)s;
+                        total += samples[x][y][i-1];
+                        count++;
+                    }
+            }
+            System.out.println("done reading samples; average sample is " + (total/count));
 
-            new Matrix(new Vec( width,           0,    0)),
-            new Matrix(new Vec(-width,           0,    0)),
             /*
-            new Matrix(new Vec(     0,           0,    depth)),
-            new Matrix(new Vec(     0,           0,   -depth)),
+            PrintWriter pw = new PrintWriter(new FileOutputStream("/tmp/out"));
+            pw.println("new short[][][] {");
+            for(int x=0; x<256; x++) {
+                if (x>0) pw.println("  ,");
+                pw.println("  {");
+                for(int y=0; y<256; y++) {
+                    if (y>0) pw.println("    ,");
+                    pw.print("    {");
+                    for(int z=0; z<124; z++) {
+                        if (z>0) pw.print(", ");
+                        if ((z % 20) == 0) {
+                            pw.println();
+                            pw.print("      ");
+                        }
+                        pw.print(shorts[x][y][z]);
+                    }
+                    pw.println();
+                    pw.println("    }");
+                }
+                pw.println("  }");
+            }
+            pw.println("};");
+            pw.flush();
+            pw.close();
             */
-        };
-
-
-        Point ltf = new Point(-(width/2),  (height/2),  (depth/2));
-        Point mtf = new Point( 0.0,        (height/2),  (depth/2));
-        Point rtf = new Point( (width/2),  (height/2),  (depth/2));
-        Point ltn = new Point(-(width/2),  (height/2), -(depth/2));
-        Point mtn = new Point( 0.0,        (height/2), -(depth/2));
-        Point rtn = new Point( (width/2),  (height/2), -(depth/2));
-        Point lbf = new Point(-(width/2), -(height/2),  (depth/2));
-        Point mbf = new Point( 0.0,       -(height/2),  (depth/2));
-        Point rbf = new Point( (width/2), -(height/2),  (depth/2));
-        Point lbn = new Point(-(width/2), -(height/2), -(depth/2));
-        Point mbn = new Point( 0.0,       -(height/2), -(depth/2));
-        Point rbn = new Point( (width/2), -(height/2), -(depth/2));
-        
-        Point[] points = new Point[] {
-            ltf,
-            mtf,
-            rtf,
-            ltn,
-            mtn,
-            rtn,
-            lbf,
-            mbf,
-            rbf,
-            lbn,
-            mbn,
-            rbn
-        };
-
-
-        // top
-        tile.newT(ltf, mtf, mtn, null);
-        tile.newT(mtn, ltn, ltf, null);
-        tile.newT(mtf, rtf, rtn, null);
-        tile.newT(rtn, mtn, mtf, null);
-
-        // bottom (swap normals)
-        tile.newT(mbf, lbf, mbn, null);
-        tile.newT(lbn, mbn, lbf, null);
-        tile.newT(rbf, mbf, rbn, null);
-        tile.newT(mbn, rbn, mbf, null);
-        
-        // left
-        tile.newT(ltf, ltn, lbn, null);
-        tile.newT(lbn, lbf, ltf, null);
-
-        // right (swap normals)
-        tile.newT(rtn, rtf, rbn, null);
-        tile.newT(rbf, rbn, rtf, null);
-
-        // front
-        tile.newT(ltn, mtn, mbn, null);
-        tile.newT(ltn, mbn, lbn, null);
-        tile.newT(mtn, rtn, rbn, null);
-        tile.newT(mtn, rbn, mbn, null);
-
-        // back
-        tile.newT(mtf, ltf, mbf, null);
-        tile.newT(mbf, ltf, lbf, null);
-        tile.newT(rtf, mtf, rbf, null);
-        tile.newT(rbf, mtf, mbf, null);
-
-        for(Matrix m : translations) {
-            for(Mesh.T t1 : tile) {
-                for(Mesh.T t2 : tile) {
-                    if (t1==t2) continue;
-
-                    if ((t1.v1().p.times(m).minus(t2.v1().p).mag() < Mesh.EPSILON) &&
-                        (t1.v2().p.times(m).minus(t2.v3().p).mag() < Mesh.EPSILON) &&
-                        (t1.v3().p.times(m).minus(t2.v2().p).mag() < Mesh.EPSILON)) {
-                        t1.e1().bind(t2.e3().pair);
-                        t1.e2().bind(t2.e2().pair);
-                        t1.e3().bind(t2.e1().pair);
+
+            Mesh mesh = new Mesh(false);
+            mesh.coalesce = true;
+            MarchingCubes.march(new VoxelData() {
+                    float radius = 1.0f;
+                    public float getMaxX()        { return  2.4f; }
+                    public float getMinX()        { return    0f; }
+                    public int   getNumSamplesX() { return   256/10; }
+                    public float getMaxY()        { return  2.4f; }
+                    public float getMinY()        { return    0f; }
+                    public int   getNumSamplesY() { return   256/10; }
+                    public float getMaxZ()        { return 1.86f; }
+                    public float getMinZ()        { return    0f; }
+                    public int   getNumSamplesZ() { return   124/10; }
+                    public float getSample(Point p) {
+                        int x = (int)Math.floor(p.x / ((double)getMaxX() / (double)256));
+                        int y = (int)Math.floor(p.y / ((double)getMaxY() / (double)256));
+                        int z = (int)Math.floor(p.z / ((double)getMaxZ() / (double)124));
+                        if ( (x<0) || (x>=samples.length) ) return 0;
+                        if ( (y<0) || (y>=samples[x].length) ) return 0;
+                        if ( (z<0) || (z>=samples[x][y].length) ) return 0;
+                        return samples[x][y][z];
                     }
-                    if ((t1.v2().p.times(m).minus(t2.v1().p).mag() < Mesh.EPSILON) &&
-                        (t1.v3().p.times(m).minus(t2.v3().p).mag() < Mesh.EPSILON) &&
-                        (t1.v1().p.times(m).minus(t2.v2().p).mag() < Mesh.EPSILON)) {
-                        t1.e2().bind(t2.e3().pair);
-                        t1.e3().bind(t2.e2().pair);
-                        t1.e1().bind(t2.e1().pair);
+                },
+                200,
+                mesh);
+            setTile(mesh);
+            //fixupTile();
+
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    public void hexBrick(boolean offset, boolean rotated) {
+        setTile(new Mesh(false));
+                float width  = (float)0.8;
+                float depth  = (float)0.08;
+                float height = (float)0.4;
+                float rshift =   width/2;
+                float lshift = -(width/2);
+                float halfup = 0;
+                Point ltf = new Point(lshift,  (depth/2),  (height/2));
+                Point mtf = new Point( 0.0,    (depth/2),  (height/2));
+                Point rtf = new Point(rshift,  (depth/2),  (height/2));
+                Point lbf = new Point(lshift, -(depth/2),  (height/2));
+                Point mbf = new Point( 0.0,   -(depth/2),  (height/2));
+                Point rbf = new Point(rshift, -(depth/2),  (height/2));
+
+                Point ltc = new Point(lshift,  (depth/2), 0);
+                Point mtc = new Point( 0.0,    (depth/2), 0);
+                Point rtc = new Point(rshift,  (depth/2), 0);
+                Point lbc = new Point(lshift, -(depth/2), 0);
+                Point mbc = new Point( 0.0,   -(depth/2), 0);
+                Point rbc = new Point(rshift, -(depth/2), 0);
+
+                Point ltn = new Point(lshift,  (depth/2), -(height/2));
+                Point mtn = new Point( 0.0,    (depth/2), -(height/2));
+                Point rtn = new Point(rshift,  (depth/2), -(height/2));
+                Point lbn = new Point(lshift, -(depth/2), -(height/2));
+                Point mbn = new Point( 0.0,   -(depth/2), -(height/2));
+                Point rbn = new Point(rshift, -(depth/2), -(height/2));
+
+        
+                Point[] points = new Point[] {
+                    ltf,
+                    mtf,
+                    rtf,
+                    lbf,
+                    mbf,
+                    rbf,
+
+                    ltc,
+                    mtc,
+                    rtc,
+                    lbc,
+                    mbc,
+                    rbc,
+
+                    ltn,
+                    mtn,
+                    rtn,
+                    lbn,
+                    mbn,
+                    rbn
+                };
+
+
+                // top
+                tile.newT(ltf, mtf, mtc, null, 1);
+                tile.newT(mtc, ltc, ltf, null, 1);
+                tile.newT(mtf, rtf, rtc, null, 1);
+                tile.newT(rtc, mtc, mtf, null, 1);
+
+                tile.newT(ltc, mtc, mtn, null, 1);
+                tile.newT(mtn, ltn, ltc, null, 1);
+                tile.newT(mtc, rtc, rtn, null, 1);
+                tile.newT(rtn, mtn, mtc, null, 1);
+
+                // bottom (swap normals)
+                tile.newT(mbf, lbf, mbc, null, 2);
+                tile.newT(lbc, mbc, lbf, null, 2);
+                tile.newT(rbf, mbf, rbc, null, 2);
+                tile.newT(mbc, rbc, mbf, null, 2);
+
+                tile.newT(mbc, lbc, mbn, null, 2);
+                tile.newT(lbn, mbn, lbc, null, 2);
+
+                tile.newT(rbc, mbc, rbn, null, 2);
+                tile.newT(mbn, rbn, mbc, null, 2);
+
+
+                // left
+                tile.newT(ltf, ltc, lbc, null, 3);
+                tile.newT(lbc, lbf, ltf, null, 3);
+                tile.newT(ltc, ltn, lbn, null, 3);
+                tile.newT(lbn, lbc, ltc, null, 3);
+
+                // right (swap normals)
+                tile.newT(rtc, rtf, rbc, null, 4);
+                tile.newT(rbf, rbc, rtf, null, 4);
+                tile.newT(rtn, rtc, rbn, null, 4);
+                tile.newT(rbc, rbn, rtc, null, 4);
+
+                // front
+                tile.newT(ltn, mtn, mbn, null, 5);
+                tile.newT(ltn, mbn, lbn, null, 5);
+                tile.newT(mtn, rtn, rbn, null, 5);
+                tile.newT(mtn, rbn, mbn, null, 5);
+
+                // back
+                tile.newT(mtf, ltf, mbf, null, 6);
+                tile.newT(mbf, ltf, lbf, null, 6);
+                tile.newT(rtf, mtf, rbf, null, 6);
+                tile.newT(rbf, mtf, mbf, null, 6);
+
+                if (offset) {
+                  transforms = new Matrix[] {
+                      Matrix.translate(new Vec(lshift,      0,    height)),
+                      Matrix.translate(new Vec(lshift,      0,   -height)),
+                      Matrix.translate(new Vec(rshift,      0,    height)),
+                      Matrix.translate(new Vec(rshift,      0,   -height)),
+                      Matrix.translate(new Vec( width,      0,         0)),
+                      Matrix.translate(new Vec(-width,      0,         0)),
+                      Matrix.translate(new Vec(lshift,  depth, 0)),
+                      Matrix.translate(new Vec(lshift, -depth, 0)),
+                      Matrix.translate(new Vec(rshift,  depth, 0)),
+                      Matrix.translate(new Vec(rshift, -depth, 0)),
+                      Matrix.ONE,
+                  };
+                } else if (rotated) {
+                    HashSet<Mesh.E> es = new HashSet<Mesh.E>();
+                    for(Mesh.T t : tile) {
+                        es.add(t.e1());
+                        es.add(t.e2());
+                        es.add(t.e3());
                     }
-                    if ((t1.v3().p.times(m).minus(t2.v1().p).mag() < Mesh.EPSILON) &&
-                        (t1.v1().p.times(m).minus(t2.v3().p).mag() < Mesh.EPSILON) &&
-                        (t1.v2().p.times(m).minus(t2.v2().p).mag() < Mesh.EPSILON)) {
-                        t1.e3().bind(t2.e3().pair);
-                        t1.e1().bind(t2.e2().pair);
-                        t1.e2().bind(t2.e1().pair);
+                    for(Mesh.E e : es) {
+                        if (e.v1.p.x == e.v2.p.x && e.v1.p.y == e.v2.p.y) continue;
+                        if (e.v1.p.z == e.v2.p.z && e.v1.p.y == e.v2.p.y) continue;
+                        if (e.v1.p.x == e.v2.p.x && e.v1.p.z == e.v2.p.z) continue;
+                        e.shatter();
                     }
+                    transforms = new Matrix[] {
+                        Matrix.translate(new Vec(0,   0,    height)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+                        Matrix.translate(new Vec(0,   0,   -height)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+                        Matrix.translate(new Vec(0,  depth, 0)),
+                        Matrix.translate(new Vec(0, -depth, 0)),
+                        Matrix.translate(new Vec( width,  0,    0)),
+                        Matrix.translate(new Vec(-width,  0,    0)),
+                      Matrix.ONE,
+                  };
+                } else {
+                  transforms = new Matrix[] {
+                      Matrix.translate(new Vec(lshift,      0,    height)),
+                      Matrix.translate(new Vec(lshift,      0,   -height)),
+                      Matrix.translate(new Vec(rshift,      0,    height)),
+                      Matrix.translate(new Vec(rshift,      0,   -height)),
+                      Matrix.translate(new Vec( width,      0,         0)),
+                      Matrix.translate(new Vec(-width,      0,         0)),
+                      Matrix.translate(new Vec(0,  depth, 0)),
+                      Matrix.translate(new Vec(0, -depth, 0)),
+                      Matrix.ONE,
+                  };
                 }
-            }
-        }
+                
+                fixupTile();
+    }
 
-        //xMesh.Vert mid = lbf.getE(mbn).shatter();
+    public class MyMenuBar extends JMenuBar {
 
-        // rescale to match volume
-        float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
-        goal.transform(new Matrix(factor));
+        public MyMenuBar() {
 
-        // translate to match centroid
-        goal.transform(new Matrix(tile.centroid().minus(goal.centroid())));
+            JMenu tileMenu = new JMenu("Tile");
+            JMenu goalMenu = new JMenu("Goal");
+            JMenu hideMenu = new JMenu("Actions");
 
-        //tx.e2.shatter();
-        //tx.e3.shatter();
+            hideMenu.add(new MyMenuItem("Start Anneal") { public void hit() { anneal = true; }});
+            hideMenu.add(new MyMenuItem("Stop Anneal") { public void hit() { anneal = false; }});
+            hideMenu.add(new MyMenuItem("Reset to high temperature") { public void hit() { temp = 1; }});
+            hideMenu.add(new MyMenuItem("Subdivide surface") { public void hit() { breaks++; }});
+            hideMenu.add(new MyMenuItem("Show Goal") { public void hit() { goalon = true; }});
+            hideMenu.add(new MyMenuItem("Hide Goal") { public void hit() { goalon = false; }});
+            hideMenu.add(new MyMenuItem("Show All Neighbors") { public void hit() { neighbors = true; }});
+            hideMenu.add(new MyMenuItem("Show One Neighbor Wireframe") { public void hit() { neighborsWireOne = true; }});
+            hideMenu.add(new MyMenuItem("Show All Neighbors Wireframe") { public void hit() { neighborsWire = true; neighborsWireOne = false;}});
+            hideMenu.add(new MyMenuItem("Hide Neighbors") { public void hit() { neighborsWire = false; neighborsWireOne = false; neighbors = false; }});
 
+            goalMenu.add(new MyMenuItem("Fish with face") { public void hit() {
+                loadGoal("face.stl");
+                //goal.transform(Matrix.rotate(new Vec(0, 1, 0), (float)(Math.PI/2)));
+                goal.transform(Matrix.rotate(new Vec(0, 0, 1), (float)(Math.PI/2)));
+                //goal.transform(Matrix.scale(1, 2.2f, 1));
+                float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
+                //factor = factor * 0.8f;
+                goal.transform(Matrix.scale(0.3f));
+                //goal.transform(Matrix.rotate(new Vec(0,1,0), (float)(Math.PI*1/3)));
+                goal.transform(Matrix.rotate(new Vec(1,0,0), (float)(Math.PI*1/3)));
+                fixupGoal(true, false);
+                //goal.transform(Matrix.translate(new Vec(0.145f, 0, 0)));
+                fixupGoal(false, true);
+            }});
+            goalMenu.add(new MyMenuItem("Fish") { public void hit() {
+                loadGoal("fish.stl");
+                //goal.transform(Matrix.rotate(new Vec(0, 1, 0), (float)(Math.PI/2)));
+                goal.transform(Matrix.rotate(new Vec(0, 0, 1), (float)(Math.PI/2)));
+                goal.transform(Matrix.scale(1, 2.2f, 1));
+                float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
+                factor = factor * 0.8f;
+                goal.transform(Matrix.scale(factor));
+                fixupGoal(true, false);
+                //goal.transform(Matrix.translate(new Vec(0.145f, 0, 0)));
+                fixupGoal(false, true);
+            }});
+            goalMenu.add(new MyMenuItem("Hammerhead Fish") { public void hit() {
+                loadGoal("fish.stl");
+                goal.transform(Matrix.rotate(new Vec(0, 1, 0), (float)(Math.PI/2)));
+                goal.transform(Matrix.rotate(new Vec(0, 0, 1), (float)(3*Math.PI/2)));
+                float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
+                factor *= 0.75f;
+                goal.transform(Matrix.scale(factor));
+                fixupGoal();
+            }});
+            goalMenu.add(new MyMenuItem("Vertical Fish") { public void hit() {
+                loadGoal("fish.stl");
+                //goal.transform(Matrix.rotate(new Vec(0, 0, 1), (float)(Math.PI/2)));
+                //goal.transform(Matrix.rotate(new Vec(1, 0, 0), (float)(Math.PI/2)));
+                float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
+                goal.transform(Matrix.scale(factor/1.6f));
+                fixupGoal();
+            }});
+            goalMenu.add(new MyMenuItem("Torus") { public void hit() {
+                loadGoal("torus.stl");
+                float factor = (float)Math.pow(tile.volume() / goal.volume(), 1.0/3.0);
+                goal.transform(Matrix.scale(factor/2.5f));
+                goal.transform(Matrix.rotate(new Vec(0, 1, 0), (float)(Math.PI/2)));
+                fixupGoal();
+            }});
+            tileMenu.add(new MyMenuItem("Hex Brick") { public void hit() {
+                hexBrick(false, false);
+            }});
+            tileMenu.add(new MyMenuItem("Hex Brick, offset planes") { public void hit() {
+                hexBrick(true, false);
+            }});
+            tileMenu.add(new MyMenuItem("Hex Brick, rotated") { public void hit() {
+                hexBrick(false, true);
+            }});
+            tileMenu.add(new MyMenuItem("Temp (do not use)") { public void hit() {
+                setTile(new Mesh(false));
+                float width  = (float)0.8;
+                float depth  = (float)0.08;
+                float height = (float)0.4;
 
-        tile.bind();
+                float rshift =   width/2;
+                float lshift = -(width/2);
+                float halfup = 0;
+                //float shift = height/2;
+                //width = (width*2)/3;
+                float shift = 0;
+                transforms = new Matrix[] {
 
-        //mid.move(new Vec((float)0,0,(float)-0.05));
-        //ltn.move(new Vec((float)0,0,(float)-0.05));
+                    Matrix.translate(new Vec(lshift/2,  depth,    -shift)),
+                    Matrix.translate(new Vec(rshift/2,  depth,    -shift)),
+                    Matrix.translate(new Vec(lshift/2, -depth,    -shift)),
+                    Matrix.translate(new Vec(rshift/2, -depth,    -shift)),
 
-        //mtf.move(new Vec(0, (float)-0.05, (float)0.05));
+                    Matrix.translate(new Vec(lshift,  depth/2,    -shift)),
+                    Matrix.translate(new Vec(rshift,  depth/2,    -shift)),
+                    Matrix.translate(new Vec(lshift, -depth/2,    -shift)),
+                    Matrix.translate(new Vec(rshift, -depth/2,    -shift)),
 
 
-        System.out.println("tile volume: " + tile.volume());
-        System.out.println("goal volume: " + goal.volume());
+                    /*
+                      Matrix.translate(new Vec(lshift,  depth,    -shift)),
+                      Matrix.translate(new Vec(rshift,  depth,    -shift)),
+                      Matrix.translate(new Vec(lshift, -depth,    -shift)),
+                      Matrix.translate(new Vec(rshift, -depth,    -shift)),
+                    */
+                    /*
+                      Matrix.translate(new Vec(lshift,  depth,    shift)),
+                      Matrix.translate(new Vec(rshift,  depth,    shift)),
+                      Matrix.translate(new Vec(lshift, -depth,    shift)),
+                      Matrix.translate(new Vec(rshift, -depth,    shift)),
+                    */
+                    //Matrix.translate(new Vec(0,  depth,    0)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+                    //Matrix.translate(new Vec(0, -depth,    0)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+                    //Matrix.translate(new Vec(0,   0,    height)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+                    //Matrix.translate(new Vec(0,   0,   -height)).times(Matrix.rotate(new Vec(0, 0, 1), (float)Math.PI)),
+
+                    //Matrix.translate(new Vec(0,  depth, 0)),
+                    //Matrix.translate(new Vec(0, -depth, 0)),
+                    Matrix.translate(new Vec(0,      0,  height)),
+                    Matrix.translate(new Vec(0,      0, -height)),
+
+                    //Matrix.translate(new Vec(lshift,        depth,  height/2)),
+                    //Matrix.translate(new Vec(lshift,        depth, -height/2)),
+                    //Matrix.translate(new Vec(rshift,       -depth,  height/2)),
+                    //Matrix.translate(new Vec(rshift,       -depth, -height/2)),
+                    //Matrix.translate(new Vec(rshift,       0,  height)),
+                    //Matrix.translate(new Vec(rshift,       0, -height)),
+
+                    Matrix.translate(new Vec( width,           0,    0)),
+                    Matrix.translate(new Vec(-width,           0,    0)),
+
+                    Matrix.ONE
+                };
+                fixupTile();
+            } });
+            tileMenu.add(new MyMenuItem("Dense Packing (hex)") { public void hit() {
+                setTile(new Mesh(false));
+                float width  = (float)3.2;
+                float depth  = (float)0.32;
+                float height = (float)1.6;
+                float unit = 0.4f;
+                float r = unit/2;
+                float sin = (float)(unit * Math.sin(Math.PI/3));
+                float cos = (float)(unit * Math.cos(Math.PI/3));
+                float x = (float)(r*Math.tan(Math.PI/6));
+                float z = (float)(r/Math.cos(Math.PI/6));
+                height = 2*r*(float)Math.sqrt(2f/3f);
+
+                /*
+                r *= 0.3f;
+                cos *= 0.3f;
+                unit *= 0.3f;
+                */
+
+                /*
+                  sin *= 0.3f;
+                  x *= 0.3f;
+                  z *= 0.3f;
+                */
+                transforms = new Matrix[] {
+                    Matrix.translate(new Vec(-unit, 0, 0)),
+                    Matrix.translate(new Vec( unit, 0, 0)),
+                    Matrix.translate(new Vec(-cos,  0,  sin)),
+                    Matrix.translate(new Vec( cos,  0,  sin)),
+                    Matrix.translate(new Vec(-cos,  0, -sin)),
+                    Matrix.translate(new Vec( cos,  0, -sin)),
+                    Matrix.translate(new Vec( 0,  height, z)),
+                    Matrix.translate(new Vec(-r,  height, -x)),
+                    Matrix.translate(new Vec( r,  height, -x)),
+                    Matrix.translate(new Vec( 0, -height, -z)),
+                    Matrix.translate(new Vec(-r, -height, x)),
+                    Matrix.translate(new Vec( r, -height, x)),
+                    Matrix.ONE,
+                };
+                generateTile(transforms, tile);
+                fixupTile();
+            } });
+
+            tileMenu.add(new MyMenuItem("Slim Dense Packing (Cubic)") { public void hit() {
+                setTile(new Mesh(false));
+                float unit = 0.4f;
+                float r = unit/2;
+                float sin = (float)(unit * Math.sin(Math.PI/3));
+                float cos = (float)(unit * Math.cos(Math.PI/3));
+                float x = (float)(r*Math.tan(Math.PI/6));
+                float z = (float)(r/Math.cos(Math.PI/6));
+                float height = 2*r*(float)Math.sqrt(2f/3f);
+
+                transforms = new Matrix[] {
+
+                    //Matrix.reflect(new Vec( 0,  height, -z).norm()),
+
+                    Matrix.translate(new Vec(-unit, 0, 0)),
+                    Matrix.translate(new Vec( unit, 0, 0)),
+                    Matrix.translate(new Vec(-cos,  0,  sin)),
+                    Matrix.translate(new Vec( cos,  0,  sin)),
+                    Matrix.translate(new Vec(-cos,  0, -sin)),
+                    Matrix.translate(new Vec( cos,  0, -sin)),
+
+                    Matrix.translate(new Vec( 0,  height, -z)),
+                    Matrix.translate(new Vec(-r,  height,  x)),
+                    Matrix.translate(new Vec( r,  height,  x)),
+                    Matrix.translate(new Vec( 0, -height,  z)),
+                    Matrix.translate(new Vec(-r, -height, -x)),
+                    Matrix.translate(new Vec( r, -height, -x)),
+
+                    /*
+                    Matrix.translate(new Vec( 0,  height, -z)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    Matrix.translate(new Vec(-r,  height,  x)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    Matrix.translate(new Vec( r,  height,  x)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    Matrix.translate(new Vec( 0, -height, -z)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    Matrix.translate(new Vec(-r, -height,  x)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    Matrix.translate(new Vec( r, -height,  x)).times(Matrix.rotate(new Vec(0,1,0), (float)Math.PI)),
+                    */
+
+                    /*
+                    Matrix.translate(new Vec( 0,  height, -z)).times(Matrix.scale(-1,1,-1)),
+                    Matrix.translate(new Vec(-r,  height,  x)).times(Matrix.scale(-1,1,-1)),
+                    Matrix.translate(new Vec( r,  height,  x)).times(Matrix.scale(-1,1,-1)),
+                    Matrix.translate(new Vec( 0, -height, -z)).times(Matrix.scale(-1,1,-1)),
+                    Matrix.translate(new Vec(-r, -height,  x)).times(Matrix.scale(-1,1,-1)),
+                    Matrix.translate(new Vec( r, -height,  x)).times(Matrix.scale(-1,1,-1)),
+                    */
+                    Matrix.ONE
+                };
+                generateTile(transforms, tile);
+
+
+                transforms = new Matrix[] {
+                    Matrix.reflect(new Vec( 0,  height, -z).norm()),
+                    //Matrix.reflect(new Vec( 0, -height,  z)),
+                    Matrix.ONE,
+                    Matrix.translate(new Vec(-unit, 0, 0)),
+                    Matrix.translate(new Vec( unit, 0, 0)),
+                    /*
+                    Matrix.translate(new Vec(-cos,  0,  sin)),
+                    Matrix.translate(new Vec( cos,  0,  sin)),
+                    Matrix.translate(new Vec(-cos,  0, -sin)),
+                    Matrix.translate(new Vec( cos,  0, -sin)),
+
+                    Matrix.translate(new Vec( 0,  height, -z)),
+                    Matrix.translate(new Vec(-r,  height,  x)),
+                    Matrix.translate(new Vec( r,  height,  x)),
+                    Matrix.translate(new Vec( 0, -height,  z)),
+                    Matrix.translate(new Vec(-r, -height, -x)),
+                    Matrix.translate(new Vec( r, -height, -x)),
+                    */
+                };
+
+
+                //for(int i=0; i<transforms.length; i++) transforms[i] = Matrix.translate(m.times(vecs[i]));
+
+                Matrix m = Matrix.scale(1.9f, 1f ,1);
+                //Matrix m = Matrix.scale(1f, 2.1f, 1f);
+                tile.transform(m);
+                for(int i=0; i<transforms.length; i++)
+                    transforms[i] = preMultiplyTranslationalComponentBy(transforms[i], m);
+
+
+                fixupTile();
+
+            } });
+            tileMenu.add(new MyMenuItem("Genus-1") { public void hit() {
+                synchronized(this) {
+                    setTile(new Mesh(false));
+                    Matrix mm = Matrix.scale(0.1f);
+                    float height = 4;
+                    float width  = 4;
+                    float depth  = 1;
+                    // top
+                    quad(tile, mm, 
+                         new Point( 2,  2,  0),
+                         new Point( 1,  1, -1),
+                         new Point(-1,  1, -1),
+                         new Point(-2,  2,  0));
+                    quad(tile, mm, 
+                         new Point(-2,  2,  0),
+                         new Point(-1,  1,  1),
+                         new Point( 1,  1,  1),
+                         new Point( 2,  2,  0));
+                    quad(tile, mm, 
+                         new Point( 1,  1, -1),
+                         new Point( 1,  1,  1),
+                         new Point(-1,  1,  1),
+                         new Point(-1,  1, -1));
+
+                    // bottom
+                    quad(tile, mm, 
+                         new Point(-2, -2,  0),
+                         new Point(-1, -1, -1),
+                         new Point( 1, -1, -1),
+                         new Point( 2, -2,  0));
+                    quad(tile, mm, 
+                         new Point( 2, -2,  0),
+                         new Point( 1, -1,  1),
+                         new Point(-1, -1,  1),
+                         new Point(-2, -2,  0));
+                    quad(tile, mm, 
+                         new Point(-1, -1, -1),
+                         new Point(-1, -1,  1),
+                         new Point( 1, -1,  1),
+                         new Point( 1, -1, -1));
+
+                    // left
+                    quad(tile, mm, 
+                         new Point( 2, -2,  0),
+                         new Point( 1, -1, -1),
+                         new Point( 1,  1, -1),
+                         new Point( 2,  2,  0));
+                    quad(tile, mm, 
+                         new Point( 2,  2,  0),
+                         new Point( 1,  1,  1),
+                         new Point( 1, -1,  1),
+                         new Point( 2, -2,  0));
+                    quad(tile, mm, 
+                         new Point( 1, -1, -1),
+                         new Point( 1, -1,  1),
+                         new Point( 1,  1,  1),
+                         new Point( 1,  1, -1));
+
+                    // bottom
+                    quad(tile, mm, 
+                         new Point(-2,  2,  0),
+                         new Point(-1,  1, -1),
+                         new Point(-1, -1, -1),
+                         new Point(-2, -2,  0));
+                    quad(tile, mm, 
+                         new Point(-2, -2,  0),
+                         new Point(-1, -1,  1),
+                         new Point(-1,  1,  1),
+                         new Point(-2,  2,  0));
+                    quad(tile, mm, 
+                         new Point(-1,  1, -1),
+                         new Point(-1,  1,  1),
+                         new Point(-1, -1,  1),
+                         new Point(-1, -1, -1));
+
+                    height = 4;
+                    width  = 4;
+                    depth  = 1;
+
+
+                    transforms = new Matrix[] {
+                        Matrix.translate(new Vec(0, 0.2f,0))
+                        .times(Matrix.rotate(new Vec(0,1,0), (float)(1*Math.PI/2))),
+
+                        Matrix.translate(new Vec(0,-0.2f,0))
+                        .times(Matrix.rotate(new Vec(0,1,0), (float)(-1*Math.PI/2))),
+
+                        Matrix.translate(new Vec( 0.2f,0,0))
+                        .times(Matrix.rotate(new Vec(1,0,0), (float)(1*Math.PI/2))),
+
+                        Matrix.translate(new Vec(-0.2f,0,0))
+                        .times(Matrix.rotate(new Vec(1,0,0), (float)(-1*Math.PI/2))),
+
+
+                        //Matrix.rotate(new Vec(0,0,1), (float)(1*Math.PI/2)),
+
+                        /*
+                          Matrix.rotate(new Vec(0,0,1), (float)(1*Math.PI/2)),
+
+                          Matrix.rotate(new Vec(0,0,1), (float)(3*Math.PI/2)),
+                          Matrix.rotate(new Vec(1,0,0), (float)(2*Math.PI/2)),
+                        */
+
+                        //Matrix.rotate(new Vec(0,0,1), (float)(2*Math.PI/2)),
+                        //Matrix.scale(1,-1,1),
+
+                        //Matrix.translate(new Vec( 0.2f, 0,0))
+                        //.times(Matrix.rotate(new Vec(0,0,1), (float)( 1*Math.PI/2)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 3*Math.PI/2))),
+
+                        //Matrix.translate(new Vec(-0.2f, 0,0))
+                        //.times(Matrix.rotate(new Vec(0,0,1), (float)( 3*Math.PI/2)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 3*Math.PI/2))),
+            
+                        //Matrix.rotate(new Vec(0,0,1), (float)( 0*Math.PI/2))
+                        //.times(Matrix.translate(new Vec(0, -0.2f, 0)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 1*Math.PI/2))),
+                        //Matrix.rotate(new Vec(0,0,1), (float)( 1*Math.PI/2))
+                        //.times(Matrix.translate(new Vec(0, -0.2f, 0)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 1*Math.PI/2))),
+
+                        //Matrix.rotate(new Vec(0,0,1), (float)( 0*Math.PI/2))
+                        //.times(Matrix.translate(new Vec(0, -0.2f, 0)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 1*Math.PI/2))),
+                        //Matrix.rotate(new Vec(0,0,1), (float)( 0*Math.PI/2))
+                        //.times(Matrix.translate(new Vec(0, -0.2f, 0)))
+                        //.times(Matrix.rotate(new Vec(0,1,0), (float)( 1*Math.PI/2))),
+
+                        Matrix.ONE,
+                    };
+                    fixupTile();
+                }}});
+            tileMenu.add(new MyMenuItem("Hammerhead") { public void hit() {
+                synchronized(this) {
+                    setTile(new Mesh(false));
+                    Matrix mm = Matrix.ONE;
+                    float height1 = .1f;
+                    float height2 = .1f;
+                    float width  = .4f;
+                    float depth  = .1f;
+                    // top
+                    Point a1 = new Point( -width/2,         height2/2, -depth/2);
+                    Point b1 = new Point(        0,         height2/2, -depth/2);
+                    Point c1 = new Point(        0, height1+height2/2, -depth/2);
+                    Point d1 = new Point(  width/2, height1+height2/2, -depth/2);
+                    Point e1 = new Point(  width/2,         height2/2, -depth/2);
+                    Point f1 = new Point(  width/2,        -height2/2, -depth/2);
+                    Point g1 = new Point(  width/2,-height1-height2/2, -depth/2);
+                    Point h1 = new Point(        0,-height1-height2/2, -depth/2);
+                    Point i1 = new Point(        0,        -height2/2, -depth/2);
+                    Point j1 = new Point( -width/2,        -height2/2, -depth/2);
+                    Point a2 = new Point( -width/2,         height2/2,  depth/2);
+                    Point b2 = new Point(        0,         height2/2,  depth/2);
+                    Point c2 = new Point(        0, height1+height2/2,  depth/2);
+                    Point d2 = new Point(  width/2, height1+height2/2,  depth/2);
+                    Point e2 = new Point(  width/2,         height2/2,  depth/2);
+                    Point f2 = new Point(  width/2,        -height2/2,  depth/2);
+                    Point g2 = new Point(  width/2,-height1-height2/2,  depth/2);
+                    Point h2 = new Point(        0,-height1-height2/2,  depth/2);
+                    Point i2 = new Point(        0,        -height2/2,  depth/2);
+                    Point j2 = new Point( -width/2,        -height2/2,  depth/2);
+
+                    quad(tile, mm, a1, b1, i1, j1);
+                    quad(tile, mm, c1, d1, e1, b1);
+                    quad(tile, mm, b1, e1, f1, i1);
+                    quad(tile, mm, i1, f1, g1, h1);
 
-        tile.score_against = goal;
-        goal.score_against = tile;
+                    quad(tile, mm, j2, i2, b2, a2);
+                    quad(tile, mm, b2, e2, d2, c2);
+                    quad(tile, mm, i2, f2, e2, b2);
+                    quad(tile, mm, h2, g2, f2, i2);
+
+                    quad(tile, mm, d1, d2, e2, e1);
+                    quad(tile, mm, e1, e2, f2, f1);
+                    quad(tile, mm, f1, f2, g2, g1);
+                    quad(tile, mm, h1, g1, g2, h2);
+                    quad(tile, mm, i2, i1, h1, h2);
+                    quad(tile, mm, j1, i1, i2, j2);
+                    quad(tile, mm, a2, a1, j1, j2);
+                    quad(tile, mm, a1, a2, b2, b1);
+                    quad(tile, mm, c2, c1, b1, b2);
+                    quad(tile, mm, c1, c2, d2, d1);
+
+                    transforms = new Matrix[] {
+
+                        mm.times(Matrix.translate(new Vec(   width,     0, 0))),
+                        mm.times(Matrix.translate(new Vec(  -width,     0, 0))),
+                        mm.times(Matrix.translate(new Vec(-width/2, height1+height2, 0))),
+                        mm.times(Matrix.translate(new Vec( width/2, height1+height2, 0))),
+                        mm.times(Matrix.translate(new Vec(-width/2,-height1-height2, 0))),
+                        mm.times(Matrix.translate(new Vec( width/2,-height1-height2, 0))),
+
+                        mm.times(Matrix.translate(new Vec(   width/2,     0,  depth))),
+                        mm.times(Matrix.translate(new Vec(  -width/2,     0,  depth))),
+                        mm.times(Matrix.translate(new Vec(         0, height1+height2,  depth))),
+                        mm.times(Matrix.translate(new Vec(         0,-height1-height2,  depth))),
+
+                        mm.times(Matrix.translate(new Vec(   width/2,     0, -depth))),
+                        mm.times(Matrix.translate(new Vec(  -width/2,     0, -depth))),
+                        mm.times(Matrix.translate(new Vec(         0, height1+height2, -depth))),
+                        mm.times(Matrix.translate(new Vec(         0,-height1-height2, -depth))),
+
+                        Matrix.ONE
+                    };
+                    fixupTile();
+                }}});
+            tileMenu.add(new MyMenuItem("Marching Cubes") { public void hit() {
+                marchingCubes();
+            }});
+            tileMenu.add(new MyMenuItem("Brain") { public void hit() {
+                marchingCubes2();
+            }});
+
+            // Finally, add all the menus to the menu bar.
+            add(tileMenu);
+            //add(goalMenu);
+            //add(hideMenu);
+        }
+
+    }
+
+    private static Matrix preMultiplyTranslationalComponentBy(Matrix mthis, Matrix mm) {
+        Vec v = mm.times(mthis.getTranslationalComponent());
+        return new Matrix(mthis.a, mthis.b, mthis.c, v.x,
+                          mthis.e, mthis.f, mthis.g, v.y,
+                          mthis.i, mthis.j, mthis.k, v.z,
+                          mthis.m, mthis.n, mthis.o, 1);
     }
-        Random random = new Random();
 
-    public synchronized void breakit() {
-        if (verts > 300) return;
-        //double min = (tile.avgedge/tile.numedges)*(1+(4/(double)verts));
-        //if (verts>0 && tile.es.peek().length() < min) return;
+//////////////////////////////////////////////////////////////////////////////
+    public void breakit() {
+        int oldverts = verts;
+        if (verts > 2000 && !force) return;
+        force = false;
+        System.out.println("doubling vertices.");
         PriorityQueue<Mesh.E> es = new PriorityQueue<Mesh.E>();
-        for(Mesh.E e : tile.edges()) es.add(e);
-        for(int i=0; i<10; i++) {
+        for(Mesh.T t : tile) {
+            es.add(t.e1());
+            es.add(t.e2());
+            es.add(t.e3());
+            Thread.yield();
+            repaint();
+        }
+        for(int i=0; i<Math.min(oldverts,50); i++) {
             Mesh.E e = es.poll();
             verts++;
-            System.out.println("shatter " + e);
             e.shatter();
-            tile.unbind();
-            tile.bind();
+            Thread.yield();
+            repaint();
         }
+        System.out.println("now have " + verts + " vertices; max is 2000");
+        tile.rebindPoints();
     }
 
-    public synchronized void rand(double temperature, Mesh.Vert p) {
-        double tile_score = tile.score();
-        double goal_score = goal.score();
-        
-        p.rescore();
-        //if (p.watch==null) return;
-        float r1 = Math.abs(random.nextFloat());
-        r1 = r1 - (float)Math.floor(r1);
-        r1 = r1 * (float)0.01;
-        r1 = r1 - (float)0.005;
+    public boolean rand(double temp, Mesh.Vertex p) {
 
-        Vec v = p.nearest_vert_in_other_mesh().minus(p.p).norm().times(r1);
+        p.reComputeErrorAround();
+        double tile_error = tile.error();
+        double goal_error = goal.error();
 
-        //v = p.norm().times(v.dot(p.norm()));
+        float max = p.averageEdgeLength()/5;
+        Vec v = new Vec(random.nextFloat(), random.nextFloat(), random.nextFloat());
+        v = v.norm().times((random.nextFloat() - 0.5f) * max);
+        Matrix m = Matrix.translate(v);
+        boolean good = p.move(v, false);
+        if (!good) { return false; }
 
-        boolean aspect = false;//(Math.abs(random.nextInt()) % 100) <= 2;
-        Matrix old_tile_aspect = null;//goal.aspect;
-        boolean good = true;
-        if (aspect) {
-            /*
-            v = v.times(10);
-            tile.aspect = new Matrix(tile.aspect.a / (v.x+1), tile.aspect.f / (v.y+1), tile.aspect.k / (v.z+1));
-            tile.invaspect = new Matrix(1/tile.aspect.a, 1/tile.aspect.f, 1/tile.aspect.k);
-            goal.rescore();
-            tile.rescore();
-            */
-        } else {
-            good = p.move(v);
-        }
-        double new_tile_score = tile.score();
-        double new_goal_score = goal.score();
-        double tile_delta = new_tile_score - tile_score;
-        double goal_delta = new_goal_score - goal_score;
+        double new_tile_error = tile.error();
+        double new_goal_error = goal.error();
+        double tile_delta = (new_tile_error - tile_error) / tile_error;
+        double goal_delta = (new_goal_error - goal_error) / goal_error;
         double delta = tile_delta + goal_delta;
-        double swapProbability = Math.exp((-1 * delta) / temperature);
-        //boolean doSwap = Math.random() < swapProbability;
-        boolean doSwap = good && (tile_delta <= 0 && goal_delta <= 0);
+        double swapProbability = Math.exp((-1 * delta) / temp);
+
+        //boolean doSwap = good && (tile_delta <= 0 && goal_delta <= 0);
+        //boolean doSwap = good && (tile_delta + goal_delta <= 0);
+        //if (temp < 0.000001) doSwap = good && (tile_delta <= 0 && goal_delta <= 0);
+        boolean doSwap = good && (Math.random() < swapProbability);
+
+        // always move uphill if possible -- potential idea
+        if (tile_delta <= 0 && goal_delta <= 0 && good) doSwap = true;
+        if (hillclimb)
+            doSwap = tile_delta <= 0 && goal_delta <= 0 && good;
+
         if (doSwap) {
-            tile_score = new_tile_score;
-            goal_score = new_goal_score;
-            //System.out.println("score: " + tile_score + " / " + goal_score);
-            if (aspect) System.out.println("aspect " + v);
+            tile_error = new_tile_error;
+            goal_error = new_goal_error;
+            hits++;
+            p.goodp = p.p;
         } else {
-            if (aspect) {
-                //tile.aspect = old_tile_aspect;
-                //tile.invaspect = new Matrix(1/tile.aspect.a, 1/tile.aspect.f, 1/tile.aspect.k);
-                goal.rescore();
-                tile.rescore();
-            } else {
-                p.move(v.times(-1));
-            }
+            p.move(v.times(-1), true);
+            misses++;
         }
+        p.reComputeErrorAround();
+        return true;
     }
 
-    /**
-     * Take care of initialization here.
-     */
-    public void init(GLAutoDrawable gld) {
-        GL gl = gld.getGL();
-        gl.glClearColor(0.0f, 0.0f, 0.0f, 1.0f);
-        gl.glViewport(0, 0, 500, 300);
-        gl.glEnable(GL.GL_DEPTH_TEST);
-        gl.glClearDepth(1.0);
-        gl.glDepthFunc(GL.GL_LEQUAL);
-        gl.glMatrixMode(GL.GL_PROJECTION);
-        gl.glLoadIdentity();
-        gl.glMatrixMode(GL.GL_MODELVIEW);
-        display(gld);
-    }
+    float hits = 0;
+    float misses = 0;
+    public void anneal() throws Exception {
+        double hightemp = 1;
+        temp = hightemp;
+        double last = 10;
+        boolean seek_upward = false;
+        double acceptance = 1;
+        while(true) {
+            synchronized(this) {
+                if (!anneal) { repaint(); Thread.sleep(10); continue; }
 
-    public void reshape(GLAutoDrawable drawable, int x, int y, int width, int height) { }
-    public void displayChanged(GLAutoDrawable drawable, boolean modeChanged, boolean deviceChanged) { }
-    public synchronized void display(GLAutoDrawable drawable) {
-        GL gl = drawable.getGL();
-        GLU glu = new GLU();
-        gl.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT);
-        gl.glPointSize(5.0f);
-        gl.glLoadIdentity();
-        glu.gluPerspective(50-tz, ((float)drawable.getWidth())/drawable.getHeight(), 0.5, 10);
-        glu.gluLookAt(0, 0, -1, 0, 0, 0, 0, 1, 0);
-        gl.glTranslatef(tx/(float)20, ty/(float)20, 0);
-        gl.glRotatef(anglex/3, 0, 1, 0);
-        gl.glRotatef(angley/3, 1, 0, 0);
-
-        gl.glBegin(GL.GL_TRIANGLES);
-        draw(gl, true, tile);
-        gl.glEnd();
-
-        gl.glBegin(GL.GL_TRIANGLES);
-        gl.glColor4f((float)0.5, (float)0.5, (float)0.5, (float)0.8);
-        //draw(gl, false, goal);
-        gl.glEnd();
-
-
-        int i = 0;
-        //gl.glDisable(GL.GL_DEPTH_TEST);
-        gl.glColor4f(1,1,1,1);
-        for(Matrix m : translations) {
-            //if (v1.z==0 && v1.y==0) continue;
-            i++;
-            if (i != 1 /*&& i!=4*/) continue;
-            Point p = new Point(0, 0, 0).times(m);
-            Vec v = new Vec(p.x, p.y, p.z);
-            v = v.times((float)1.04);
-            gl.glTranslatef(v.x, v.y, v.z);
-            draw(gl, false, tile);
-            gl.glTranslatef(-v.x, -v.y, -v.z);
-        }
-        //gl.glEnable(GL.GL_DEPTH_TEST);
-    }
+            double ratio = (hits+misses==0) ? 1 : (hits / (hits+misses));
+            hits = 0;
+            misses = 0;
+            double gamma = 1;
+            acceptance = (ratio+acceptance)/2;
+            accepts = (int)(Math.ceil(ratio*100));
+            temps = (int)(Math.ceil(temp*1000));
+            vertss = tile.size();
+            if (breaks > 0) {
+                while (breaks>0) {
+                    breaks--;
+                    breakit();
+                }
+                seek_upward = true;
+                continue;
+            } else if (acceptance > 0.96) gamma = 0.1f;
+            else if (acceptance > 0.9)    gamma = 0.2f;
+            else if (acceptance > 0.8)    gamma = 0.3f;
+            else if (acceptance > 0.6)    gamma = 0.4f;
+            else if (acceptance > 0.3)    gamma = 0.8f;
+            else if (acceptance > 0.15)   gamma = 0.94f;
+            else if (acceptance > 0.10)   gamma = 0.98f;
 
-    private synchronized void draw(GL gl, boolean triangles, Mesh mesh) {
-        float red = 0.0f;
-        float green = 0.0f;
-        float blue = 0.0f;
-        for(Mesh.T t : mesh) {
-            if (red < 0.15) red = 1.0f;
-            if (green < 0.15) green = 1.0f;
-            if (blue < 0.15) blue = 1.0f;
-            red -= .09f;
-            green -= .12f;
-            blue -= .15f;
-
-            if (triangles) switch(t.color) {
-                case 0: gl.glColor4f((float)0.25, (float)0.25, (float)0.75, (float)0.3); break;
-                case 1: gl.glColor4f((float)0.25, (float)0.75, (float)0.25, (float)0.3); break;
-                case 2: gl.glColor4f((float)0.75, (float)0.25, (float)0.25, (float)0.3); break;
-                case 3: gl.glColor4f((float)0.50, (float)0.50, (float)0.50, (float)0.3); break;
-            }
-            //gl.glBegin(GL.GL_LINES);
-
-            if (triangles) {
-                gl.glBegin(GL.GL_TRIANGLES);
-                t.glVertices(gl);
-                gl.glEnd();
-            } else {
-                gl.glBegin(GL.GL_LINES);
-                t.e1().p1.p.glVertex(gl);
-                t.e1().p2.p.glVertex(gl);
-                t.e2().p1.p.glVertex(gl);
-                t.e2().p2.p.glVertex(gl);
-                t.e3().p1.p.glVertex(gl);
-                t.e3().p2.p.glVertex(gl);
-                gl.glEnd();
+            else if (acceptance < 0.01)   breaks++;
+
+            if (seek_upward) {
+                if (acceptance > 0.25) seek_upward = false;
+                else gamma = 2-gamma;
             }
 
-            Point centroid = t.centroid();
-            gl.glBegin(GL.GL_LINES);
-            gl.glColor3f(1, 1, 1);
-            /*
-            centroid.glVertex(gl);
-            centroid.plus(t.norm().times(t.diameter())).glVertex(gl);
-            */
+            if (anneal)
+                temp = temp * gamma;
 
-            if (mesh==goal)
-                for(Mesh.Vert p : new Mesh.Vert[] { t.v1(), t.v2(), t.v3() }) {
-                    p.p.glVertex(gl);
-                    //p.plus(p.norm().times(p.score()*10)).glVertex(gl);
-                    p.partner().p.glVertex(gl);
-                    //tile.nearest(p).centroid().glVertex(gl);
-                }
 
-            gl.glEnd();
+            HashSet<Mesh.Vertex> hs = new HashSet<Mesh.Vertex>();
+            for(Mesh.Vertex p : tile.vertices()) hs.add(p);
+            Mesh.Vertex[] pts = (Mesh.Vertex[])hs.toArray(new Mesh.Vertex[0]);
 
+            int count = 0;
+            long then = System.currentTimeMillis();
+            for(int i=0; i<300; i++) {
+                if (anneal) {
+                    Mesh.Vertex v = pts[Math.abs(random.nextInt()) % pts.length];
+                    if (breaks>0) break;
+                    if (!rand(temp,v)) { i--; continue; }
+                    v.recomputeFundamentalQuadricIfStale();
+                    v.recomputeFundamentalQuadricIfNeighborChanged();
+                    count++;
+                }
+                Thread.yield();
+                repaint();
+            }
+
+            System.out.println("temp="+temp + " ratio="+(Math.ceil(acceptance*100)) + " " +
+                               "points_per_second=" +
+                               (count*1000)/((double)(System.currentTimeMillis()-then)));
+            for(Mesh.Vertex p : goal.vertices()) {
+                p.quadricStale = true;
+                p.recomputeFundamentalQuadricIfNeighborChanged();
+            }
+            }
         }
     }
 
+
     public static void main(String[] s) throws Exception {
-        StlFile stlf = new StlFile();
-        stlf.load("simplefish.stl");
-        Main main = new Main(stlf);
-        Frame f = new Frame();
-        GLCapabilities glcaps = new GLCapabilities();
-        GLCanvas glcanvas = new GLCanvas();
-        glcanvas.addGLEventListener(main);
-        f.add(glcanvas, BorderLayout.CENTER);
+        JFrame f = new JFrame();
+        f.setLayout(new BorderLayout());
+        Main main = new Main(f);
+        f.add(main, BorderLayout.CENTER);
+
+        f.addWindowListener(new WindowListener() {
+                public void windowActivated(WindowEvent e) { }
+                public void windowClosed(WindowEvent e) { System.exit(0); }
+                public void windowClosing(WindowEvent e) { System.exit(0); }
+                public void windowDeactivated(WindowEvent e)  { }
+                public void windowDeiconified(WindowEvent e)  { }
+                public void windowIconified(WindowEvent e)  { }
+                public void windowOpened(WindowEvent e) { }
+            });
+
         f.pack();
         f.show();
         f.setSize(900, 900);
         f.doLayout();
 
-        glcanvas.addMouseListener(main);
-        glcanvas.addMouseMotionListener(main);
-        glcanvas.addMouseWheelListener(main);
-        glcanvas.addKeyListener(main);
+        JFrame f2 = new JFrame();
+        f2.setJMenuBar(main.new MyMenuBar());
+        f2.setSize(100,100);
+        f2.show();
 
-        main.anneal(glcanvas);
+        main.anneal();
     }
-    public static int verts = 0;
-    public void anneal(GLCanvas glcanvas) throws Exception {
-        int verts = 0;
-        while(true) {
-            //Thread.sleep(10);
-            for(int i=0; i<1; i++) {
-                glcanvas.repaint();
-                //tile.ts.get(Math.abs(random.nextInt()) % tile.ts.size()).e1().p1
-                for(Mesh.T t : tile)
-                    for(Mesh.Vert p : new Mesh.Vert[] { t.v1(), t.v2(), t.v3() }) {
-                        rand(10,p);
-                    }
-                goal.rescore();
-                tile.rescore();
-            }
-            breakit();
-       }
 
-    }
 
 }
\ No newline at end of file