Updated copyright dates.

[trakem2.git] / ini / trakem2 / display / LayerSet.java

/**

TrakEM2 plugin for ImageJ(C).
Copyright (C) 2005-2009 Albert Cardona and Rodney Douglas.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.txt )

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 

You may contact Albert Cardona at acardona at ini.phys.ethz.ch
Institute of Neuroinformatics, University of Zurich / ETH, Switzerland.
**/

package ini.trakem2.display;


import ij.gui.GenericDialog;
import ij.measure.Calibration;
import ij.ImagePlus;
import ij.ImageStack;

import ini.trakem2.ControlWindow;
import ini.trakem2.Project;
import ini.trakem2.persistence.DBObject;
import ini.trakem2.utils.ProjectToolbar;
import ini.trakem2.utils.Utils;
import ini.trakem2.utils.IJError;
import ini.trakem2.imaging.LayerStack;
import ini.trakem2.tree.LayerThing;
import ini.trakem2.tree.Thing;

import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Composite;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.Rectangle;
import java.awt.geom.AffineTransform;
import java.awt.geom.Area;
import java.util.ArrayList;
import java.util.List;
import java.util.HashMap;
import java.util.TreeMap;
import java.util.Iterator;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.Map;
import java.util.Set;
import java.util.Collection;


/** A LayerSet represents an axis on which layers can be stacked up. Paints with 0.67 alpha transparency when not active. */
public final class LayerSet extends Displayable implements Bucketable { // Displayable is already extending DBObject

        // the anchors for resizing
        static public final int NORTH = 0;
        static public final int NORTHEAST = 1;
        static public final int EAST = 2;
        static public final int SOUTHEAST = 3;
        static public final int SOUTH = 4;
        static public final int SOUTHWEST = 5;
        static public final int WEST = 6;
        static public final int NORTHWEST = 7;
        static public final int CENTER = 8;

        // the possible rotations
        static public final int R90 = 9;
        static public final int R270 = 10;
        // the posible flips
        static public final int FLIP_HORIZONTAL = 11;
        static public final int FLIP_VERTICAL = 12;

        // postions in the stack
        static public final int TOP = 13;
        static public final int UP = 14;
        static public final int DOWN = 15;
        static public final int BOTTOM = 16;

        static public final String[] snapshot_modes = new String[]{"Full","Outlines","Disabled"};

        /** 0, 1, 2 -- corresponding to snapshot_modes entries above. */
        private int snapshots_mode = 0;

        static public final String[] ANCHORS =  new String[]{"north", "north east", "east", "southeast", "south", "south west", "west", "north west", "center"};
        static public final String[] ROTATIONS = new String[]{"90 right", "90 left", "Flip horizontally", "Flip vertically"};

        private double layer_width; // the Displayable.width is for the representation, not for the dimensions of the LayerSet!
        private double layer_height;
        private double rot_x;
        private double rot_y;
        private double rot_z; // should be equivalent to the Displayable.rot
        private final ArrayList<Layer> al_layers = new ArrayList<Layer>();
        /** The layer in which this LayerSet lives. If null, this is the root LayerSet. */
        private Layer parent = null;
        /** A LayerSet can contain Displayables that are show in every single Layer, such as Pipe objects. */
        private final ArrayList<ZDisplayable> al_zdispl = new ArrayList<ZDisplayable>();

        /** For creating snapshots. */
        private boolean snapshots_quality = true;

        /** Tool to manually register using landmarks across two layers. Uses the toolbar's 'Align tool'. */
        private Align align = null;

        /** The scaling applied to the Layers when painting them for presentation as a LayerStack. If -1, automatic mode (default) */
        private double virtual_scale = -1;
        /** The maximum size of either width or height when virtuzaling pixel access to the layers.*/
        private int max_dimension = 1024;
        private boolean virtualization_enabled = false;

        private Calibration calibration = new Calibration(); // default values

        /** Dummy. */
        protected LayerSet(Project project, long id) {
                super(project, id, null, false, null, 20, 20);
        }

        /** Create a new LayerSet with a 0,0,0 rotation vector and default 20,20 px Displayable width,height. */
        public LayerSet(Project project, String title, double x, double y, Layer parent, double layer_width, double layer_height) {
                super(project, title, x, y);
                rot_x = rot_y = rot_z = 0.0D;
                this.width = 20;
                this.height = 20; // for the label that paints into the parent Layer
                this.parent = parent;
                this.layer_width = layer_width;
                this.layer_height = layer_height;
                addToDatabase();
        }

        /** Reconstruct from the database. */
        public LayerSet(Project project, long id, String title, double width, double height, double rot_x, double rot_y, double rot_z, double layer_width, double layer_height, boolean locked, int shapshots_mode, AffineTransform at) {
                super(project, id, title, locked, at, width, height);
                this.rot_x = rot_x;
                this.rot_y = rot_y;
                this.rot_z = rot_z;
                this.layer_width = layer_width;
                this.layer_height= layer_height;
                this.snapshots_mode = snapshots_mode;
                // the parent will be set by the LayerThing.setup() calling Layer.addSilently()
                // the al_layers will be filled idem.
        }

        /** Reconstruct from an XML entry. */
        public LayerSet(Project project, long id, HashMap ht_attributes, HashMap ht_links) {
                super(project, id, ht_attributes, ht_links);
                for (Iterator it = ht_attributes.entrySet().iterator(); it.hasNext(); ) {
                        Map.Entry entry = (Map.Entry)it.next();
                        String key = (String)entry.getKey();
                        String data = (String)entry.getValue();
                        if (key.equals("layer_width")) {
                                this.layer_width = Double.parseDouble(data);
                        } else if (key.equals("layer_height")) {
                                this.layer_height = Double.parseDouble(data);
                        } else if (key.equals("rot_x")) {
                                this.rot_x = Double.parseDouble(data);
                        } else if (key.equals("rot_y")) {
                                this.rot_y = Double.parseDouble(data);
                        } else if (key.equals("rot_z")) {
                                this.rot_z = Double.parseDouble(data);
                        } else if (key.equals("snapshots_quality")) {
                                snapshots_quality = Boolean.valueOf(data.trim().toLowerCase());
                        } else if (key.equals("snapshots_mode")) {
                                String smode = data.trim();
                                for (int i=0; i<snapshot_modes.length; i++) {
                                        if (smode.equals(snapshot_modes[i])) {
                                                snapshots_mode = i;
                                                break;
                                        }
                                }
                        }
                        // the above would be trivial in Jython, and can be done by reflection! The problem would be in the parsing, that would need yet another if/else if/ sequence was any field to change or be added.
                }
        }

        /** For reconstruction purposes: set the active layer to the ZDisplayable objects. Recurses through LayerSets in the children layers. */
        public void setup() {
                final Layer la0 = al_layers.get(0);
                for (ZDisplayable zd : al_zdispl) zd.setLayer(la0); // just any Layer
                for (Layer layer : al_layers) {
                        for (Iterator itl = layer.getDisplayables().iterator(); itl.hasNext(); ) {
                                Object ob = itl.next();
                                if (ob instanceof LayerSet) {
                                        ((LayerSet)ob).setup();
                                }
                        }
                }
        }

        /** Create a new LayerSet in the middle of the parent Layer. */
        public LayerSet create(Layer parent_layer) {
                if (null == parent_layer) return null;
                GenericDialog gd = ControlWindow.makeGenericDialog("New Layer Set");
                gd.addMessage("In pixels:");
                gd.addNumericField("width: ", this.layer_width, 3);
                gd.addNumericField("height: ", this.layer_height, 3);
                gd.showDialog();
                if (gd.wasCanceled()) return null;
                try {
                        double width = gd.getNextNumber();
                        double height = gd.getNextNumber();
                        if (Double.isNaN(width) || Double.isNaN(height)) return null;
                        if (0 == width || 0 == height) {
                                Utils.showMessage("Cannot accept zero width or height for LayerSet dimensions.");
                                return null;
                        }
                        // make a new LayerSet with x,y in the middle of the parent_layer
                        return new LayerSet(project, "Layer Set", parent_layer.getParent().getLayerWidth() / 2, parent_layer.getParent().getLayerHeight() / 2, parent_layer, width/2, height/2);
                } catch (Exception e) { Utils.log("LayerSet.create: " + e); }
                return null;
        }

        /** Add a new Layer silently, ordering by z as well.*/
        public void addSilently(final Layer layer) {
                if (null == layer || al_layers.contains(layer)) return;
                try {
                        double z = layer.getZ();
                        int i = 0;
                        for (Layer la : al_layers) {
                                if (! (la.getZ() < z) ) {
                                        al_layers.add(i, layer);
                                        layer.setParentSilently(this);
                                        return;
                                }
                                i++;
                        }
                        // else, add at the end
                        al_layers.add(layer);
                        layer.setParentSilently(this);
                } catch (Exception e) {
                        Utils.log("LayerSet.addSilently: Not a Layer, not adding DBObject id=" + layer.getId());
                        return;
                }
        }

        /** Add a new Layer, inserted according to its Z. */
        public void add(final Layer layer) {
                if (-1 != al_layers.indexOf(layer)) return;
                final double z = layer.getZ();
                final int n = al_layers.size();
                int i = 0;
                for (; i<n; i++) {
                        Layer l = (Layer)al_layers.get(i);
                        if (l.getZ() < z) continue;
                        break;
                }
                if (i < n) {
                        al_layers.add(i, layer);
                } else {
                        al_layers.add(layer);
                }
                layer.setParent(this);
                Display.updateLayerScroller(this);
                //debug();
        }

        private void debug() {
                Utils.log("LayerSet debug:");
                for (int i=0; i<al_layers.size(); i++)
                        Utils.log(i + " : " + ((Layer)al_layers.get(i)).getZ());
        }

        public Layer getParent() {
                return parent;
        }

        /** 'update' in database or not. */
        public void setLayer(Layer layer, boolean update) {
                super.setLayer(layer, update);
                if (null != layer) this.parent = layer; // repeated pointer, eliminate 'parent' !
        }

        public void setParent(Layer layer) {
                if (null == layer || layer == parent) return;
                this.parent = layer;
                updateInDatabase("parent_id");
        }

        public void mousePressed(MouseEvent me, int x_p, int y_p, Rectangle srcRect, double mag) {
                if (ProjectToolbar.SELECT != ProjectToolbar.getToolId()) return;
                Display.setActive(me, this);
                if (2 == me.getClickCount() && al_layers.size() > 0) {
                        new Display(project, al_layers.get(0));
                }
        }

        public void mouseDragged(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old, Rectangle srcRect, double mag) {
                if (ProjectToolbar.SELECT != ProjectToolbar.getToolId()) return;
                super.translate(x_d - x_d_old, y_d - y_d_old);
                Display.repaint(layer, this, 0);
        }

        public void mouseReleased(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r, Rectangle srcRect, double mag) {
                // nothing
        }

        public void keyPressed(KeyEvent ke) {
                Utils.log("LayerSet.keyPressed: not yet implemented.");
                // TODO
        }

        public String toString() {
                return this.title;
        }

        public void paint(Graphics2D g, double magnification, boolean active, int channels, Layer active_layer) {
                //arrange transparency
                Composite original_composite = null;
                if (alpha != 1.0f) {
                        original_composite = g.getComposite();
                        g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha));
                }

                //set color
                g.setColor(this.color);
                // fill a background box
                g.fillRect(0, 0, (int)(this.width), (int)(this.height));
                g.setColor(new Color(255 - color.getRed(), 255 - color.getGreen(), 255 - color.getBlue()).brighter()); // the "opposite", but brighter, so it won't fail to generate contrast if the color is 127 in all channels
                int x = (int)(this.width/5);
                int y = (int)(this.height/5);
                int width = (int)(this.width/5);
                int height = (int)(this.height/5 * 3);

                g.fillRect(x, y, width, height);

                x = (int)(this.width/5 * 2);
                y = (int)(this.height/5 * 3);
                width = (int)(this.width/5 * 2);
                height = (int)(this.height/5);

                g.fillRect(x, y, width, height);

                //Transparency: fix composite back to original.
                if (alpha != 1.0f) {
                        g.setComposite(original_composite);
                }
        }

        public double getLayerWidth() { return layer_width; }
        public double getLayerHeight() { return layer_height; }
        public double getRotX() { return rot_x; }
        public double getRotY() { return rot_y; }
        public double getRotZ() { return rot_z; }

        public int size() {
                return al_layers.size();
        }

        public void setRotVector(double rot_x, double rot_y, double rot_z) {
                if (Double.isNaN(rot_x) || Double.isNaN(rot_y) || Double.isNaN(rot_z)) {
                        Utils.showMessage("LayerSet: Rotation vector contains NaNs. Not updating.");
                        return;
                } else if (rot_x == this.rot_x && rot_y == this.rot_y && rot_z == this.rot_z) {
                        return;
                }
                this.rot_x = rot_x;
                this.rot_y = rot_y;
                this.rot_z = rot_z;
                updateInDatabase("rot");
        }

        /** Used by the Loader after loading blindly a lot of Patches. Will crop the canvas to the minimum size possible. */
        public boolean setMinimumDimensions() {
                // find current x,y,width,height that crops the canvas without cropping away any Displayable
                double x = Double.NaN;
                double y = Double.NaN;
                double xe = 0; // lower right corner (x end)
                double ye = 0;
                double tx = 0;
                double ty = 0;
                double txe = 0;
                double tye = 0;
                // collect all Displayable and ZDisplayable objects
                final ArrayList al = new ArrayList();
                for (int i=al_layers.size() -1; i>-1; i--) {
                        al.addAll(((Layer)al_layers.get(i)).getDisplayables());
                }
                al.addAll(al_zdispl);

                // find minimum bounding box
                Rectangle b = new Rectangle();
                for (Iterator it = al.iterator(); it.hasNext(); ) {
                        Displayable d = (Displayable)it.next();
                        b = d.getBoundingBox(b); // considers rotation
                        tx = b.x;//d.getX();
                        ty = b.y;//d.getY();
                        // set first coordinates
                        if (Double.isNaN(x) || Double.isNaN(y)) { // Double.NaN == x fails!
                                x = tx;
                                y = ty;
                        }
                        txe = tx + b.width;//d.getWidth();
                        tye = ty + b.height;//d.getHeight();
                        if (tx < x) x = tx;
                        if (ty < y) y = ty;
                        if (txe > xe) xe = txe;
                        if (tye > ye) ye = tye;
                }
                // if none, then stop
                if (Double.isNaN(x) || Double.isNaN(y)) {
                        Utils.showMessage("No displayable objects, don't know how to resize the canvas and Layerset.");
                        return false;
                }

                double w = xe - x;
                double h = ye - y;
                if (w <= 0 || h <= 0) {
                        Utils.log("LayerSet.setMinimumDimensions: zero width or height, NOT resizing.");
                        return false;
                }

                // Record previous state
                if (prepareStep(this)) {
                        addEditStep(new LayerSet.DoResizeLayerSet(this));
                }

                // translate
                if (0 != x || 0 != y) {
                        project.getLoader().startLargeUpdate();
                        try {
                                final AffineTransform at2 = new AffineTransform();
                                at2.translate(-x, -y);
                                //Utils.log2("translating all displayables by " + x + "," + y);
                                for (Iterator it = al.iterator(); it.hasNext(); ) {
                                        //((Displayable)it.next()).translate(-x, -y, false); // drag regardless of getting off current LayerSet bounds
                                        // optimized to avoid creating so many AffineTransform instances:
                                        final Displayable d = (Displayable)it.next();
                                        //Utils.log2("BEFORE: " + d.getBoundingBox());
                                        d.getAffineTransform().preConcatenate(at2);
                                        //Utils.log2("AFTER: " + d.getBoundingBox());
                                        d.updateInDatabase("transform");
                                }
                                project.getLoader().commitLargeUpdate();
                        } catch (Exception e) {
                                IJError.print(e);
                                project.getLoader().rollback();
                                return false;
                        }
                }

                //Utils.log("x,y  xe,ye : " + x + "," + y + "  " + xe + "," + ye);
                // finally, accept:
                if (w != layer_width || h != layer_height) {
                        this.layer_width = Math.ceil(w); // stupid int to double conversions ... why floating point math is a non-solved problem? Well, it is for SBCL
                        this.layer_height = Math.ceil(h);
                        updateInDatabase("layer_dimensions");
                        if (null != root) recreateBuckets(true);
                        // and notify the Displays, if any
                        Display.update(this);
                        Display.pack(this);
                }

                // Record current state:
                addEditStep(new LayerSet.DoResizeLayerSet(this));

                return true;
        }

        /** Enlarges the display in the given direction; the anchor is the point to keep still, and can be any of LayerSet.NORTHWEST (top-left), etc. */
        public boolean enlargeToFit(final Displayable d, final int anchor) {
                final Rectangle r = new Rectangle(0, 0, (int)Math.ceil(layer_width), (int)Math.ceil(layer_height));
                final Rectangle b = d.getBoundingBox(null);
                // check if necessary
                if (r.contains(b)) return false;
                // else, enlarge to fit it
                r.add(b);
                return setDimensions(r.width, r.height, anchor);
        }

        /** May leave objects beyond the visible window. */
        public void setDimensions(double x, double y, double layer_width, double layer_height) {
                // Record previous state
                if (prepareStep(this)) {
                        addEditStep(new LayerSet.DoResizeLayerSet(this));
                }

                this.layer_width = layer_width;
                this.layer_height = layer_height;
                final AffineTransform affine = new AffineTransform();
                affine.translate(-x, -y);
                for (ZDisplayable zd : al_zdispl) {
                        zd.getAffineTransform().preConcatenate(affine);
                        zd.updateInDatabase("transform");
                }
                for (Layer la : al_layers) la.apply(Displayable.class, affine);
                if (null != root) {
                        recreateBuckets(true);
                }
                Display.update(this);

                // Record new state
                addEditStep(new LayerSet.DoResizeLayerSet(this));
        }

        /** Returns false if any Displayables are being partially or totally cropped away. */
        public boolean setDimensions(double layer_width, double layer_height, int anchor) {
                // check preconditions
                if (Double.isNaN(layer_width) || Double.isNaN(layer_height)) { Utils.log("LayerSet.setDimensions: NaNs! Not adjusting."); return false; }
                if (layer_width <=0 || layer_height <= 0) { Utils.showMessage("LayerSet: can't accept zero or a minus for layer width or height"); return false; }
                if (anchor < NORTH || anchor > CENTER) {  Utils.log("LayerSet: wrong anchor, not resizing."); return false; }

                // Record previous state
                if (prepareStep(this)) {
                        addEditStep(new LayerSet.DoResizeLayerSet(this));
                }

                // new coordinates:
                double new_x = 0;// the x,y of the old 0,0
                double new_y = 0;
                switch (anchor) {
                        case NORTH:
                        case SOUTH:
                        case CENTER:
                                new_x = (layer_width - this.layer_width) / 2; // (this.layer_width - layer_width) / 2;
                                break;
                        case NORTHWEST:
                        case WEST:
                        case SOUTHWEST:
                                new_x = 0;
                                break;
                        case NORTHEAST:
                        case EAST:
                        case SOUTHEAST:
                                new_x = layer_width - this.layer_width; // (this.layer_width - layer_width);
                                break;
                }
                switch (anchor) {
                        case WEST:
                        case EAST:
                        case CENTER:
                                new_y = (layer_height - this.layer_height) / 2;
                                break;
                        case NORTHWEST:
                        case NORTH:
                        case NORTHEAST:
                                new_y = 0;
                                break;
                        case SOUTHWEST:
                        case SOUTH:
                        case SOUTHEAST:
                                new_y = (layer_height - this.layer_height);
                                break;
                }

                /*
                Utils.log("anchor: " + anchor);
                Utils.log("LayerSet: existing w,h = " + this.layer_width + "," + this.layer_height);
                Utils.log("LayerSet: new      w,h = " + layer_width + "," + layer_height);
                */

                // collect all Displayable and ZDisplayable objects
                ArrayList al = new ArrayList();
                for (int i=al_layers.size() -1; i>-1; i--) {
                        al.addAll(((Layer)al_layers.get(i)).getDisplayables());
                }
                al.addAll(al_zdispl);

                // check that no displayables are being cropped away
                if (layer_width < this.layer_width || layer_height < this.layer_height) {
                        for (Iterator it = al.iterator(); it.hasNext(); ) {
                                Displayable d = (Displayable)it.next();
                                Rectangle b = d.getBoundingBox(null);
                                double dw = b.getWidth();
                                double dh = b.getHeight();
                                // respect 10% margins
                                if (b.x + dw + new_x < 0.1 * dw || b.x + 0.9 * dw + new_x > layer_width || b.y + dh + new_y < 0.1 * dh || b.y + 0.9 * dh + new_y > layer_height) {
                                        // cropping!
                                        Utils.showMessage("Cropping " + d + "\nLayerSet: not resizing.");
                                        return false;
                                }
                        }
                }
                this.layer_width = layer_width;
                this.layer_height = layer_height;
                //Utils.log("LayerSet.setDimensions: new_x,y: " + new_x + "," + new_y);
                // translate all displayables
                if (0 != new_x || 0 != new_y) {
                        for (Iterator it = al.iterator(); it.hasNext(); ) {
                                Displayable d = (Displayable)it.next();
                                Rectangle b = d.getBoundingBox(null);
                                //Utils.log("d x,y = " + b.x + ", " + b.y);
                                d.setLocation(b.x + new_x, b.y + new_y);
                        }
                }

                updateInDatabase("layer_dimensions");
                if (null != root) recreateBuckets(true);
                // and notify the Display
                Display.update(this);
                Display.pack(this);

                // Record new state
                addEditStep(new LayerSet.DoResizeLayerSet(this));

                return true;
        }

        protected boolean remove2(boolean check) {
                if (check) {
                        if (!Utils.check("Really delete " + this.toString() + (null != al_layers && al_layers.size() > 0 ? " and all its children?" : ""))) return false;
                }
                LayerThing lt = project.findLayerThing(this);
                if (null == lt) return false;
                return project.getLayerTree().remove(check, lt, null); // will end up calling remove(boolean) on this object
        }

        public boolean remove(boolean check) {
                if (check) {
                        if (!Utils.check("Really delete " + this.toString() + (null != al_layers && al_layers.size() > 0 ? " and all its children?" : ""))) return false;
                }
                // delete all layers
                while (0 != al_layers.size()) {
                        if (!((DBObject)al_layers.get(0)).remove(false)) {
                                Utils.showMessage("LayerSet id= " + id + " : Deletion incomplete, check database.");
                                return false;
                        }
                }
                // delete the ZDisplayables
                Iterator it = al_zdispl.iterator();
                while (it.hasNext()) {
                        ((ZDisplayable)it.next()).remove(false); // will call back the LayerSet.remove(ZDisplayable)
                }
                // remove the self
                if (null != parent) parent.remove(this);
                removeFromDatabase();
                return true;
        }

        /** Remove a child. Does not destroy it or delete it from the database. */
        public void remove(Layer layer) {
                if (null == layer || -1 == al_layers.indexOf(layer)) return;
                al_layers.remove(layer);
                Display.updateLayerScroller(this);
                Display.updateTitle(this);
        }

        public Layer next(Layer layer) {
                int i = al_layers.indexOf(layer);
                if (-1 == i) {
                        Utils.log("LayerSet.next: no such Layer " + layer);
                        return layer;
                }
                if (al_layers.size() -1 == i) return layer;
                else return (Layer)al_layers.get(i+1);
        }

        public Layer previous(Layer layer) {
                int i = al_layers.indexOf(layer);
                if (-1 == i) {
                        Utils.log("LayerSet.previous: no such Layer " + layer);
                        return layer;
                }
                if (0 == i) return layer;
                else return (Layer)al_layers.get(i-1);
        }

        public Layer nextNonEmpty(Layer layer) {
                Layer next = layer;
                Layer given = layer;
                do {
                        layer = next;
                        next = next(layer);
                        if (!next.isEmpty()) return next;
                } while (next != layer);
                return given;
        }
        public Layer previousNonEmpty(Layer layer) {
                Layer previous = layer;
                Layer given = layer;
                do {
                        layer = previous;
                        previous = previous(layer);
                        if (!previous.isEmpty()) return previous;
                } while (previous != layer);
                return given;
        }

        public int getLayerIndex(final long id) {
                for (int i=al_layers.size()-1; i>-1; i--) {
                        if (((Layer)al_layers.get(i)).getId() == id) return i;
                }
                return -1;
        }

        /** Find a layer by index, or null if none. */
        public Layer getLayer(final int i) {
                if (i >=0 && i < al_layers.size()) return (Layer)al_layers.get(i);
                return null;
        }

        /** Find a layer with the given id, or null if none. */
        public Layer getLayer(final long id) {
                for (Layer layer : al_layers) {
                        if (layer.getId() == id) return layer;
                }
                return null;
        }

        /** Returns the first layer found with the given Z coordinate, rounded to seventh decimal precision, or null if none found. */
        public Layer getLayer(final double z) {
                double error = 0.0000001; // TODO adjust to an optimal
                for (Layer layer : al_layers) {
                        if (error > Math.abs(layer.getZ() - z)) { // floating-point arithmetic is still not a solved problem!
                                return layer;
                        }
                }
                return null;
        }

        public Layer getNearestLayer(final double z) {
                double min_dist = Double.MAX_VALUE;
                Layer closest = null;
                for (Layer layer : al_layers) {
                        double dist = Math.abs(layer.getZ() - z);
                        if (dist < min_dist) {
                                min_dist = dist;
                                closest = layer;
                        }
                }
                return closest;
        }

        /** Returns null if none has the given z and thickness. If 'create' is true and no layer is found, a new one with the given Z is created and added to the LayerTree. */
        public Layer getLayer(double z, double thickness, boolean create) {
                Iterator it = al_layers.iterator();
                Layer layer = null;
                double error = 0.0000001; // TODO adjust to an optimal
                while (it.hasNext()) {
                        Layer l = (Layer)it.next();
                        if (error > Math.abs(l.getZ() - z) && error > Math.abs(l.getThickness() - thickness)) { // floating point is still not a solved problem.
                                //Utils.log("LayerSet.getLayer: found layer with z=" + l.getZ());
                                layer = l;
                        }
                }
                if (create && null == layer && !Double.isNaN(z) && !Double.isNaN(thickness)) {
                        //Utils.log("LayerSet.getLayer: creating new Layer with z=" + z);
                        layer = new Layer(project, z, thickness, this);
                        add(layer);
                        project.getLayerTree().addLayer(this, layer);
                }
                return layer;
        }

        /** Add a Displayable to be painted in all Layers, such as a Pipe. Also updates open displays of the fact. */
        public void add(final ZDisplayable zdispl) {
                if (null == zdispl || -1 != al_zdispl.indexOf(zdispl)) {
                        Utils.log2("LayerSet: not adding zdispl");
                        return;
                }
                al_zdispl.add(0, zdispl); // at the top

                zdispl.setLayerSet(this);
                // The line below can fail (and in the addSilently as well) if one can add zdispl objects while no Layer has been created. But the ProjectThing.createChild prevents this situation.
                zdispl.setLayer(al_layers.get(0));
                zdispl.updateInDatabase("layer_set_id"); // TODO: update stack index?

                // insert into bucket
                if (null != root) {
                        // add as last, then update
                        root.put(al_zdispl.size()-1, zdispl, zdispl.getBoundingBox(null));
                        root.update(this, zdispl, 0, al_zdispl.size()-1);
                }

                Display.add(this, zdispl);
        }

        public void addAll(final Collection<? extends ZDisplayable> coll) {
                if (null == coll || 0 == coll.size()) return;
                for (final ZDisplayable zd : coll) {
                        al_zdispl.add(0, zd);
                        zd.setLayerSet(this);
                        zd.setLayer(al_layers.get(0));
                        zd.updateInDatabase("layer_set_id");
                        if (null != root) {
                                // add as last, then update
                                root.put(al_zdispl.size()-1, zd, zd.getBoundingBox(null));
                                root.update(this, zd, 0, al_zdispl.size()-1);
                        }
                }
                Display.addAll(this, coll);
        }

        /** Used for reconstruction purposes, avoids repainting or updating. */
        public void addSilently(final ZDisplayable zdispl) {
                if (null == zdispl || -1 != al_zdispl.indexOf(zdispl)) return;
                try {
                        zdispl.setLayer(0 == al_layers.size() ? null : al_layers.get(0));
                        zdispl.setLayerSet(this, false);
                        //Utils.log2("setLayerSet to ZDipl id=" + zdispl.getId());
                        al_zdispl.add(zdispl);
                } catch (Exception e) {
                        Utils.log("LayerSet.addSilently: not adding ZDisplayable with id=" + zdispl.getId());
                        IJError.print(e);
                        return;
                }
        }

        /** Remove a child. Does not destroy the child nor remove it from the database, only from the Display. */
        public boolean remove(final ZDisplayable zdispl) {
                if (null == zdispl || null == al_zdispl || -1 == al_zdispl.indexOf(zdispl)) return false;
                // remove from Bucket before modifying stack index
                if (null != root) Bucket.remove(zdispl, db_map);
                // now remove proper, so stack_index hasn't changed yet
                al_zdispl.remove(zdispl);
                Display.remove(zdispl);
                return true;
        }

        public ArrayList<ZDisplayable> getZDisplayables(final Class c) {
                return getZDisplayables(c, false);
        }

        /** Returns a list of ZDisplayable of class c only.*/
        public ArrayList<ZDisplayable> getZDisplayables(final Class c, final boolean instance_of) {
                final ArrayList<ZDisplayable> al = new ArrayList<ZDisplayable>();
                if (null == c) return al;
                if (Displayable.class == c || ZDisplayable.class == c) {
                        al.addAll(al_zdispl);
                        return al;
                }
                if (instance_of) {
                        for (ZDisplayable zd : al_zdispl) {
                                if (c.isInstance(zd)) al.add(zd);
                        }
                } else {
                        for (ZDisplayable zd : al_zdispl) {
                                if (zd.getClass() == c) al.add(zd);
                        }
                }
                return al;
        }

        public ArrayList<ZDisplayable> getZDisplayables(final Class c, final Layer layer, final Area aroi, final boolean visible_only) {
                final ArrayList<ZDisplayable> al = getZDisplayables(c);
                final double z = layer.getZ();
                for (Iterator<ZDisplayable> it = al.iterator(); it.hasNext(); ) {
                        ZDisplayable zd = it.next();
                        if (visible_only && !zd.isVisible()) { it.remove(); continue; }
                        if (!zd.intersects(aroi, z, z)) it.remove();
                }
                return al;
        }

        public boolean contains(final Layer layer) {
                if (null == layer) return false;
                return -1 != al_layers.indexOf(layer);
        }

        public boolean contains(final Displayable zdispl) {
                if (null == zdispl) return false;
                return -1 != al_zdispl.indexOf(zdispl);
        }

        /** Returns a copy of the layer list. */
        public ArrayList<Layer> getLayers() {
                return (ArrayList<Layer>)al_layers.clone(); // for integrity and safety, return a copy.
        }

        public boolean isDeletable() {
                return false;
        }

        /** Overiding. The alpha is used to show whether the LayerSet object is selected or not. */
        public void setAlpha(float alpha) { return; }

        /** Move the given Displayable to the next layer if possible. */
        public void moveDown(Layer layer, Displayable d) {
                int i = al_layers.indexOf(layer);
                if (al_layers.size() -1 == i || -1 == i) return;
                layer.remove(d);
                ((Layer)(al_layers.get(i +1))).add(d);
        }
        /** Move the given Displayable to the previous layer if possible. */
        public void moveUp(Layer layer, Displayable d) {
                int i = al_layers.indexOf(layer);
                if (0 == i || -1 == i) return;
                layer.remove(d);
                ((Layer)(al_layers.get(i -1))).add(d);
        }

        /** Move all Displayable objects in the HashSet to the given target layer. */
        public void move(final HashSet hs_d, final Layer source, final Layer target) {
                if (0 == hs_d.size() || null == source || null == target || source == target) return;
                Display.setRepaint(false); // disable repaints
                for (Iterator it = hs_d.iterator(); it.hasNext(); ) {
                        Displayable d = (Displayable)it.next();
                        if (source == d.getLayer()) {
                                source.remove(d);
                                target.add(d, false, false); // these contortions to avoid repeated DB traffic
                                d.updateInDatabase("layer_id");
                                Display.add(target, d, false); // don't activate
                        }
                }
                Display.setRepaint(true); // enable repaints
                source.updateInDatabase("stack_index");
                target.updateInDatabase("stack_index");
                Display.repaint(source); // update graphics: true
                Display.repaint(target);
        }

        /** Find ZDisplayable objects that contain the point x,y in the given layer. */
        public Collection<Displayable> findZDisplayables(final Layer layer, final int x, final int y, final boolean visible_only) {
                if (null != root) return root.find(x, y, layer, visible_only);
                final ArrayList<Displayable> al = new ArrayList<Displayable>();
                for (ZDisplayable zd : al_zdispl) {
                        if (zd.contains(layer, x, y)) al.add(zd);
                }
                return al;
        }
        public Collection<Displayable> findZDisplayables(final Layer layer, final Rectangle r, final boolean visible_only) {
                if (null != root) return root.find(r, layer, visible_only);
                final ArrayList<Displayable> al = new ArrayList<Displayable>();
                for (ZDisplayable zd : al_zdispl) {
                        if (zd.getBounds(null, layer).intersects(r)) al.add(zd);
                }
                return al;
        }

        /** Returns the hash set of objects whose visibility has changed. */
        public HashSet<Displayable> setVisible(String type, final boolean visible, final boolean repaint) {
                type = type.toLowerCase();
                final HashSet<Displayable> hs = new HashSet<Displayable>();
                try {
                        project.getLoader().startLargeUpdate();
                        if (type.equals("pipe") || type.equals("ball") || type.equals("arealist") || type.equals("polyline")) {
                                for (ZDisplayable zd : al_zdispl) {
                                        if (visible != zd.isVisible() && zd.getClass().getName().toLowerCase().endsWith(type)) { // endsWith, because DLabel is called as Label
                                                zd.setVisible(visible, false); // don't repaint
                                                hs.add(zd);
                                        }
                                }
                        } else {
                                if (type.equals("image")) type = "patch";
                                for (Layer layer : al_layers) {
                                        hs.addAll(layer.setVisible(type, visible, false)); // don't repaint
                                }
                        }
                } catch (Exception e) {
                        IJError.print(e);
                } finally {
                        project.getLoader().commitLargeUpdate();
                }
                if (repaint) {
                        Display.repaint(this); // this could be optimized to repaint only the accumulated box
                }
                return hs;
        }
        /** Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged. Returns the list of displayables made hidden. */
        public HashSet<Displayable> hideExcept(ArrayList<Class> type, boolean repaint) {
                final HashSet<Displayable> hs = new HashSet<Displayable>();
                for (ZDisplayable zd : al_zdispl) {
                        if (!type.contains(zd.getClass()) && zd.isVisible()) {
                                zd.setVisible(false, repaint);
                                hs.add(zd);
                        }
                }
                for (Layer la : al_layers) hs.addAll(la.hideExcept(type, repaint));
                return hs;
        }
        public void setAllVisible(boolean repaint) {
                for (ZDisplayable zd : al_zdispl) {
                        if (!zd.isVisible()) zd.setVisible(true, repaint);
                }
                for (Layer la : al_layers) la.setAllVisible(repaint);
        }

        /** Returns true if any of the ZDisplayable objects are of the given class. */
        public boolean contains(final Class c) {
                for (ZDisplayable zd : al_zdispl) {
                        if (zd.getClass() == c) return true;
                }
                return false;
        }
        /** Check in all layers. */
        public boolean containsDisplayable(Class c) {
                for (Iterator it = al_layers.iterator(); it.hasNext(); ) {
                        Layer la = (Layer)it.next();
                        if (la.contains(c)) return true;
                }
                return false;
        }

        /** Returns the distance from the first layer's Z to the last layer's Z. */
        public double getDepth() {
                if (null == al_layers || al_layers.isEmpty()) return 0;
                return ((Layer)al_layers.get(al_layers.size() -1)).getZ() - ((Layer)al_layers.get(0)).getZ();
        }

        /** Return all the Displayable objects from all the layers of this LayerSet. Does not include the ZDisplayables. */
        public ArrayList<Displayable> getDisplayables() {
                final ArrayList<Displayable> al = new ArrayList<Displayable>();
                for (Layer layer : al_layers) {
                        al.addAll(layer.getDisplayables());
                }
                return al;
        }
        /** Return all the Displayable objects from all the layers of this LayerSet of the given class. Does not include the ZDisplayables. */
        public ArrayList<Displayable> getDisplayables(Class c) {
                final ArrayList<Displayable> al = new ArrayList<Displayable>();
                for (Layer layer : al_layers) {
                        al.addAll(layer.getDisplayables(c));
                }
                return al;
        }
        /** Return all the Displayable objects from all the layers of this LayerSet of the given class that intersect the given area. Does not include the ZDisplayables. */
        public ArrayList<Displayable> getDisplayables(final Class c, final Area aroi, final boolean visible_only) {
                final ArrayList<Displayable> al = new ArrayList<Displayable>();
                for (Layer layer : al_layers) {
                        al.addAll(layer.getDisplayables(c, aroi, visible_only));
                }
                return al;
        }

        /** From zero to size-1. */
        public int indexOf(Layer layer) {
                return al_layers.indexOf(layer);
        }

        public void exportXML(final java.io.Writer writer, final String indent, final Object any) throws Exception {
                final StringBuffer sb_body = new StringBuffer();
                sb_body.append(indent).append("<t2_layer_set\n");
                final String in = indent + "\t";
                super.exportXML(sb_body, in, any);
                sb_body.append(in).append("layer_width=\"").append(layer_width).append("\"\n")
                       .append(in).append("layer_height=\"").append(layer_height).append("\"\n")
                       .append(in).append("rot_x=\"").append(rot_x).append("\"\n")
                       .append(in).append("rot_y=\"").append(rot_y).append("\"\n")
                       .append(in).append("rot_z=\"").append(rot_z).append("\"\n")
                       .append(in).append("snapshots_quality=\"").append(snapshots_quality).append("\"\n")
                       .append(in).append("snapshots_mode=\"").append(snapshot_modes[snapshots_mode]).append("\"\n")
                       // TODO: alpha! But it's not necessary.
                ;
                sb_body.append(indent).append(">\n");
                if (null != calibration) {
                        sb_body.append(in).append("<t2_calibration\n")
                               .append(in).append("\tpixelWidth=\"").append(calibration.pixelWidth).append("\"\n")
                               .append(in).append("\tpixelHeight=\"").append(calibration.pixelHeight).append("\"\n")
                               .append(in).append("\tpixelDepth=\"").append(calibration.pixelDepth).append("\"\n")
                               .append(in).append("\txOrigin=\"").append(calibration.xOrigin).append("\"\n")
                               .append(in).append("\tyOrigin=\"").append(calibration.yOrigin).append("\"\n")
                               .append(in).append("\tzOrigin=\"").append(calibration.zOrigin).append("\"\n")
                               .append(in).append("\tinfo=\"").append(calibration.info).append("\"\n")
                               .append(in).append("\tvalueUnit=\"").append(calibration.getValueUnit()).append("\"\n")
                               .append(in).append("\ttimeUnit=\"").append(calibration.getTimeUnit()).append("\"\n")
                               .append(in).append("\tunit=\"").append(calibration.getUnit()).append("\"\n")
                               .append(in).append("/>\n")
                        ;
                }
                writer.write(sb_body.toString());
                // export ZDisplayable objects
                if (null != al_zdispl) {
                        for (Iterator it = al_zdispl.iterator(); it.hasNext(); ) {
                                ZDisplayable zd = (ZDisplayable)it.next();
                                sb_body.setLength(0);
                                zd.exportXML(sb_body, in, any);
                                writer.write(sb_body.toString()); // each separately, for they can be huge
                        }
                }
                // export Layer and contained Displayable objects
                if (null != al_layers) {
                        //Utils.log("LayerSet " + id + " is saving " + al_layers.size() + " layers.");
                        for (Iterator it = al_layers.iterator(); it.hasNext(); ) {
                                sb_body.setLength(0);
                                ((Layer)it.next()).exportXML(sb_body, in, any);
                                writer.write(sb_body.toString());
                        }
                }
                super.restXML(sb_body, in, any);
                writer.write("</t2_layer_set>\n");
        }

        /** Includes the !ELEMENT */
        static public void exportDTD(StringBuffer sb_header, HashSet hs, String indent) {
                String type = "t2_layer_set";
                if (!hs.contains(type)) {
                        sb_header.append(indent).append("<!ELEMENT t2_layer_set (").append(Displayable.commonDTDChildren()).append(",t2_layer,t2_pipe,t2_ball,t2_area_list,t2_calibration)>\n");
                        Displayable.exportDTD(type, sb_header, hs, indent);
                        sb_header.append(indent).append(TAG_ATTR1).append(type).append(" layer_width").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" layer_height").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" rot_x").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" rot_y").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" rot_z").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" snapshots_quality").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append(type).append(" snapshots_mode").append(TAG_ATTR2)
                        ;
                        sb_header.append(indent).append("<!ELEMENT t2_calibration EMPTY>\n")
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration pixelWidth").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration pixelHeight").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration pixelDepth").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration xOrigin").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration yOrigin").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration zOrigin").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration info").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration valueUnit").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration timeUnit").append(TAG_ATTR2)
                                 .append(indent).append(TAG_ATTR1).append("t2_calibration unit").append(TAG_ATTR2)
                        ;
                }
        }

        public void setSnapshotsMode(final int mode) {
                if (mode == snapshots_mode) return;
                this.snapshots_mode = mode;
                Display.repaintSnapshots(this);
                updateInDatabase("snapshots_mode");
        }

        public int getSnapshotsMode() {
                return this.snapshots_mode;
        }

        public void destroy() {
                for (Iterator it = al_layers.iterator(); it.hasNext(); ) {
                        Layer layer = (Layer)it.next();
                        layer.destroy();
                }
                for (Iterator it = al_zdispl.iterator(); it.hasNext(); ) {
                        ZDisplayable zd = (ZDisplayable)it.next();
                        zd.destroy();
                }
                this.al_layers.clear();
                this.al_zdispl.clear();
                if (null != align) {
                        align.destroy();
                        align = null;
                }
        }

        public boolean isAligning() {
                return null != align;
        }

        public void cancelAlign() {
                if (null != align) {
                        align.cancel(); // will repaint
                        align = null;
                }
        }

        public void applyAlign(final boolean post_register) {
                if (null != align) align.apply(post_register);
        }

        public void applyAlign(final Layer la_start, final Layer la_end, final Selection selection) {
                if (null != align) align.apply(la_start, la_end, selection);
        }

        public void startAlign(Display display) {
                align = new Align(display);
        }

        public Align getAlign() {
                return align;
        }

        /** Used by the Layer.setZ method. */
        protected void reposition(Layer layer) {
                if (null == layer || !al_layers.contains(layer)) return;
                al_layers.remove(layer);
                addSilently(layer);
        }

        /** Get up to 'n' layers before and after the given layers. */
        public ArrayList getNeighborLayers(final Layer layer, final int n) {
                final int i_layer = al_layers.indexOf(layer);
                final ArrayList al = new ArrayList();
                if (-1 == i_layer) return al;
                int start = i_layer - n;
                if (start < 0) start = 0;
                int end = i_layer + n;
                if (end > al_layers.size()) end = al_layers.size();
                for (int i=start; i<i_layer; i++) al.add(al_layers.get(i));
                for (int i=i_layer+1; i<= i_layer + n || i < end; i++) al.add(al_layers.get(i));
                return al;
        }

        public boolean isTop(ZDisplayable zd) {
                if (null != zd && al_zdispl.size() > 0 && al_zdispl.indexOf(zd) == al_zdispl.size() -1) return true;
                return false;
        }

        public boolean isBottom(ZDisplayable zd) {
                if (null != zd && al_zdispl.size() > 0 && al_zdispl.indexOf(zd) == 0) return true;
                return false;
        }

        /** Hub method: ZDisplayable or into the Displayable's Layer. */
        protected boolean isTop(Displayable d) {
                if (d instanceof ZDisplayable) return isTop((ZDisplayable)d);
                else return d.getLayer().isTop(d);
        }
        /** Hub method: ZDisplayable or into the Displayable's Layer. */
        protected boolean isBottom(Displayable d) {
                if (d instanceof ZDisplayable) return isBottom((ZDisplayable)d);
                else return d.getLayer().isBottom(d);
        }

        /** Change z position in the layered stack, which defines the painting order. */ // the BOTTOM of the stack is the first element in the al_zdispl array
        protected void move(final int place, final Displayable d) {
                if (d instanceof ZDisplayable) {
                        int i = al_zdispl.indexOf(d);
                        if (-1 == i) {
                                Utils.log("LayerSet.move: object does not belong here");
                                return;
                        }
                        int size = al_zdispl.size();
                        if (1 == size) return;
                        switch(place) {
                                case LayerSet.TOP:
                                        al_zdispl.add(al_zdispl.remove(i));
                                        break;
                                case LayerSet.UP:
                                        if (size -1 == i) return;
                                        al_zdispl.add(i+1, al_zdispl.remove(i));
                                        break;
                                case LayerSet.DOWN:
                                        if (0 == i) return;
                                        al_zdispl.add(i, al_zdispl.remove(i-1)); //swap
                                        break;
                                case LayerSet.BOTTOM:
                                        al_zdispl.add(0, al_zdispl.remove(i));
                                        break;
                        }
                        updateInDatabase("stack_index");
                        Display.updatePanelIndex(d.getLayer(), d);
                } else {
                        switch (place) {
                                case LayerSet.TOP: d.getLayer().moveTop(d); break;
                                case LayerSet.UP: d.getLayer().moveUp(d); break;
                                case LayerSet.DOWN: d.getLayer().moveDown(d); break;
                                case LayerSet.BOTTOM: d.getLayer().moveBottom(d); break;
                        }
                }
        }

        public int indexOf(final ZDisplayable zd) {
                int k = al_zdispl.indexOf(zd);
                if (-1 == k) return -1;
                return al_zdispl.size() - k -1;
        }

        public boolean isEmptyAt(Layer la) {
                for (Iterator it = al_zdispl.iterator(); it.hasNext(); ) {
                        if (((ZDisplayable)it.next()).paintsAt(la)) return false;
                }
                return true;
        }

        public Displayable clone(final Project pr, final boolean copy_id) {
                return clone(pr, (Layer)al_layers.get(0), (Layer)al_layers.get(al_layers.size()-1), new Rectangle(0, 0, (int)Math.ceil(getLayerWidth()), (int)Math.ceil(getLayerHeight())), false, copy_id);
        }

        /** Clone the contents of this LayerSet, from first to last given layers, and cropping for the given rectangle. */
        public Displayable clone(Project pr, Layer first, Layer last, Rectangle roi, boolean add_to_tree, boolean copy_id) {
                // obtain a LayerSet
                final long nid = copy_id ? this.id : pr.getLoader().getNextId();
                final LayerSet copy = new LayerSet(pr, nid, getTitle(), this.width, this.height, this.rot_x, this.rot_y, this.rot_z, roi.width, roi.height, this.locked, this.snapshots_mode, (AffineTransform)this.at.clone());
                copy.setCalibration(getCalibrationCopy());
                copy.snapshots_quality = this.snapshots_quality;
                // copy objects that intersect the roi, from within the given range of layers
                final java.util.List<Layer> al = ((ArrayList<Layer>)al_layers.clone()).subList(indexOf(first), indexOf(last) +1);
                Utils.log2("al.size() : " + al.size());
                for (Layer layer : al) {
                        Layer layercopy = layer.clone(pr, copy, roi, copy_id);
                        copy.addSilently(layercopy);
                        if (add_to_tree) pr.getLayerTree().addLayer(copy, layercopy);
                }
                // copy ZDisplayable objects if they intersect the roi, and translate them properly
                final AffineTransform trans = new AffineTransform();
                trans.translate(-roi.x, -roi.y);
                for (ZDisplayable zd : find(first, last, new Area(roi))) {
                        ZDisplayable zdcopy = (ZDisplayable)zd.clone(pr, copy_id);
                        zdcopy.getAffineTransform().preConcatenate(trans);
                        copy.addSilently(zdcopy);
                }
                // fix links:
                copy.linkPatchesR();
                return (Displayable)copy;
        }

        /** Create a virtual layer stack that acts as a virtual ij.ImageStack, in RGB and set to a scale of max_dimension / Math.max(layer_width, layer_height). */
        public LayerStack createLayerStack(Class clazz, int type, int c_alphas) {
                return new LayerStack(this,
                                      getVirtualizationScale(),
                                      type,
                                      clazz,
                                      c_alphas);
        }

        public int getPixelsMaxDimension() { return max_dimension; }
        /** From 0.000... to 1. */
        public double getVirtualizationScale() {
                double scale = max_dimension / Math.max(layer_width, layer_height);
                return scale > 1 ? 1 : scale;
        }
        public void setPixelsMaxDimension(int d) {
                if (d > 2 && d != max_dimension) {
                        max_dimension = d;
                        Polyline.flushTraceCache(project); // depends on the scale value
                } else Utils.log("Can't set virtualization max pixels dimension to smaller than 2!");
        }

        public void setPixelsVirtualizationEnabled(boolean b) { this.virtualization_enabled = b; }
        public boolean isPixelsVirtualizationEnabled() { return virtualization_enabled; }


        /** Returns a new Rectangle of 0, 0, layer_width, layer_height. */
        public Rectangle get2DBounds() {
                return new Rectangle(0, 0, (int)Math.ceil(layer_width), (int)Math.ceil(layer_height));
        }

        /** Set the calibration to a clone of the given calibration. */
        public void setCalibration(Calibration cal) {
                if (null == cal) return;
                this.calibration = (Calibration)cal.clone();
        }

        public Calibration getCalibration() {
                return this.calibration;
        }

        public Calibration getCalibrationCopy() {
                return calibration.copy();
        }

        public boolean isCalibrated() {
                Calibration identity = new Calibration();
                if (identity.equals(this.calibration)) return false;
                return true;
        }

        /** Restore calibration from the given XML attributes table.*/
        public void restoreCalibration(HashMap ht_attributes) {
                for (Iterator it = ht_attributes.entrySet().iterator(); it.hasNext(); ) {
                        Map.Entry entry = (Map.Entry)it.next();
                        String key = (String)entry.getKey();
                        String value = (String)entry.getValue();
                        // remove the prefix 't2_'
                        key.substring(3).toLowerCase(); // case-resistant
                        try {
                                if (key.equals("pixelwidth")) {
                                        calibration.pixelWidth = Double.parseDouble(value);
                                } else if (key.equals("pixelheight")) {
                                        calibration.pixelHeight = Double.parseDouble(value);
                                } else if (key.equals("pixeldepth")) {
                                        calibration.pixelDepth = Double.parseDouble(value);
                                } else if (key.equals("xorigin")) {
                                        calibration.xOrigin = Double.parseDouble(value);
                                } else if (key.equals("yorigin")) {
                                        calibration.yOrigin = Double.parseDouble(value);
                                } else if (key.equals("zorigin")) {
                                        calibration.zOrigin = Double.parseDouble(value);
                                } else if (key.equals("info")) {
                                        calibration.info = value;
                                } else if (key.equals("valueunit")) {
                                        calibration.setValueUnit(value);
                                } else if (key.equals("timeunit")) {
                                        calibration.setTimeUnit(value);
                                } else if (key.equals("unit")) {
                                        calibration.setUnit(value);
                                }
                        } catch (Exception e) {
                                Utils.log2("LayerSet.restoreCalibration, key/value failed:" + key + "=\"" + value +"\"");
                                IJError.print(e);
                        }
                }
                //Utils.log2("Restored LayerSet calibration: " + calibration);
        }

        /** For creating snapshots, using a very slow but much better scaling algorithm (the Image.SCALE_AREA_AVERAGING method). */
        public boolean snapshotsQuality() {
                return snapshots_quality;
        }

        public void setSnapshotsQuality(boolean b) {
                this.snapshots_quality = b;
                updateInDatabase("snapshots_quality");
                // TODO this is obsolete
        }

        /** Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c. Includes the ZDisplayables. */
        public ArrayList get(final Class c) {
                return get(new ArrayList(), c);
        }

        /** Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c, which are stored in the given ArrayList; returns the same ArrayList, or a new one if its null. Includes the ZDisplayables. */
        public ArrayList get(ArrayList all, final Class c) {
                if (null == all) all = new ArrayList();
                // check whether to include all the ZDisplayable objects
                if (Displayable.class == c || ZDisplayable.class == c) all.addAll(al_zdispl);
                else {
                        for (Iterator it = al_zdispl.iterator(); it.hasNext(); ){
                                Object ob = it.next();
                                if (ob.getClass() == c) all.add(ob);
                        }
                }
                for (Layer layer : al_layers) {
                        all.addAll(layer.getDisplayables(c));
                        ArrayList al_ls = layer.getDisplayables(LayerSet.class);
                        for (Iterator i2 = al_ls.iterator(); i2.hasNext(); ) {
                                LayerSet ls = (LayerSet)i2.next();
                                ls.get(all, c);
                        }
                }
                return all;
        }

        /** Returns the region defined by the rectangle as an image in the type and format specified.
         *  The type is either ImagePlus.GRAY8 or ImagePlus.COLOR_RGB.
         *  The format is either Layer.IMAGE (an array) or Layer.ImagePlus (it returns an ImagePlus containing an ImageStack), from which any ImageProcessor or pixel arrays can be retrieved trivially.
         */
        public Object grab(final int first, final int last, final Rectangle r, final double scale, final Class c, final int c_alphas, final int format, final int type) {
                // check preconditions
                if (first < 0 || first > last || last >= al_layers.size()) {
                        Utils.log("Invalid first and/or last layers.");
                        return null;
                }
                // check that it will fit in memory
                if (!project.getLoader().releaseToFit(r.width, r.height, type, 1.1f)) {
                        Utils.log("LayerSet.grab: Cannot fit an image stack of " + (long)(r.width*r.height*(ImagePlus.GRAY8==type?1:4)*1.1) + " bytes in memory.");
                        return null;
                }
                if (Layer.IMAGEPLUS == format) {
                        ImageStack stack = new ImageStack((int)(r.width*scale), (int)(r.height*scale));
                        for (int i=first; i<=last; i++) {
                                Layer la = (Layer)al_layers.get(i);
                                Utils.log2("c is " + c);
                                ImagePlus imp = project.getLoader().getFlatImage(la, r, scale, c_alphas, type, c, null, true);
                                if (null != imp) try {
                                        //if (0 == stack.getSize()) stack.setColorModel(imp.getProcessor().getColorModel());
                                        stack.addSlice(imp.getTitle(), imp.getProcessor()); //.getPixels());
                                } catch (IllegalArgumentException iae) {
                                        IJError.print(iae);
                                } else Utils.log("LayerSet.grab: Ignoring layer " + la);
                        }
                        if (0 == stack.getSize()) {
                                Utils.log("LayerSet.grab: could not make slices.");
                                return null;
                        }
                        return new ImagePlus("Stack " + first + "-" + last, stack);
                } else if (Layer.IMAGE == format) {
                        final Image[] image = new Image[last - first + 1];
                        for (int i=first, j=0; i<=last; i++, j++) {
                                image[j] = project.getLoader().getFlatAWTImage((Layer)al_layers.get(i), r, scale, c_alphas, type, c, null, true, Color.black);
                        }
                        return image;
                }
                return null;
        }


        /** Searches in all layers. Ignores the ZDisplaybles. */
        public Displayable findDisplayable(final long id) {
                for (Layer la : al_layers) {
                        for (Displayable d : la.getDisplayables()) {
                                if (d.getId() == id) return d;
                        }
                }
                return null;
        }

        /** Searches in all ZDisplayables and in all layers, recursively into nested LayerSets. */
        public DBObject findById(final long id) {
                if (this.id == id) return this;
                for (ZDisplayable zd : al_zdispl) {
                        if (zd.getId() == id) return zd;
                }
                for (Layer la : al_layers) {
                        DBObject dbo = la.findById(id);
                        if (null != dbo) return dbo;
                }
                return null;
        }

        // private to the package
        void linkPatchesR() {
                for (Layer la : al_layers) la.linkPatchesR();
                for (ZDisplayable zd : al_zdispl) zd.linkPatches();
        }

        /** Recursive into nested LayerSet objects.*/
        public void updateLayerTree() {
                for (Layer la : al_layers) {
                        la.updateLayerTree();
                }
        }

        /** Find the ZDisplayable objects that intersect with the 3D roi defined by the first and last layers, and the area -all in world coordinates. */
        public ArrayList<ZDisplayable> find(final Layer first, final Layer last, final Area area) {
                final ArrayList<ZDisplayable> al = new ArrayList<ZDisplayable>();
                for (ZDisplayable zd : al_zdispl) {
                        if (zd.intersects(area, first.getZ(), last.getZ())) {
                                al.add(zd);
                        }
                }
                return al;
        }

        /** For fast search. */
        Bucket root = null;
        private HashMap<Displayable,ArrayList<Bucket>> db_map = null;

        /** Returns a copy of the list of ZDisplayable objects. */
        public ArrayList<ZDisplayable> getZDisplayables() { return (ArrayList<ZDisplayable>)al_zdispl.clone(); }

        /** Returns the real list of displayables, not a copy. If you modify this list, Thor may ground you with His lightning. */
        public ArrayList<ZDisplayable> getDisplayableList() {
                return al_zdispl;
        }

        public HashMap<Displayable, ArrayList<Bucket>> getBucketMap() {
                return db_map;
        }

        public void updateBucket(final Displayable d) {
                if (null != root) root.updatePosition(d, db_map);
        }

        public void recreateBuckets(final boolean layers) {
                this.root = new Bucket(0, 0, (int)(0.00005 + getLayerWidth()), (int)(0.00005 + getLayerHeight()), Bucket.getBucketSide(this));
                this.db_map = new HashMap<Displayable,ArrayList<Bucket>>();
                this.root.populate(this, db_map);
                if (layers) {
                        for (final Layer la : al_layers) {
                                // recreate only if there were any already
                                if (null != la.root) la.recreateBuckets();
                        }
                }
        }

        /** Checks only buckets for ZDisplayable, not any related to any layer. */
        public void checkBuckets() {
                if (null == root || null == db_map) recreateBuckets(false);
        }

        public Rectangle getMinimalBoundingBox(final Class c) {
                Rectangle r = null;
                for (final Layer la : al_layers) {
                        if (null == r) r = la.getMinimalBoundingBox(c);
                        else {
                                Rectangle box = la.getMinimalBoundingBox(c); // may be null if Layer is empty
                                if (null != box) r.add(box);
                        }
                }
                return r;
        }

        /** Time vs DoStep. Not all steps may be specific for a single Displayable. */
        final private TreeMap<Long,DoStep> edit_history = new TreeMap<Long,DoStep>();

        /** The step representing the current diff state. */
        private long current_edit_time = 0;
        private DoStep current_edit_step = null;

        /** Displayable vs its own set of time vs DoStep, for quick access, for those edits that are specific of a Displayable.
         *  It's necessary to set a ground, starting point for any Displayable whose data will be edited. */
        final private Map<Displayable,TreeMap<Long,DoStep>> dedits = new HashMap<Displayable,TreeMap<Long,DoStep>>();

        /** Time vs DoStep; as steps are removed from the end of edit_history, they are put here. */
        final private TreeMap<Long,DoStep> redo = new TreeMap<Long,DoStep>();

        /** Whether an initial step should be added or not. */
        final boolean prepareStep(final Object ob) {
                synchronized (edit_history) {
                        if (0 == edit_history.size() || redo.size() > 0) return true;
                        // Check if the last added entry contains the exact same elements and data
                        DoStep step = edit_history.get(edit_history.lastKey());
                        boolean b = step.isIdenticalTo(ob);
                        Utils.log2(b + " == prepareStep for " + ob);
                        // If identical, don't prepare one!
                        return !b;
                }
        }

        /** If last step is not a DoEdit "data" step for d, then call addDataEditStep(d). */
        boolean addPreDataEditStep(final Displayable d) {
                if (  null == current_edit_step
                  || (current_edit_step.getD() != d || !((DoEdit)current_edit_step).containsKey("data"))) {
                        //Utils.log2("Adding pre-data edit step");
                        //return addDataEditStep(d);
                        return addEditStep(new Displayable.DoEdit(d).init(d, new String[]{"data"}));
                }
                return false;
        }

        /** A new undo step for the "data" field of Displayable d. */
        boolean addDataEditStep(final Displayable d) {
                //Utils.log2("Adding data edit step");
                // Adds "data", which contains width,height,affinetransform,links, and the data (points, areas, etc.)
                return addEditStep(new Displayable.DoEdit(d).init(d, new String[]{"data"}));
        }

        /** A new undo step for the "data" field of all Displayable in the set. */
        boolean addDataEditStep(final Set<Displayable> ds) {
                return addDataEditStep(ds, new String[]{"data"});
        }

        boolean addDataEditStep(final Set<Displayable> ds, final String[] fields) {
                final Displayable.DoEdits edits = new Displayable.DoEdits(ds);
                edits.init(fields);
                return addEditStep(edits);
        }

        /** Add an undo step for the transformations of all Displayable in the layer. */
        public void addTransformStep(final Layer layer) {
                addTransformStep(layer.getDisplayables());
        }
        /** Add an undo step for the transformations of all Displayable in hs. */
        public void addTransformStep(final Collection<Displayable> col) {
                Utils.log2("Added transform step for col");
                addEditStep(new Displayable.DoTransforms().addAll(col));
        }
        /** Add an undo step for the transformations of all Displayable in all layers. */
        public void addTransformStep() {
                Utils.log2("Added transform step for all");
                Displayable.DoTransforms dt = new Displayable.DoTransforms();
                for (final Layer la : al_layers) {
                        dt.addAll(la.getDisplayables());
                }
                addEditStep(dt);
        }

        /** Add a step to undo the addition or deletion of one or more objects in this project and LayerSet. */
        public void addChangeTreesStep() {
                DoStep step = new LayerSet.DoChangeTrees(this);
                if (prepareStep(step)) {
                        Utils.log2("Added change trees step.");
                        addEditStep(step);
                }
        }
        /** For the Displayable contained in a Layer: their number, and their stack order. */
        public void addLayerContentStep(final Layer la) {
                DoStep step = new Layer.DoContentChange(la);
                if (prepareStep(step)) {
                        Utils.log2("Added layer content step.");
                        addEditStep(step);
                }
        }
        /** For the Z and thickness of a layer. */
        public void addLayerEditedStep(final Layer layer) {
                addEditStep(new Layer.DoEditLayer(layer));
        }
        /** For the Z and thickness of a list of layers. */
        public void addLayerEditedStep(final List<Layer> al) {
                addEditStep(new Layer.DoEditLayers(al));
        }

        boolean addEditStep(final DoStep step) {
                if (null == step || step.isEmpty()) {
                        Utils.log2("Warning: can't add empty step " + step);
                        return false;
                }

                synchronized (edit_history) {
                        // Check if it's identical to current step
                        if (step.isIdenticalTo(current_edit_step)) {
                                Utils.log2("Skipping identical undo step of class " + step.getClass() + ": " + step);
                                return false;
                        }

                        // Store current in undo queue
                        if (null != current_edit_step) {
                                edit_history.put(current_edit_time, current_edit_step);
                                // Store for speedy access, if its Displayable-specific:
                                final Displayable d = current_edit_step.getD();
                                if (null != d) {
                                        TreeMap<Long,DoStep> edits = dedits.get(d);
                                        if (null == edits) {
                                                edits = new TreeMap<Long,DoStep>();
                                                dedits.put(d, edits);
                                        }
                                        edits.put(current_edit_time, current_edit_step);
                                }

                                // prune if too large
                                while (edit_history.size() > project.getProperty("n_undo_steps", 32)) {
                                        long t = edit_history.firstKey();
                                        DoStep st = edit_history.remove(t);
                                        if (null != st.getD()) {
                                                TreeMap<Long,DoStep> m = dedits.get(st.getD());
                                                m.remove(t);
                                                if (0 == m.size()) dedits.remove(st.getD());
                                        }
                                }
                        }

                        // Set step as current
                        current_edit_time = System.currentTimeMillis();
                        current_edit_step = step;

                        // Bye bye redo! Can't branch.
                        redo.clear();
                }

                return true;
        }

        public boolean canUndo() {
                return edit_history.size() > 0;
        }
        public boolean canRedo() {
                return redo.size() > 0 || null != current_edit_step;
        }

        /** Undoes one step of the ongoing transformation history, otherwise of the overall LayerSet history. */
        public boolean undoOneStep() {
                synchronized (edit_history) {
                        if (0 == edit_history.size()) {
                                Utils.log2("Empty undo history.");
                                return false;
                        }

                        //Utils.log2("Undoing one step");

                        // Add current (if any) to redo queue
                        if (null != current_edit_step) {
                                redo.put(current_edit_time, current_edit_step);
                        }

                        // Remove last step from undo queue, and set it as current
                        current_edit_time = edit_history.lastKey();
                        current_edit_step = edit_history.remove(current_edit_time);

                        // Remove as well from dedits
                        if (null != current_edit_step.getD()) {
                                dedits.get(current_edit_step.getD()).remove(current_edit_time);
                        }

                        if (!current_edit_step.apply(DoStep.UNDO)) {
                                Utils.log("Undo: could not apply step!");
                                return false;
                        }
                }
                return true;
        }

        /** Redoes one step of the ongoing transformation history, otherwise of the overall LayerSet history. */
        public boolean redoOneStep() {
                synchronized (edit_history) {
                        if (0 == redo.size()) {
                                Utils.log2("Empty redo history.");
                                if (null != current_edit_step) {
                                        return current_edit_step.apply(DoStep.REDO);
                                }
                                return false;
                        }

                        //Utils.log2("Redoing one step");

                        // Add current (if any) to undo queue
                        if (null != current_edit_step) {
                                edit_history.put(current_edit_time, current_edit_step);
                                if (null != current_edit_step.getD()) {
                                        dedits.get(current_edit_step.getD()).put(current_edit_time, current_edit_step);
                                }
                        }

                        // Remove one step from undo queue and set it as current
                        current_edit_time = redo.firstKey();
                        current_edit_step = redo.remove(current_edit_time);

                        if (!current_edit_step.apply(DoStep.REDO)) {
                                Utils.log("Undo: could not apply step!");
                                return false;
                        }
                }
                return true;
        }

        static public void applyTransforms(final Map<Displayable,AffineTransform> m) {
                for (final Map.Entry<Displayable,AffineTransform> e : m.entrySet()) {
                        e.getKey().setAffineTransform(e.getValue()); // updates buckets
                }
        }

        static {
                // Undo background tasks: should be done in background threads,
                // but on attempting to undo/redo, the undo/redo should wait
                // until all tasks are done. For example, updating mipmaps when
                // undoing/redoing min/max or CoordinateTransform.
                // This could be done with futures: spawn and do in the
                // background, but on redo/undo, call for the Future return
                // value, which will block until there is one to return.
                // Since blocking would block the EventDispatchThread, just refuse to undo/redo and notify the user.
                //
                // TODO
        }

        /** Keeps the width,height of a LayerSet and the AffineTransform of every Displayable in it. */
        static private class DoResizeLayerSet implements DoStep {

                final LayerSet ls;
                final HashMap<Displayable,AffineTransform> affines;
                final double width, height;

                DoResizeLayerSet(final LayerSet ls) {
                        this.ls = ls;
                        this.width = ls.layer_width;
                        this.height = ls.layer_height;
                        this.affines = new HashMap<Displayable,AffineTransform>();

                        final ArrayList<Displayable> col = ls.getDisplayables(); // it's a new list
                        col.addAll(ls.getZDisplayables());
                        for (final Displayable d : col) {
                                this.affines.put(d, d.getAffineTransformCopy());
                        }
                }
                public boolean isIdenticalTo(final Object ob) {
                        if (!(ob instanceof LayerSet)) return false;
                        final LayerSet layerset = (LayerSet) ob;
                        if (layerset.layer_width != this.width || layerset.height != this.height || layerset != this.ls) return false;
                        final ArrayList<Displayable> col = ls.getDisplayables();
                        col.addAll(ls.getZDisplayables());
                        for (final Displayable d : col) {
                                final AffineTransform aff = this.affines.get(d);
                                if (null == aff) return false;
                                if (!aff.equals(d.getAffineTransform())) return false;
                        }
                        return true;
                }

                public boolean apply(int action) {
                        ls.layer_width = width;
                        ls.layer_height = height;
                        for (final Map.Entry<Displayable,AffineTransform> e : affines.entrySet()) {
                                e.getKey().getAffineTransform().setTransform(e.getValue());
                        }
                        if (null != ls.root) ls.recreateBuckets(true);
                        Display.updateSelection();
                        Display.update(ls); //so it's not left out painted beyond borders
                        return true;
                }
                public boolean isEmpty() { return false; }
                public Displayable getD() { return null; }
        }

        /** Records the state of the LayerSet.al_layers, each Layer.al_displayables and all the trees and unique types of Project. */
        static private class DoChangeTrees implements DoStep {
                final LayerSet ls;
                final HashMap<Thing,Boolean> ttree_exp, ptree_exp, ltree_exp;
                final Thing troot, proot, lroot;
                final ArrayList<Layer> all_layers;
                final HashMap<Layer,ArrayList<Displayable>> all_displ;
                final ArrayList<ZDisplayable> all_zdispl;
                final HashMap<Displayable,Set<Displayable>> links;

                // TODO: does not consider recursive LayerSets!
                public DoChangeTrees(final LayerSet ls) {
                        this.ls = ls;
                        final Project p = ls.getProject();

                        this.ttree_exp = new HashMap<Thing,Boolean>();
                        this.troot = p.getTemplateTree().duplicate(ttree_exp);
                        this.ptree_exp = new HashMap<Thing,Boolean>();
                        this.proot = p.getProjectTree().duplicate(ptree_exp);
                        this.ltree_exp = new HashMap<Thing,Boolean>();
                        this.lroot = p.getProjectTree().duplicate(ltree_exp);

                        this.all_layers = ls.getLayers(); // a copy
                        this.all_zdispl = ls.getZDisplayables(); // a copy

                        this.links = new HashMap<Displayable,Set<Displayable>>();
                        for (final ZDisplayable zd : this.all_zdispl) {
                                this.links.put(zd, zd.hs_linked); // LayerSet is a Displayable
                        }

                        this.all_displ = new HashMap<Layer,ArrayList<Displayable>>();
                        for (final Layer layer : all_layers) {
                                final ArrayList<Displayable> al = layer.getDisplayables(); // a copy
                                this.all_displ.put(layer, al);
                                for (final Displayable d : al) {
                                        this.links.put(d, null == d.hs_linked ? null : new HashSet<Displayable>(d.hs_linked));
                                }
                        }
                }
                public Displayable getD() { return null; }
                public boolean isEmpty() { return false; }
                public boolean isIdenticalTo(final Object ob) {
                        // TODO
                        return false;
                }
                public boolean apply(int action) {
                        // Replace all layers
                        ls.al_layers.clear();
                        ls.al_layers.addAll(this.all_layers);

                        final ArrayList<Displayable> patches = new ArrayList<Displayable>();

                        // Replace all Displayable in each Layer
                        for (final Map.Entry<Layer,ArrayList<Displayable>> e : all_displ.entrySet()) {
                                // Acquire pointer to the actual instance list in each Layer
                                final ArrayList<Displayable> al = e.getKey().getDisplayableList(); // the real one!
                                // Create a list to contain those Displayable present in old list but not in list to use now
                                final HashSet<Displayable> diff = new HashSet<Displayable>(al); // create with all Displayable of old list
                                diff.removeAll(e.getValue()); // remove all Displayable present in list to use now, to leave the diff or remainder only
                                // Clear current list
                                al.clear();
                                // Insert all to the current list
                                al.addAll(e.getValue());
                                // Add to remove-on-shutdown queue all those Patch no longer in the list to use now:
                                for (final Displayable d : diff) {
                                        if (d.getClass() == Patch.class) {
                                                d.getProject().getLoader().tagForMipmapRemoval((Patch)d, true);
                                        }
                                }
                                // Remove from queue all those Patch in the list to use now:
                                for (final Displayable d : al) {
                                        if (d.getClass() == Patch.class) {
                                                d.getProject().getLoader().tagForMipmapRemoval((Patch)d, false);
                                        }
                                }
                        }

                        // Replace all ZDisplayable
                        ls.al_zdispl.clear();
                        ls.al_zdispl.addAll(this.all_zdispl);

                        // Replace all trees
                        final Project p = ls.getProject();
                        p.getTemplateTree().set(this.troot, this.ttree_exp);
                        p.getProjectTree().set(this.proot, this.ptree_exp);
                        p.getLayerTree().set(this.lroot, this.ltree_exp);

                        // Replace all links
                        for (final Map.Entry<Displayable,Set<Displayable>> e : this.links.entrySet()) {
                                final Set<Displayable> hs = e.getKey().hs_linked;
                                if (null != hs) {
                                        final Set<Displayable> hs2 = e.getValue();
                                        if (null == hs2) e.getKey().hs_linked = null;
                                        else {
                                                hs.clear();
                                                hs.addAll(hs2);
                                        }
                                }
                        }

                        ls.recreateBuckets(true);

                        Display.update(ls);

                        return true;
                }
        }
}