fixed improper generic parameter use in Tree.duplicateAs > Map, necessary

[trakem2.git] / TrakEM2_ / src / main / java / ini / trakem2 / display / Display3D.java

package ini.trakem2.display;

import java.awt.Color;
import java.awt.Cursor;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.FutureTask;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;

import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.View;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;

import customnode.CustomLineMesh;
import customnode.CustomMesh;
import customnode.CustomMultiMesh;
import customnode.CustomTriangleMesh;
import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.measure.Calibration;
import ij3d.Content;
import ij3d.Image3DUniverse;
import ij3d.ImageWindow3D;
import ij3d.UniverseListener;
import ini.trakem2.display.d3d.ControlClickBehavior;
import ini.trakem2.display.d3d.Display3DGUI;
import ini.trakem2.imaging.PatchStack;
import ini.trakem2.tree.ProjectThing;
import ini.trakem2.utils.IJError;
import ini.trakem2.utils.Utils;
import ini.trakem2.vector.VectorString3D;


/** One Display3D instance for each LayerSet (maximum). */
public final class Display3D {

        /** Table of LayerSet and Display3D - since there is a one to one relationship.  */
        static private Hashtable<LayerSet,Display3D> ht_layer_sets = new Hashtable<LayerSet,Display3D>();
        /**Control calls to new Display3D. */
        static private Object htlock = new Object();

        /** The sky will fall on your head if you modify any of the objects contained in this table -- which is a copy of the original, but the objects are the originals. */
        static public Hashtable<LayerSet,Display3D> getMasterTable() {
                return new Hashtable<LayerSet,Display3D>(ht_layer_sets);
        }

        /** Table of ProjectThing keys versus names of Content objects in the universe. */
        private Map<ProjectThing,String> ht_pt_meshes = Collections.synchronizedMap(new HashMap<ProjectThing,String>());

        private Image3DUniverse universe;

        private LayerSet layer_set;
        /** The dimensions of the LayerSet in 2D. */
        private double width, height;
        private int resample = -1; // unset
        static private final int DEFAULT_RESAMPLE = 4;
        /** If the LayerSet dimensions are too large, then limit to max 2048 for width or height and setup a scale.*/
        private final double scale = 1.0; // OBSOLETE: meshes are now generated with imglib ShapeList images.


        // To fork away from the EventDispatchThread
        static private ExecutorService launchers = Utils.newFixedThreadPool(Runtime.getRuntime().availableProcessors(), "Display3D-launchers");

        // To build meshes, or edit them
        private ExecutorService executors = Utils.newFixedThreadPool(Runtime.getRuntime().availableProcessors(), "Display3D-executors");

        /*
        static private KeyAdapter ka = new KeyAdapter() {
                public void keyPressed(KeyEvent ke) {
                        // F1 .. F12 keys to set tools
                        ProjectToolbar.keyPressed(ke);
                }
        };
        */

        /** Defaults to parallel projection. */
        private Display3D(final LayerSet ls) {
                this.layer_set = ls;
                this.width = ls.getLayerWidth();
                this.height = ls.getLayerHeight();
                this.universe = new Image3DUniverse(512, 512); // size of the initial canvas, not the universe itself
                this.universe.getViewer().getView().setProjectionPolicy(View.PERSPECTIVE_PROJECTION); // (View.PERSPECTIVE_PROJECTION);

                //this.universe.show();

                final Display3DGUI gui = new Display3DGUI(this.universe);
                final ImageWindow3D win = gui.init();
                this.universe.init(win);
                win.pack();
                win.setVisible(true);

                this.universe.getWindow().addWindowListener(new IW3DListener(this, ls));
                this.universe.getWindow().setTitle(ls.getProject().toString() + " -- 3D Viewer");
                // it ignores the listeners:
                //preaddKeyListener(this.universe.getWindow(), ka);
                //preaddKeyListener(this.universe.getWindow().getCanvas(), ka);

                // register
                Display3D.ht_layer_sets.put(ls, this);

                // Add a behavior to catch control + mouse-click on
                // objects in the 3D viewer and centre the front Display
                // on that point:
                this.universe.addInteractiveBehavior(new ControlClickBehavior(universe, ls));

                this.universe.addUniverseListener(new UniverseListener() {
                        @Override
                        public void universeClosed() {
                                synchronized (ht_pt_meshes) {
                                        ht_pt_meshes.clear();
                                }
                        }
                        @Override
                        public void transformationUpdated(final View arg0) {
                        }
                        @Override
                        public void transformationStarted(final View arg0) {
                        }
                        @Override
                        public void transformationFinished(final View arg0) {
                        }
                        @Override
                        public void contentSelected(final Content arg0) {
                                // TODO could select in TrakEM2's Display
                        }
                        @Override
                        public void contentRemoved(final Content arg0) {
                                final String name = arg0.getName();
                                synchronized (ht_pt_meshes) {
                                        for (final Iterator<Map.Entry<ProjectThing,String>> it = ht_pt_meshes.entrySet().iterator(); it.hasNext(); ) {
                                                if (name.equals(it.next().getValue())) {
                                                        it.remove();
                                                        break;
                                                }
                                        }
                                }
                        }
                        @Override
                        public void contentChanged(final Content arg0) {
                        }
                        @Override
                        public void contentAdded(final Content arg0) {
                        }
                        @Override
                        public void canvasResized() {
                        }
                });
        }

        /*
        private void preaddKeyListener(Component c, KeyListener kl) {
                KeyListener[] all = c.getKeyListeners();
                if (null != all) {
                        for (KeyListener k : all) c.removeKeyListener(k);
                }
                c.addKeyListener(kl);
                if (null != all) {
                        for (KeyListener k : all) c.addKeyListener(k);
                }
        }
        */

        public Image3DUniverse getUniverse() {
                return universe;
        }

        /* Take a snapshot know-it-all mode. Each Transform3D given as argument gets assigned to the (nearly) homonimous TransformGroup, which have the following relationships:
         *
         *  scaleTG contains rotationsTG
         *  rotationsTG contains translateTG
         *  translateTG contains centerTG
         *  centerTG contains the whole scene, with all meshes, etc.
         *
         *  Any null arguments imply the current transform in the open Display3D.
         *
         *  By default, a newly created Display3D has the scale and center transforms modified to make the scene fit nicely centered (and a bit scaled down) in the given Display3D window. The translate and rotate transforms are set to identity.
         *
         *  The TransformGroup instances may be reached like this:
         *
         *  LayerSet layer_set = Display.getFrontLayer().getParent();
         *  Display3D d3d = Display3D.getDisplay(layer_set);
         *  TransformGroup scaleTG = d3d.getUniverse().getGlobalScale();
         *  TransformGroup rotationsTG = d3d.getUniverse().getGlobalRotate();
         *  TransformGroup translateTG = d3d.getUniverse().getGlobalTranslate();
         *  TransformGroup centerTG = d3d.getUniverse().getCenterTG();
         *
         *  ... and the Transform3D from each may be read out indirectly like this:
         *
         *  Transform3D t_scale = new Transform3D();
         *  scaleTG.getTransform(t_scale);
         *  ...
         *
         * WARNING: if your java3d setup does not support offscreen rendering, the Display3D window will be brought to the front and a screen snapshot cropped to it to perform the snapshot capture. Don't cover the Display3D window with any other windows (not even an screen saver).
         *
         */
        /*public ImagePlus makeSnapshot(final Transform3D scale, final Transform3D rotate, final Transform3D translate, final Transform3D center) {
                return universe.makeSnapshot(scale, rotate, translate, center);
        }*/

        /** Uses current scaling, translation and centering transforms! */
        /*public ImagePlus makeSnapshotXY() { // aka posterior
                // default view
                return universe.makeSnapshot(null, new Transform3D(), null, null);
        }*/
        /** Uses current scaling, translation and centering transforms! */
        /*public ImagePlus makeSnapshotXZ() { // aka dorsal
                Transform3D rot1 = new Transform3D();
                rot1.rotZ(-Math.PI/2);
                Transform3D rot2 = new Transform3D();
                rot2.rotX(Math.PI/2);
                rot1.mul(rot2);
                return universe.makeSnapshot(null, rot1, null, null);
        }
        */
        /** Uses current scaling, translation and centering transforms! */
        /*
        public ImagePlus makeSnapshotYZ() { // aka lateral
                Transform3D rot = new Transform3D();
                rot.rotY(Math.PI/2);
                return universe.makeSnapshot(null, rot, null, null);
        }*/

        /*
        public ImagePlus makeSnapshotZX() { // aka frontal
                Transform3D rot = new Transform3D();
                rot.rotX(-Math.PI/2);
                return universe.makeSnapshot(null, rot, null, null);
        }
        */

        /** Uses current scaling, translation and centering transforms! Opposite side of XZ. */
        /*
        public ImagePlus makeSnapshotXZOpp() {
                Transform3D rot1 = new Transform3D();
                rot1.rotX(-Math.PI/2); // 90 degrees clockwise
                Transform3D rot2 = new Transform3D();
                rot2.rotY(Math.PI); // 180 degrees around Y, to the other side.
                rot1.mul(rot2);
                return universe.makeSnapshot(null, rot1, null, null);
        }*/

        private class IW3DListener extends WindowAdapter {
                private Display3D d3d;
                private LayerSet ls;
                IW3DListener(final Display3D d3d, final LayerSet ls) {
                        this.d3d = d3d;
                        this.ls = ls;
                }
                @Override
                public void windowClosing(final WindowEvent we) {
                        //Utils.log2("Display3D.windowClosing");
                        d3d.executors.shutdownNow();
                        /*Object ob =*/ ht_layer_sets.remove(ls);
                        /*if (null != ob) {
                                Utils.log2("Removed Display3D from table for LayerSet " + ls);
                        }*/
                }
                @Override
                public void windowClosed(final WindowEvent we) {
                        //Utils.log2("Display3D.windowClosed");
                        ht_layer_sets.remove(ls);
                }
        }

        static private boolean check_j3d = true;
        static private boolean has_j3d_3dviewer = false;

        static private boolean hasLibs() {
                if (check_j3d) {
                        check_j3d = false;
                        try {
                                Class.forName("javax.vecmath.Point3f");
                                has_j3d_3dviewer = true;
                        } catch (final ClassNotFoundException cnfe) {
                                Utils.log("Java 3D not installed.");
                                has_j3d_3dviewer = false;
                                return false;
                        }
                        try {
                                Class.forName("ij3d.ImageWindow3D");
                                has_j3d_3dviewer = true;
                        } catch (final ClassNotFoundException cnfe) {
                                Utils.log("3D Viewer not installed.");
                                has_j3d_3dviewer = false;
                                return false;
                        }
                }
                return has_j3d_3dviewer;
        }

        /** Get an existing Display3D for the given LayerSet, or create a new one for it (and cache it). */
        static public Display3D get(final LayerSet ls) {
                synchronized (htlock) {
                        try {
                                // test:
                                if (!hasLibs()) return null;
                                //
                                final Display3D d3d = ht_layer_sets.get(ls);
                                if (null != d3d) return d3d;
                                // Else, new:
                                final boolean[] done = new boolean[]{false};
                                javax.swing.SwingUtilities.invokeAndWait(new Runnable() { @Override
                                public void run() {
                                        ht_layer_sets.put(ls, new Display3D(ls));
                                        done[0] = true;
                                }});
                                // wait to avoid crashes in amd64
                                // try { Thread.sleep(500); } catch (Exception e) {}
                                while (!done[0]) {
                                        try { Thread.sleep(10); } catch (final Exception e) {}
                                }
                                return ht_layer_sets.get(ls);
                        } catch (final Exception e) {
                                IJError.print(e);
                        }
                }
                return null;
        }

        /** Get the Display3D instance that exists for the given LayerSet, if any. */
        static public Display3D getDisplay(final LayerSet ls) {
                return ht_layer_sets.get(ls);
        }

        static public void setWaitingCursor() {
                Utils.invokeLater(new Runnable() { @Override
                public void run() {
                        for (final Display3D d3d : ht_layer_sets.values()) {
                                d3d.universe.getWindow().setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
                        }
                }});
        }

        static public void doneWaiting() {
                Utils.invokeLater(new Runnable() { @Override
                public void run() {
                        for (final Display3D d3d : ht_layer_sets.values()) {
                                d3d.universe.getWindow().setCursor(Cursor.getDefaultCursor());
                        }
                }});
        }

        static public Future<Vector<Future<Content>>> show(final ProjectThing pt) {
                return show(pt, false, -1);
        }

        static public void showAndResetView(final ProjectThing pt) {
                launchers.submit(new Runnable() {
                        @Override
                        public void run() {
                                // wait until done
                                final Future<Vector<Future<Content>>> fu = show(pt, true, -1);
                                Vector<Future<Content>> vc;
                                try {
                                        vc = fu.get(); // wait until done
                                } catch (final Exception e) {
                                        IJError.print(e);
                                        return;
                                }
                                for (final Future<Content> fc : vc) {
                                        try {
                                                final Content c = fc.get();
                                                if (null == c) continue;
                                                final ArrayList<Display3D> d3ds = new ArrayList<Display3D>();
                                                synchronized (ht_layer_sets) {
                                                        d3ds.addAll(ht_layer_sets.values());
                                                }
                                                /* // Disabled, it's annoying
                                                for (Display3D d3d : d3ds) {
                                                        synchronized (d3d) {
                                                                if (d3d.universe.getContents().contains(c)) {
                                                                        d3d.universe.resetView(); // reset the absolute center
                                                                        d3d.universe.adjustView(); // zoom out to bring all elements in universe within view
                                                                }
                                                        }
                                                }*/
                                        } catch (final Exception e) {
                                                IJError.print(e);
                                        }
                                }
                                Utils.logAll("Reset 3D view if not within field of view!");
                        }
                });
        }

        /** Scan the ProjectThing children and assign the renderable ones to an existing Display3D for their LayerSet, or open a new one. If true == wait && -1 != resample, then the method returns only when the mesh/es have been added. */
        static public Future<Vector<Future<Content>>> show(final ProjectThing pt, final boolean wait, final int resample) {
                if (null == pt) return null;

                final Future<Vector<Future<Content>>> fu = launchers.submit(new Callable<Vector<Future<Content>>>() {
                        @Override
                        public Vector<Future<Content>> call() {

                // Scan the given ProjectThing for 3D-viewable items
                // So: find arealist, pipe, ball, and profile_list types
                final HashSet<ProjectThing> hs = pt.findBasicTypeChildren();
                if (null == hs || 0 == hs.size()) {
                        Utils.logAll("Node " + pt + " does not contain any 3D-displayable children");
                        return null;
                }

                // Remove profile if it lives under a profile_list
                for (final Iterator<ProjectThing> it = hs.iterator(); it.hasNext(); ) {
                        final ProjectThing pt = it.next();
                        if (null != pt.getObject() && pt.getObject().getClass() == Profile.class && pt.getParent().getType().equals("profile_list")) {
                                it.remove();
                        }
                }

                setWaitingCursor();

                // Start new scheduler to publish/add meshes to the 3D Viewer every 5 seconds and when done.
                final Hashtable<Display3D,Vector<Content>> contents = new Hashtable<Display3D,Vector<Content>>();
                final ScheduledExecutorService updater = Executors.newScheduledThreadPool(1);
                final AtomicInteger counter = new AtomicInteger();
                updater.scheduleWithFixedDelay(new Runnable() {
                        @Override
                        public void run() {
                                // Obtain a copy of the contents queue
                                final HashMap<Display3D,Vector<Content>> m = new HashMap<Display3D,Vector<Content>>();
                                synchronized (contents) {
                                        m.putAll(contents);
                                        contents.clear();
                                }
                                if (m.isEmpty()) return;
                                // Add all to the corresponding Display3D
                                for (final Map.Entry<Display3D,Vector<Content>> e : m.entrySet()) {
                                        e.getKey().universe.addContentLater(e.getValue());
                                        counter.getAndAdd(e.getValue().size());
                                }
                                Utils.showStatus(new StringBuilder("Rendered ").append(counter.get()).append('/').append(hs.size()).toString());
                        }
                }, 100, 4000, TimeUnit.MILLISECONDS);

                // A list of all generated Content objects
                final Vector<Future<Content>> list = new Vector<Future<Content>>();

                for (final Iterator<ProjectThing> it = hs.iterator(); it.hasNext(); ) {
                        // obtain the Displayable object under the node
                        final ProjectThing child = it.next();

                        final Object obc = child.getObject();
                        final Displayable displ = obc.getClass().equals(String.class) ? null : (Displayable)obc;
                        if (null != displ) {
                                if (displ.getClass().equals(Profile.class)) {
                                        //Utils.log("Display3D can't handle Bezier profiles at the moment.");
                                        // handled by profile_list Thing
                                        continue;
                                }
                                if (!displ.isVisible()) {
                                        Utils.log("Skipping non-visible node " + displ);
                                        continue;
                                }
                        }
                        // obtain the containing LayerSet
                        final Display3D d3d;
                        if (null != displ) d3d = Display3D.get(displ.getLayerSet());
                        else if (child.getType().equals("profile_list")) {
                                final ArrayList<ProjectThing> al_children = child.getChildren();
                                if (null == al_children || 0 == al_children.size()) continue;
                                // else, get the first Profile and get its LayerSet
                                d3d = Display3D.get(((Displayable)((ProjectThing)al_children.get(0)).getObject()).getLayerSet());
                        } else {
                                Utils.log("Don't know what to do with node " + child);
                                d3d = null;
                        }
                        if (null == d3d) {
                                Utils.log("Could not get a proper 3D display for node " + displ);
                                return null; // java3D not installed most likely
                        }

                        boolean already;
                        synchronized (d3d.ht_pt_meshes) {
                                already = d3d.ht_pt_meshes.containsKey(child);
                        }
                        if (already) {
                                if (child.getObject() instanceof ZDisplayable) {
                                        Utils.log("Updating 3D view of " + child.getObject());
                                } else {
                                        Utils.log("Updating 3D view of " + child);
                                }
                        }

                        list.add(d3d.executors.submit(new Callable<Content>() {
                                @Override
                                public Content call() {
                                        Content c = null;
                                        try {
                                                c = d3d.createMesh(child, displ, resample).call();
                                                Vector<Content> vc;
                                                synchronized (contents) {
                                                        vc = contents.get(d3d);
                                                        if (null == vc) vc = new Vector<Content>();
                                                        contents.put(d3d, vc);
                                                }
                                                vc.add(c);
                                        } catch (final Exception e) {
                                                IJError.print(e);
                                        }
                                        return c;
                                }
                        }));

                        // If it's the last one:
                        if (!it.hasNext()) {
                                // Add the concluding task, that waits on all and shuts down the scheduler
                                d3d.executors.submit(new Runnable() {
                                        @Override
                                        public void run() {
                                                // Wait until all are done
                                                for (final Future<Content> c : list) {
                                                        try {
                                                                c.get();
                                                        } catch (final Throwable t) {
                                                                IJError.print(t);
                                                        }
                                                }
                                                try {
                                                        // Shutdown scheduler and execute remaining tasks
                                                        for (final Runnable r : updater.shutdownNow()) {
                                                                r.run();
                                                        }
                                                } catch (final Throwable e) {
                                                        IJError.print(e);
                                                }
                                                // Reset cursor
                                                doneWaiting();
                                                Utils.showStatus(new StringBuilder("Done rendering ").append(counter.get()).append('/').append(hs.size()).toString());
                                        }
                                });
                        }
                }

                return list;

                }});

                if (wait && -1 != resample) {
                        try {
                                fu.get();
                        } catch (final Throwable t) {
                                IJError.print(t);
                        }
                }

                return fu;
        }

        static public void resetView(final LayerSet ls) {
                final Display3D d3d = ht_layer_sets.get(ls);
                if (null != d3d) d3d.universe.resetView();
        }

        static public void showOrthoslices(final Patch p) {
                final Display3D d3d = get(p.getLayerSet());
                d3d.adjustResampling();
                //d3d.universe.resetView();
                final String title = makeTitle(p) + " orthoslices";
                // remove if present
                d3d.universe.removeContent(title);
                final PatchStack ps = p.makePatchStack();
                final ImagePlus imp = get8BitStack(ps);
                final Content ct = d3d.universe.addOrthoslice(imp, null, title, 0, new boolean[]{true, true, true}, d3d.resample);
                setTransform(ct, ps.getPatch(0));
                ct.setLocked(true); // locks the added content
        }

        static public void showVolume(final Patch p) {
                final Display3D d3d = get(p.getLayerSet());
                d3d.adjustResampling();
                //d3d.universe.resetView();
                final String title = makeTitle(p) + " volume";
                // remove if present
                d3d.universe.removeContent(title);
                final PatchStack ps = p.makePatchStack();
                final ImagePlus imp = get8BitStack(ps);
                final Content ct = d3d.universe.addVoltex(imp, null, title, 0, new boolean[]{true, true, true}, d3d.resample);
                setTransform(ct, ps.getPatch(0));
                ct.setLocked(true); // locks the added content
        }

        static private void setTransform(final Content ct, final Patch p) {
                final double[] a = new double[6];
                p.getAffineTransform().getMatrix(a);
                final Calibration cal = p.getLayerSet().getCalibration();
                // a is: m00 m10 m01 m11 m02 m12
                // d expects: m01 m02 m03 m04, m11 m12 ...
                ct.applyTransform(new Transform3D(new double[]{a[0], a[2], 0, a[4] * cal.pixelWidth,
                                                               a[1], a[3], 0, a[5] * cal.pixelWidth,
                                                                  0,    0, 1, p.getLayer().getZ() * cal.pixelWidth,
                                                                  0,    0, 0, 1}));
        }

        static public void showOrthoslices(final ImagePlus imp, final String title, final int wx, final int wy, final float scale2D, final Layer first) {
                final Display3D d3d = get(first.getParent());
                d3d.universe.removeContent(title);
                final Content ct = d3d.universe.addOrthoslice(imp, null, title, 0, new boolean[]{true, true, true}, 1);
                final Calibration cal = imp.getCalibration();
                final Transform3D t = new Transform3D(new double[]{1, 0, 0, wx * cal.pixelWidth * scale2D,
                                                                                                         0, 1, 0, wy * cal.pixelHeight * scale2D,
                                                                                                         0, 0, scale2D, first.getZ() * cal.pixelWidth * scale2D, // not pixelDepth!
                                                                                                         0, 0, 0, 1});
                                                                                                // why scale2D has to be there at all reflects a horrible underlying setting of the calibration, plus of the scaling in the Display3D.
                Utils.log(t);
                ct.applyTransform(t);
                ct.setLocked(true);
        }

        /** Returns a stack suitable for the ImageJ 3D Viewer, either 8-bit gray or 8-bit color.
         *  If the PatchStack is already of the right type, it is returned,
         *  otherwise a copy is made in the proper type.
         */
        static private ImagePlus get8BitStack(final PatchStack ps) {
                switch (ps.getType()) {
                        case ImagePlus.COLOR_RGB:
                                // convert stack to 8-bit color
                                return ps.createColor256Copy();
                        case ImagePlus.GRAY16:
                        case ImagePlus.GRAY32:
                                // convert stack to 8-bit
                                return ps.createGray8Copy();
                        case ImagePlus.GRAY8:
                        case ImagePlus.COLOR_256:
                                return ps;
                        default:
                                Utils.logAll("Cannot handle stacks of type: " + ps.getType());
                                return null;
                }
        }

        /** Considers there is only one Display3D for each LayerSet. */
        static public void remove(final ProjectThing pt) {
                if (null == pt) return;
                if (null == pt.getObject()) return;
                final Object ob = pt.getObject();
                if (!(ob instanceof Displayable)) return;
                final Displayable displ = (Displayable)ob;
                final Display3D d3d = ht_layer_sets.get(displ.getLayerSet()); // TODO profile_list is going to fail here
                if (null == d3d) {
                        // there is no Display3D showing the pt to remove
                        //Utils.log2("No Display3D contains ProjectThing: " + pt);
                        return;
                }
                String name;
                synchronized (d3d.ht_pt_meshes) {
                        name = d3d.ht_pt_meshes.remove(pt);
                }
                if (null == name) {
                        Utils.log2("No mesh contained within " + d3d + " for ProjectThing " + pt);
                        return;
                }
                d3d.universe.removeContent(name);
        }


        /** Creates a mesh for the given Displayable in a separate Thread, and adds it to the universe. */
        private Future<Content> addMesh(final ProjectThing pt, final Displayable displ, final int resample) {
                return executors.submit(new Callable<Content>() {
                        @Override
                        public Content call() {
                                try {
                                        // 1 - Create content
                                        final Callable<Content> c = createMesh(pt, displ, resample);
                                        if (null == c) return null;
                                        final Content content = c.call();
                                        if (null == content) return null;
                                        final String title = content.getName();
                                        // 2 - Remove from universe any content of the same title
                                        if (universe.contains(title)) {
                                                universe.removeContent(title);
                                        }
                                        // 3 - Add to universe, and wait
                                        universe.addContentLater(content).get();

                                        return content;

                                } catch (final Exception e) {
                                        IJError.print(e);
                                        return null;
                                }
                        }
                });
        }

        static private final String makeProfileListTitle(final ProjectThing pt) {
                String title;
                final Object ob = pt.getParent().getTitle();
                if (null == ob || ob.equals(pt.getParent().getType())) title = pt.toString() + " #" + pt.getId(); // Project.getMeaningfulTitle can't handle profile_list properly
                else title = ob.toString() + " /[" + pt.getParent().getType() + "]/[profile_list] #" + pt.getId();
                return title;
        }

        /** Remove all basic type children contained in {@param pt} and its children, recursively.
         *
         * @param pt
         */
        static public void removeFrom3D(final ProjectThing pt) {
                final HashSet<ProjectThing> hs = pt.findBasicTypeChildren();
                if (null == hs || 0 == hs.size()) {
                        Utils.logAll("Nothing to remove from 3D.");
                        return;
                }
                // Ignore Profile instances ("profile_list" takes care of them)
                for (final ProjectThing child : hs) {
                        if (child.getByType().equals("profile")) continue;
                        // Find the LayerSet
                        LayerSet lset = null;
                        if (child.getType().equals("profile_list")) {
                                if (!child.hasChildren()) continue;
                                for (final ProjectThing p : child.getChildren()) {
                                        if (null != p.getObject() && p.getObject() instanceof Profile) {
                                                lset = ((Displayable)p.getObject()).getLayerSet();
                                                break;
                                        }
                                }
                                if (null == lset) continue;
                        } else if (child.getType().equals("profile")) {
                                // Taken care of by "profile list"
                                continue;
                        } else {
                                final Displayable d = (Displayable)child.getObject();
                                if (null == d) {
                                        Utils.log("Null object for ProjectThing " + child);
                                        continue;
                                }
                                lset = d.getLayerSet();
                        }
                        if (null == lset) {
                                Utils.log("No LayerSet found for " + child);
                                continue;
                        }
                        final Display3D d3d = getDisplay(lset);
                        if (null == d3d) {
                                Utils.log("No Display 3D found for " + child);
                                continue; // no Display3D window open
                        }
                        final String oldTitle = d3d.ht_pt_meshes.remove(child);
                        if (null == oldTitle) {
                                Utils.log("Could not find a title for " + child);
                                continue;
                        }
                        Utils.log("Removed from 3D view: " + oldTitle);
                        d3d.getUniverse().removeContent(oldTitle);
                }
        }


        /** Returns a function that returns a Content object.
         *  Does NOT add the Content to the universe; it merely creates it. */
        public Callable<Content> createMesh(final ProjectThing pt, final Displayable displ, final int resample) {
                final double scale = 1.0; // OBSOLETE
                return new Callable<Content>() {
                        @Override
                        public Content call() {
                                Thread.currentThread().setPriority(Thread.NORM_PRIORITY);
                                try {

                // the list 'triangles' is really a list of Point3f, which define a triangle every 3 consecutive points. (TODO most likely Bene Schmid got it wrong: I don't think there's any need to have the points duplicated if they overlap in space but belong to separate triangles.)
                final List<Point3f> triangles;
                //boolean no_culling_ = false;

                final Class<?> c;
                final boolean line_mesh;
                final int line_mesh_mode;
                if (null == displ) {
                        c = null;
                        line_mesh = false;
                        line_mesh_mode = Integer.MAX_VALUE;
                } else {
                        c = displ.getClass();
                        line_mesh = Tree.class.isAssignableFrom(c) || Polyline.class == c;
                        if (Tree.class.isAssignableFrom(c)) line_mesh_mode = CustomLineMesh.PAIRWISE;
                        else if (Polyline.class == c) line_mesh_mode = CustomLineMesh.CONTINUOUS;
                        else line_mesh_mode = Integer.MAX_VALUE; // disabled
                }

                List<Point3f> extra_triangles = null;
                List<Color3f> triangle_colors = null,
                                          extra_triangle_colors = null;

                int rs = resample;
                if (displ instanceof AreaContainer) {
                        if (-1 == resample) rs = Display3D.this.resample = adjustResampling(); // will adjust this.resample, and return it (even if it's a default value)
                        else rs = Display3D.this.resample;
                }
                if (AreaList.class == c) {
                        triangles = ((AreaList)displ).generateTriangles(scale, rs);
                        //triangles = removeNonManifold(triangles);
                } else if (Ball.class == c) {
                        final double[][][] globe = Ball.generateGlobe(12, 12);
                        triangles = ((Ball)displ).generateTriangles(scale, globe);
                } else if (displ instanceof Line3D) {
                        // Pipe and Polyline
                        // adjustResampling();  // fails horribly, needs first to correct mesh-generation code
                        triangles = ((Line3D)displ).generateTriangles(scale, 12, 1 /*Display3D.this.resample*/);
                } else if (displ instanceof Tree<?>) {
                        // A 3D wire skeleton, using CustomLineMesh
                        final Tree.MeshData skeleton = ((Tree<?>)displ).generateSkeleton(scale, 12, 1);
                        triangles = skeleton.verts;
                        triangle_colors = skeleton.colors;
                        if (displ instanceof Treeline) {
                                final Tree.MeshData tube = ((Treeline)displ).generateMesh(scale, 12);
                                extra_triangles = tube.verts;
                                extra_triangle_colors = tube.colors;
                        } else if (displ instanceof AreaTree) {
                                final Tree.MeshData mesh = ((AreaTree)displ).generateMesh(scale, rs);
                                extra_triangles = mesh.verts;
                                extra_triangle_colors = mesh.colors;
                        }
                        if (null != extra_triangles && extra_triangles.isEmpty()) extra_triangles = null; // avoid issues with MultiMesh
                } else if (Connector.class == c) {
                        final Tree.MeshData octopus = ((Connector)displ).generateMesh(scale, 12);
                        triangles = octopus.verts;
                        triangle_colors = octopus.colors;
                } else if (null == displ && pt.getType().equals("profile_list")) {
                        triangles = Profile.generateTriangles(pt, scale);
                        //no_culling_ = true;
                } else {
                        Utils.log("Unrecognized type for 3D mesh generation: " + (null != displ ? displ.getClass() : null) + " : " + displ);
                        triangles = null;
                }
                // safety checks
                if (null == triangles) {
                        Utils.log("Some error ocurred: can't create triangles for " + displ);
                        return null;
                }
                if (0 == triangles.size()) {
                        Utils.log2("Skipping empty mesh for " + displ.getTitle());
                        return null;
                }
                if (!line_mesh && 0 != triangles.size() % 3) {
                        Utils.log2("Skipping non-multiple-of-3 vertices list generated for " + displ.getTitle());
                        return null;
                }

                final Color color;
                final float alpha;
                final String title;
                if (null != displ) {
                        color = displ.getColor();
                        alpha = displ.getAlpha();
                        title = makeTitle(displ);
                } else if (pt.getType().equals("profile_list")) {
                        // for profile_list: get from the first (what a kludge; there should be a ZDisplayable ProfileList object)
                        final Object obp = ((ProjectThing)pt.getChildren().get(0)).getObject();
                        if (null == obp) return null;
                        final Displayable di = (Displayable)obp;
                        color = di.getColor();
                        alpha = di.getAlpha();
                        title = makeProfileListTitle(pt);
                } else {
                        title = pt.toString() + " #" + pt.getId();
                        color = null;
                        alpha = 1.0f;
                }

                // Why for all? Above no_culling_ is set to true or false, depending upon type. --> Because with transparencies it looks proper and better when no_culling is true.
                final boolean no_culling = true; // for ALL

                Content ct = null;

                try {
                        final Color3f c3 = new Color3f(color);

                        // If it exists, remove and add as new:
                        universe.removeContent(title);

                        final CustomMesh cm;

                        if (line_mesh) {
                                //ct = universe.createContent(new CustomLineMesh(triangles, line_mesh_mode, c3, 0), title);
                                cm = new CustomLineMesh(triangles, line_mesh_mode, c3, 0);
                        } else if (no_culling) {
                                // create a mesh with the same color and zero transparency (that is, full opacity)
                                final CustomTriangleMesh mesh = new CustomTriangleMesh(triangles, c3, 0);
                                // Set mesh properties for double-sided triangles
                                final PolygonAttributes pa = mesh.getAppearance().getPolygonAttributes();
                                pa.setCullFace(PolygonAttributes.CULL_NONE);
                                pa.setBackFaceNormalFlip(true);
                                mesh.setColor(c3);
                                // After setting properties, add to the viewer
                                //ct = universe.createContent(mesh, title);
                                cm = mesh;
                        } else {
                                //ct = universe.createContent(new CustomTriangleMesh(triangles, c3, 0), title);
                                cm = new CustomTriangleMesh(triangles, c3, 0);
                        }

                        if (null != triangle_colors) cm.setColor(triangle_colors);

                        //if (null == cm) return null;

                        if (null == extra_triangles || 0 == extra_triangles.size()) {
                                ct = universe.createContent(cm, title);
                        } else {
                                final CustomTriangleMesh extra = new CustomTriangleMesh(extra_triangles, c3, 0);
                                if (null != extra_triangle_colors) {
                                        // Set mesh properties for double-sided triangles
                                        final PolygonAttributes pa = extra.getAppearance().getPolygonAttributes();
                                        pa.setCullFace(PolygonAttributes.CULL_NONE);
                                        pa.setBackFaceNormalFlip(true);
                                        extra.setColor(extra_triangle_colors);
                                }
                                ct = universe.createContent(new CustomMultiMesh(Arrays.asList(new CustomMesh[]{cm, extra})), title);
                        }

                        // Set general content properties
                        ct.setTransparency(1f - alpha);
                        // Default is unlocked (editable) transformation; set it to locked:
                        ct.setLocked(true);

                        // register mesh title
                        synchronized (ht_pt_meshes) {
                                ht_pt_meshes.put(pt, ct.getName());
                        }

                } catch (final Throwable e) {
                        Utils.logAll("Mesh generation failed for \"" + title + "\"  from " + pt);
                        IJError.print(e);
                        e.printStackTrace();
                }

                Utils.log2(pt.toString() + " n points: " + triangles.size());

                return ct;

                                } catch (final Exception e) {
                                        IJError.print(e);
                                        return null;
                                }

                }};
        }

        static public class VectorStringContent {
                VectorString3D vs;
                String title;
                Color color;
                double[] widths;
                float alpha;
                public VectorStringContent(final VectorString3D vs, final String title, final Color color, final double[] widths, final float alpha){
                        this.vs = vs;
                        this.title = title;
                        this.color = color;
                        this.widths = widths;
                        this.alpha = alpha;
                }
                public Content asContent(final Display3D d3d) {
                        double[] wi = widths;
                        if (null == widths) {
                                wi = new double[vs.getPoints(0).length];
                                Arrays.fill(wi, 2.0);
                        } else if (widths.length != vs.length()) {
                                Utils.log("ERROR: widths.length != VectorString3D.length()");
                                return null;
                        }
                        float transp = 1 - alpha;
                        if (transp < 0) transp = 0;
                        if (transp > 1) transp = 1;
                        if (1 == transp) {
                                Utils.log("WARNING: adding a 3D object fully transparent.");
                        }
                        final List<Point3f> triangles = Pipe.generateTriangles(Pipe.makeTube(vs.getPoints(0), vs.getPoints(1), vs.getPoints(2), wi, 1, 12, null), d3d.scale);
                        final Content ct = d3d.universe.createContent(new CustomTriangleMesh(triangles, new Color3f(color), 0), title);
                        ct.setTransparency(transp);
                        ct.setLocked(true);
                        return ct;
                }
        }

        /** Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe. */
        static public Future<Collection<Future<Content>>> addMesh(final LayerSet ref_ls, final VectorString3D vs, final String title, final Color color) {
                return addMesh(ref_ls, vs, title, color, null, 1.0f);
        }

        /** Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe. */
        static public Future<Collection<Future<Content>>> addMesh(final LayerSet ref_ls, final VectorString3D vs, final String title, final Color color, final double[] widths, final float alpha) {
                final List<Content> col = new ArrayList<Content>();
                final Display3D d3d = Display3D.get(ref_ls);
                col.add(new VectorStringContent(vs, title, color, widths, alpha).asContent(d3d));
                return d3d.addContent(col);
        }

        static public Future<Collection<Future<Content>>> show(final LayerSet ref_ls, final Collection<Content> col) {
                final Display3D d3d = get(ref_ls);
                return d3d.addContent(col);
        }

        public Future<Collection<Future<Content>>> addContent(final Collection<Content> col) {

                final FutureTask<Collection<Future<Content>>> fu = new FutureTask<Collection<Future<Content>>>(new Callable<Collection<Future<Content>>>() {
                        @Override
                        public Collection<Future<Content>> call() {
                                Thread.currentThread().setPriority(Thread.NORM_PRIORITY);
                                try {
                                        return universe.addContentLater(col);
                                } catch (final Throwable e) {
                                        IJError.print(e);
                                        return null;
                                }
                }});

                launchers.submit(new Runnable() { @Override
                public void run() {
                        executors.submit(fu);
                }});

                return fu;
        }

        public Future<Content> addContent(final Content c) {
                final FutureTask<Content> fu = new FutureTask<Content>(new Callable<Content>() {
                        @Override
                        public Content call() {
                                Thread.currentThread().setPriority(Thread.NORM_PRIORITY);
                                try {
                                        return universe.addContentLater(c).get();
                                } catch (final Throwable e) {
                                        IJError.print(e);
                                        return null;
                                }
                        }
                });

                launchers.submit(new Runnable() { @Override
                public void run() {
                        executors.submit(fu);
                }});

                return fu;
        }

        static public final int estimateResamplingFactor(final LayerSet ls, final double width, final double height) {
                final int max_dimension = ls.getPixelsMaxDimension();
                return (int)(DEFAULT_RESAMPLE / (Math.max(width, height) > max_dimension ?
                          max_dimension / Math.max(width, height)
                        : 1));
        }

        /** Estimate a scaling factor, to be used as a multiplier of the suggested default resampling. */
        private final int estimateResamplingFactor() {
                return estimateResamplingFactor(layer_set, width, height);
        }

        // This method has the exclusivity in adjusting the resampling value, and it also returns it.
        synchronized private final int adjustResampling() {
                if (resample > 0) return resample;
                final GenericDialog gd = new GenericDialog("Resample");
                final int default_resample = estimateResamplingFactor();
                gd.addSlider("Resample: ", 1, Math.max(default_resample, 100), -1 != resample ? resample : default_resample);
                gd.showDialog();
                if (gd.wasCanceled()) {
                        resample = -1 != resample ? resample : default_resample; // current or default value
                        return resample;
                }
                resample = ((java.awt.Scrollbar)gd.getSliders().get(0)).getValue();
                return resample;
        }

        /** Checks if there is any Display3D instance currently showing the given Displayable. */
        static public boolean isDisplayed(final Displayable d) {
                if (null == d) return false;
                final String title = makeTitle(d);
                for (final Display3D d3d : ht_layer_sets.values()) {
                        if (null != d3d.universe.getContent(title)) return true;
                }
                if (d.getClass() == Profile.class) {
                        if (null != getProfileContent(d)) return true;
                }
                return false;
        }

        /** Checks if the given Displayable is a Profile, and tries to find a possible Content object in the Image3DUniverse of its LayerSet according to the title as created from its profile_list ProjectThing. */
        static public Content getProfileContent(final Displayable d) {
                if (null == d) return null;
                if (d.getClass() != Profile.class) return null;
                final Display3D d3d = get(d.getLayer().getParent());
                if (null == d3d) return null;
                ProjectThing pt = d.getProject().findProjectThing(d);
                if (null == pt) return null;
                pt = (ProjectThing) pt.getParent();
                return d3d.universe.getContent(new StringBuilder(pt.toString()).append(" #").append(pt.getId()).toString());
        }

        static public Future<Boolean> setColor(final Displayable d, final Color color) {
                final Display3D d3d = getDisplay(d.getLayer().getParent());
                if (null == d3d) return null; // no 3D displays open
                return d3d.executors.submit(new Callable<Boolean>() { @Override
                public Boolean call() {
                        Content content = d3d.universe.getContent(makeTitle(d));
                        if (null == content) content = getProfileContent(d);
                        if (null != content) {
                                content.setColor(new Color3f(color));
                                return true;
                        }
                        return false;
                }});
        }

        static public Future<Boolean> setTransparency(final Displayable d, final float alpha) {
                if (null == d) return null;
                final Layer layer = d.getLayer();
                if (null == layer) return null; // some objects have no layer, such as the parent LayerSet.
                final Display3D d3d = ht_layer_sets.get(layer.getParent());
                if (null == d3d) return null;
                return d3d.executors.submit(new Callable<Boolean>() { @Override
                public Boolean call() {
                        String title = makeTitle(d);
                        Content content = d3d.universe.getContent(title);
                        if (null == content) content = getProfileContent(d);
                        if (null != content) content.setTransparency(1 - alpha);
                        else if (null == content && d.getClass().equals(Patch.class)) {
                                final Patch pa = (Patch)d;
                                if (pa.isStack()) {
                                        title = pa.getProject().getLoader().getFileName(pa);
                                        for (final Display3D dd : ht_layer_sets.values()) {
                                                for (final Iterator<?> cit = dd.universe.getContents().iterator(); cit.hasNext(); ) {
                                                        final Content c = (Content)cit.next();
                                                        if (c.getName().startsWith(title)) {
                                                                c.setTransparency(1 - alpha);
                                                                // no break, since there could be a volume and an orthoslice
                                                        }
                                                }
                                        }
                                }
                        }
                        return true;
                }});
        }

        static public String makeTitle(final Displayable d) {
                return d.getProject().getMeaningfulTitle(d) + " #" + d.getId();
        }
        static public String makeTitle(final Patch p) {
                return new File(p.getProject().getLoader().getAbsolutePath(p)).getName()
                       + " #" + p.getProject().getLoader().getNextId();
        }

        /** Remake the mesh for the Displayable in a separate Thread, if it's included in a Display3D
         *  (otherwise returns null). */
        static public Future<Content> update(final Displayable d) {
                final Layer layer = d.getLayer();
                if (null == layer) return null; // some objects have no layer, such as the parent LayerSet.
                final Display3D d3d = ht_layer_sets.get(layer.getParent());
                if (null == d3d) return null;
                return d3d.addMesh(d.getProject().findProjectThing(d), d, d3d.resample);
        }

        /*
        static public final double computeTriangleArea() {
                return 0.5 *  Math.sqrt(Math.pow(xA*yB + xB*yC + xC*yA, 2) +
                                        Math.pow(yA*zB + yB*zC + yC*zA, 2) +
                                        Math.pow(zA*xB + zB*xC + zC*xA, 2));
        }
        */

        static public final boolean contains(final LayerSet ls, final String title) {
                final Display3D d3d = getDisplay(ls);
                if (null == d3d) return false;
                return null != d3d.universe.getContent(title);
        }

        static public void destroy() {
                launchers.shutdownNow();
        }

        static public void init() {
                if (launchers.isShutdown()) {
                        launchers = Utils.newFixedThreadPool(Runtime.getRuntime().availableProcessors(), "Display3D-launchers");
                }
        }

        /** Creates a calibrated sphere to represent a point at LayerSet pixel coordinates wx, wy, wz, with radius wr.*/
        public List<Point3f> createFatPoint(final double wx, final double wy, final double wz, final double wr, final Calibration cal) {
                final double[][][] globe = Ball.generateGlobe(12, 12);
                final int sign = cal.pixelDepth < 0 ? -1 : 1;
                for (int z=0; z<globe.length; z++) {
                        for (int k=0; k<globe[0].length; k++) {
                                globe[z][k][0] = (globe[z][k][0] * wr + wx) * scale * cal.pixelWidth;
                                globe[z][k][1] = (globe[z][k][1] * wr + wy) * scale * cal.pixelHeight;
                                globe[z][k][2] = (globe[z][k][2] * wr + wz) * scale * cal.pixelWidth * sign; // not pixelDepth, see day notes 20080227. Because pixelDepth is in microns/px, not in px/microns, and the z coord here is taken from the z of the layer, which is in pixels.
                        }
                }
                final ArrayList<Point3f> list = new ArrayList<Point3f>();
                // create triangular faces and add them to the list
                for (int z=0; z<globe.length-1; z++) { // the parallels
                        for (int k=0; k<globe[0].length -1; k++) { // meridian points
                                // half quadrant (a triangle)
                                list.add(new Point3f((float)globe[z][k][0], (float)globe[z][k][1], (float)globe[z][k][2]));
                                list.add(new Point3f((float)globe[z+1][k+1][0], (float)globe[z+1][k+1][1], (float)globe[z+1][k+1][2]));
                                list.add(new Point3f((float)globe[z+1][k][0], (float)globe[z+1][k][1], (float)globe[z+1][k][2]));
                                // the other half quadrant
                                list.add(new Point3f((float)globe[z][k][0], (float)globe[z][k][1], (float)globe[z][k][2]));
                                list.add(new Point3f((float)globe[z][k+1][0], (float)globe[z][k+1][1], (float)globe[z][k+1][2]));
                                list.add(new Point3f((float)globe[z+1][k+1][0], (float)globe[z+1][k+1][1], (float)globe[z+1][k+1][2]));
                        }
                }
                return list;
        }

        /** Expects uncalibrated wx,wy,wz, (i.e. pixel values), to be calibrated by @param ls calibration. */
        static public final Future<Content> addFatPoint(final String title, final LayerSet ls, final double wx, final double wy, final double wz, final double wr, final Color color) {
                final Display3D d3d = Display3D.get(ls);
                d3d.universe.removeContent(title);
                final Content ct = d3d.universe.createContent(new CustomTriangleMesh(d3d.createFatPoint(wx, wy, wz, wr, ls.getCalibrationCopy()), new Color3f(color), 0), title);
                ct.setLocked(true);
                return d3d.addContent(ct);
        }

}