Examples with Displayable ini.trakem2.display.Displayable used on opensource projects

Example 66 with Displayable

use of ini.trakem2.display.Displayable in project TrakEM2 by trakem2.

the class Loader method createLazyFlyThrough.

/**
 * Each slice is generated on demand, one slice per Region instance.
 */
public <I> ImagePlus createLazyFlyThrough(final List<? extends Region<I>> regions, final double magnification, final int type, final Displayable active) {
    final Region<I> first = regions.get(0);
    final int w = (int) (first.r.width * magnification), h = (int) (first.r.height * magnification);
    final LazyVirtualStack stack = new LazyVirtualStack(w, h, regions.size());
    for (final Region<I> r : regions) {
        stack.addSlice(new Callable<ImageProcessor>() {

            @Override
            public ImageProcessor call() {
                return getFlatImage(r.layer, r.r, magnification, 0xffffffff, type, Displayable.class, null, true, Color.black, active).getProcessor();
            }
        });
    }
    return new ImagePlus("Fly-Through", stack);
}

Example 67 with Displayable

use of ini.trakem2.display.Displayable in project TrakEM2 by trakem2.

the class Loader method getFlatAWTImage.

/**
 * @param layer The layer from which to collect visible Displayable instances that intersect the srcRect.
 * @param srcRect_ Rectangle in World coordinates representing the field of view to paint into the image, and defines the width and height of the image together with the scale.
 * @param scale Value between 0 and 1.
 * @param c_alphas Which color channels to include when painting Patch instances that hold an RGB image.
 * @param type Either ImagePlus.GRAY8 or ImagePlus.COLOR_RGB
 * @param clazz Include only Displayable instances of this class; use Displayable.class for all.
 * @param al_displ List of Displayable instances to include. Use null to include all visible intersected by srcRect.
 * @param quality Whether to attempt to create a larger image and then scale it down with area averaging for best quality.
 * @param background The color of the areas of the image where no Displayable paints.
 * @param active Whether to paint a particular Displayable instance in an active state (as if it was selected in the UI).
 * @return
 */
public Image getFlatAWTImage(final Layer layer, final Rectangle srcRect_, final double scale, final int c_alphas, final int type, final Class<?> clazz, List<? extends Displayable> al_displ, boolean quality, final Color background, final Displayable active) {
    try {
        // dimensions
        int w = 0;
        int h = 0;
        Rectangle srcRect = (null == srcRect_) ? null : (Rectangle) srcRect_.clone();
        if (null != srcRect) {
            w = srcRect.width;
            h = srcRect.height;
        } else {
            w = (int) Math.ceil(layer.getLayerWidth());
            h = (int) Math.ceil(layer.getLayerHeight());
            srcRect = new Rectangle(0, 0, w, h);
        }
        Utils.log2("Loader.getFlatImage: using rectangle " + srcRect);
        /*
			 * output size including excess space for not entirely covered
			 * pixels
			 */
        final int ww = (int) Math.ceil(w * scale);
        final int hh = (int) Math.ceil(h * scale);
        /* The size of the buffered image to be generated */
        final int biw, bih;
        final double scaleP, scalePX, scalePY;
        // on scaling down to output resolution.
        if (quality) {
            if (ww * hh >= Math.pow(2, 30)) {
                // 1 GB
                // While perhaps scale could be increased to an image size of up to 2 GB, it is not advisable
                scaleP = scalePX = scalePY = scale;
                quality = false;
                biw = ww;
                bih = hh;
                Utils.log("Can't use 'quality' flag for getFlatAWTImage: would be too large");
            // If the image is larger than 2 GB, it will thrown a NegativeArraySizeException below and stop.
            } else {
                // Max area: the smallest of the srcRect at 100x magnification and 1 GB
                final double max_area = Math.min(srcRect.width * srcRect.height, Math.pow(2, 30));
                final double ratio = ww / (double) hh;
                // area = w * h
                // ratio = w / h
                // w = ratio * h
                // area = ratio * h * h
                // h = sqrt(area / ratio)
                // scaleP is then the ratio between the real-world height and the target height
                // (And clamp to a maximum of 1.0: above makes no sense)
                scaleP = Math.min(1.0, srcRect.height / Math.sqrt(max_area / ratio));
                biw = (int) Math.ceil(ww / scale);
                bih = (int) Math.ceil(hh / scale);
                /* compensate for excess space due to ceiling */
                scalePX = (double) biw / (double) ww * scale;
                scalePY = (double) bih / (double) hh * scale;
                Utils.log("getFlatAWTImage -- scale: " + scale + "; quality scale: " + scaleP);
            }
        } else {
            scaleP = scalePX = scalePY = scale;
            biw = ww;
            bih = hh;
        }
        // estimate image size
        final long n_bytes = (long) ((biw * bih * (ImagePlus.GRAY8 == type ? 1.0 : /*byte*/
        4.0)));
        Utils.log2("Flat image estimated size in bytes: " + Long.toString(n_bytes) + "  w,h : " + (int) Math.ceil(biw) + "," + (int) Math.ceil(bih) + (quality ? " (using 'quality' flag: scaling to " + scale + " is done later with area averaging)" : ""));
        releaseToFit(n_bytes);
        // go
        BufferedImage bi = null;
        switch(type) {
            case ImagePlus.GRAY8:
                bi = new BufferedImage(biw, bih, BufferedImage.TYPE_BYTE_INDEXED, GRAY_LUT);
                break;
            case ImagePlus.COLOR_RGB:
                bi = new BufferedImage(biw, bih, BufferedImage.TYPE_INT_ARGB);
                break;
            default:
                Utils.log2("Left bi,icm as null");
                break;
        }
        final Graphics2D g2d = bi.createGraphics();
        g2d.setColor(background);
        g2d.fillRect(0, 0, bi.getWidth(), bi.getHeight());
        g2d.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_QUALITY);
        // TODO Stephan, test if that introduces offset vs nearest neighbor
        g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BICUBIC);
        // to smooth edges of the images
        g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
        g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
        g2d.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
        ArrayList<ZDisplayable> al_zdispl = null;
        if (null == al_displ) {
            al_displ = new ArrayList<Displayable>(layer.find(clazz, srcRect, true, true));
            al_zdispl = new ArrayList<ZDisplayable>((Collection) layer.getParent().findZDisplayables(clazz, layer, srcRect, true, true));
        } else {
            // separate ZDisplayables into their own array
            al_displ = new ArrayList<Displayable>(al_displ);
            final HashSet<ZDisplayable> az = new HashSet<ZDisplayable>();
            for (final Iterator<?> it = al_displ.iterator(); it.hasNext(); ) {
                final Object ob = it.next();
                if (ob instanceof ZDisplayable) {
                    it.remove();
                    az.add((ZDisplayable) ob);
                }
            }
            // order ZDisplayables by their stack order
            final ArrayList<ZDisplayable> al_zdispl2 = layer.getParent().getZDisplayables();
            for (final Iterator<ZDisplayable> it = al_zdispl2.iterator(); it.hasNext(); ) {
                if (!az.contains(it.next()))
                    it.remove();
            }
            al_zdispl = al_zdispl2;
        }
        // prepare the canvas for the srcRect and magnification
        final AffineTransform at_original = g2d.getTransform();
        final AffineTransform atc = new AffineTransform();
        atc.scale(scalePX, scalePY);
        atc.translate(-srcRect.x, -srcRect.y);
        at_original.preConcatenate(atc);
        g2d.setTransform(at_original);
        // Utils.log2("will paint: " + al_displ.size() + " displ and " + al_zdispl.size() + " zdispl");
        // int total = al_displ.size() + al_zdispl.size();
        int count = 0;
        boolean zd_done = false;
        final List<Layer> layers = layer.getParent().getColorCueLayerRange(layer);
        for (final Displayable d : al_displ) {
            // paint the ZDisplayables before the first label, if any
            if (!zd_done && d instanceof DLabel) {
                zd_done = true;
                for (final ZDisplayable zd : al_zdispl) {
                    if (!zd.isOutOfRepaintingClip(scaleP, srcRect, null)) {
                        zd.paint(g2d, srcRect, scaleP, active == zd, c_alphas, layer, layers);
                    }
                    count++;
                // Utils.log2("Painted " + count + " of " + total);
                }
            }
            if (!d.isOutOfRepaintingClip(scaleP, srcRect, null)) {
                d.paintOffscreen(g2d, srcRect, scaleP, active == d, c_alphas, layer, layers);
            // Utils.log("painted: " + d + "\n with: " + scaleP + ", " + c_alphas + ", " + layer);
            } else {
            // Utils.log2("out: " + d);
            }
            count++;
        // Utils.log2("Painted " + count + " of " + total);
        }
        if (!zd_done) {
            zd_done = true;
            for (final ZDisplayable zd : al_zdispl) {
                if (!zd.isOutOfRepaintingClip(scaleP, srcRect, null)) {
                    zd.paint(g2d, srcRect, scaleP, active == zd, c_alphas, layer, layers);
                }
                count++;
            // Utils.log2("Painted " + count + " of " + total);
            }
        }
        // ensure enough memory is available for the processor and a new awt from it
        // locks on its own
        releaseToFit((long) (n_bytes * 2.3));
        try {
            if (quality) {
                // need to scale back down
                Image scaled = null;
                if (!isMipMapsRegenerationEnabled() || scale >= 0.499) {
                    // there are no proper mipmaps above 50%, so there's need for SCALE_AREA_AVERAGING.
                    // very slow, but best by far
                    scaled = bi.getScaledInstance(ww, hh, Image.SCALE_AREA_AVERAGING);
                    if (ImagePlus.GRAY8 == type) {
                        // getScaledInstance generates RGB images for some reason.
                        final BufferedImage bi8 = new BufferedImage(ww, hh, BufferedImage.TYPE_BYTE_GRAY);
                        bi8.createGraphics().drawImage(scaled, 0, 0, null);
                        scaled.flush();
                        scaled = bi8;
                    }
                } else {
                    // faster, but requires gaussian blurred images (such as the mipmaps)
                    if (bi.getType() == BufferedImage.TYPE_BYTE_INDEXED) {
                        scaled = new BufferedImage(ww, hh, bi.getType(), GRAY_LUT);
                    } else {
                        scaled = new BufferedImage(ww, hh, bi.getType());
                    }
                    final Graphics2D gs = (Graphics2D) scaled.getGraphics();
                    // gs.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BICUBIC);
                    gs.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
                    gs.drawImage(bi, 0, 0, ww, hh, null);
                }
                bi.flush();
                return scaled;
            } else {
                // else the image was made scaled down already, and of the proper type
                return bi;
            }
        } catch (final OutOfMemoryError oome) {
            Utils.log("Not enough memory to create the ImagePlus. Try scaling it down or not using the 'quality' flag.");
        }
    } catch (final Exception e) {
        IJError.print(e);
    }
    return null;
}

Example 68 with Displayable

use of ini.trakem2.display.Displayable in project TrakEM2 by trakem2.

the class TMLHandler method makeLayerThing.

private LayerThing makeLayerThing(String type, final HashMap<String, String> ht_attributes) {
    try {
        type = type.toLowerCase();
        if (0 == type.indexOf("t2_")) {
            type = type.substring(3);
        }
        // long id = -1;
        // final String sid = ht_attributes.get("id");
        // if (null != sid) id = Long.parseLong(sid);
        long oid = -1;
        final String soid = ht_attributes.get("oid");
        if (null != soid)
            oid = Long.parseLong(soid);
        if (type.equals("node")) {
            if (null == last_tree) {
                throw new NullPointerException("Can't create a node for null last_tree!");
            }
            final Node<?> node = last_tree.newNode(ht_attributes);
            taggables.add(node);
            // Put node into the list of nodes with that layer id, to update to proper Layer pointer later
            final long ndlid = Long.parseLong(ht_attributes.get("lid"));
            List<Node<?>> list = node_layer_table.get(ndlid);
            if (null == list) {
                list = new ArrayList<Node<?>>();
                node_layer_table.put(ndlid, list);
            }
            list.add(node);
            // Set node as root node or add as child to last node in the stack
            if (null == last_root_node) {
                last_root_node = node;
            } else {
                final String sconf = ht_attributes.get("c");
                nodes.getLast().add((Node) node, null == sconf ? Node.MAX_EDGE_CONFIDENCE : Byte.parseByte(sconf));
            }
            // color?
            final String scolor = ht_attributes.get("color");
            if (null != scolor) {
                final Color color = Utils.getRGBColorFromHex(scolor);
                Collection<Node<?>> nodes = node_colors.get(color);
                if (null == nodes) {
                    nodes = new ArrayList<Node<?>>();
                    node_colors.put(color, nodes);
                }
                nodes.add(node);
            }
            // Put node into stack of nodes (to be removed on closing the tag)
            nodes.add(node);
        } else if (type.equals("profile")) {
            Profile profile = new Profile(this.project, oid, ht_attributes, ht_links);
            profile.addToDatabase();
            ht_displayables.put(oid, profile);
            addToLastOpenLayer(profile);
            last_displayable = profile;
            return null;
        } else if (type.equals("pipe")) {
            Pipe pipe = new Pipe(this.project, oid, ht_attributes, ht_links);
            pipe.addToDatabase();
            ht_displayables.put(new Long(oid), pipe);
            ht_zdispl.put(new Long(oid), pipe);
            last_displayable = pipe;
            addToLastOpenLayerSet(pipe);
            return null;
        } else if (type.equals("polyline")) {
            Polyline pline = new Polyline(this.project, oid, ht_attributes, ht_links);
            pline.addToDatabase();
            last_displayable = pline;
            ht_displayables.put(new Long(oid), pline);
            ht_zdispl.put(new Long(oid), pline);
            addToLastOpenLayerSet(pline);
            return null;
        } else if (type.equals("connector")) {
            final Connector con = new Connector(this.project, oid, ht_attributes, ht_links);
            if (ht_attributes.containsKey("origin")) {
                legacy.add(new Runnable() {

                    public void run() {
                        con.readLegacyXML(al_layer_sets.get(al_layer_sets.size() - 1), ht_attributes, ht_links);
                    }
                });
            }
            con.addToDatabase();
            last_connector = con;
            last_tree = con;
            last_displayable = con;
            ht_displayables.put(new Long(oid), con);
            ht_zdispl.put(new Long(oid), con);
            addToLastOpenLayerSet(con);
            return null;
        } else if (type.equals("path")) {
            if (null != reca) {
                reca.add(ht_attributes.get("d"));
                return null;
            }
            return null;
        } else if (type.equals("area")) {
            reca = new ReconstructArea();
            if (null != last_area_list) {
                last_area_list_layer_id = Long.parseLong(ht_attributes.get("layer_id"));
            }
            return null;
        } else if (type.equals("area_list")) {
            AreaList area = new AreaList(this.project, oid, ht_attributes, ht_links);
            // why? This looks like an onion
            area.addToDatabase();
            last_area_list = area;
            last_displayable = area;
            ht_displayables.put(new Long(oid), area);
            ht_zdispl.put(new Long(oid), area);
            addToLastOpenLayerSet(area);
            return null;
        } else if (type.equals("tag")) {
            Taggable t = taggables.getLast();
            if (null != t) {
                Object ob = ht_attributes.get("key");
                // defaults to 't'
                int keyCode = KeyEvent.VK_T;
                // KeyEvent.VK_U is char U, not u
                if (null != ob)
                    keyCode = (int) ((String) ob).toUpperCase().charAt(0);
                Tag tag = al_layer_sets.get(al_layer_sets.size() - 1).putTag(ht_attributes.get("name"), keyCode);
                // could be null if name is not found
                if (null != tag)
                    t.addTag(tag);
            }
        } else if (type.equals("ball_ob")) {
            // add a ball to the last open Ball
            if (null != last_ball) {
                last_ball.addBall(Double.parseDouble(ht_attributes.get("x")), Double.parseDouble(ht_attributes.get("y")), Double.parseDouble(ht_attributes.get("r")), Long.parseLong(ht_attributes.get("layer_id")));
            }
            return null;
        } else if (type.equals("ball")) {
            Ball ball = new Ball(this.project, oid, ht_attributes, ht_links);
            ball.addToDatabase();
            last_ball = ball;
            last_displayable = ball;
            ht_displayables.put(new Long(oid), ball);
            ht_zdispl.put(new Long(oid), ball);
            addToLastOpenLayerSet(ball);
            return null;
        } else if (type.equals("stack")) {
            Stack stack = new Stack(this.project, oid, ht_attributes, ht_links);
            stack.addToDatabase();
            last_stack = stack;
            last_displayable = stack;
            ht_displayables.put(new Long(oid), stack);
            ht_zdispl.put(new Long(oid), stack);
            addToLastOpenLayerSet(stack);
        } else if (type.equals("treeline")) {
            Treeline tline = new Treeline(this.project, oid, ht_attributes, ht_links);
            tline.addToDatabase();
            last_treeline = tline;
            last_tree = tline;
            last_treeline_data = new StringBuilder();
            last_displayable = tline;
            ht_displayables.put(oid, tline);
            ht_zdispl.put(oid, tline);
            addToLastOpenLayerSet(tline);
        } else if (type.equals("areatree")) {
            AreaTree art = new AreaTree(this.project, oid, ht_attributes, ht_links);
            art.addToDatabase();
            last_areatree = art;
            last_tree = art;
            last_displayable = art;
            ht_displayables.put(oid, art);
            ht_zdispl.put(oid, art);
            addToLastOpenLayerSet(art);
        } else if (type.equals("dd_item")) {
            if (null != last_dissector) {
                last_dissector.addItem(Integer.parseInt(ht_attributes.get("tag")), Integer.parseInt(ht_attributes.get("radius")), ht_attributes.get("points"));
            }
        } else if (type.equals("label")) {
            DLabel label = new DLabel(project, oid, ht_attributes, ht_links);
            label.addToDatabase();
            ht_displayables.put(new Long(oid), label);
            addToLastOpenLayer(label);
            last_displayable = label;
            return null;
        } else if (type.equals("annot")) {
            last_annotation = new StringBuilder();
            return null;
        } else if (type.equals("patch")) {
            Patch patch = new Patch(project, oid, ht_attributes, ht_links);
            patch.addToDatabase();
            ht_displayables.put(new Long(oid), patch);
            addToLastOpenLayer(patch);
            last_patch = patch;
            last_displayable = patch;
            checkAlphaMasks(patch);
            return null;
        } else if (type.equals("filter")) {
            last_patch_filters.add(newFilter(ht_attributes));
        } else if (type.equals("dissector")) {
            Dissector dissector = new Dissector(this.project, oid, ht_attributes, ht_links);
            dissector.addToDatabase();
            last_dissector = dissector;
            last_displayable = dissector;
            ht_displayables.put(new Long(oid), dissector);
            ht_zdispl.put(new Long(oid), dissector);
            addToLastOpenLayerSet(dissector);
        } else if (type.equals("layer")) {
            // find last open LayerSet, if any
            for (int i = al_layer_sets.size() - 1; i > -1; ) {
                LayerSet set = al_layer_sets.get(i);
                Layer layer = new Layer(project, oid, ht_attributes);
                layer.addToDatabase();
                set.addSilently(layer);
                al_layers.add(layer);
                Object ot = ht_attributes.get("title");
                return new LayerThing(template_layer_thing, project, -1, (null == ot ? null : (String) ot), layer, null);
            }
        } else if (type.equals("layer_set")) {
            LayerSet set = new LayerSet(project, oid, ht_attributes, ht_links);
            last_displayable = set;
            set.addToDatabase();
            ht_displayables.put(new Long(oid), set);
            al_layer_sets.add(set);
            addToLastOpenLayer(set);
            Object ot = ht_attributes.get("title");
            return new LayerThing(template_layer_set_thing, project, -1, (null == ot ? null : (String) ot), set, null);
        } else if (type.equals("calibration")) {
            // find last open LayerSet if any
            for (int i = al_layer_sets.size() - 1; i > -1; ) {
                LayerSet set = al_layer_sets.get(i);
                set.restoreCalibration(ht_attributes);
                return null;
            }
        } else if (type.equals("prop")) {
            // Add property to last created Displayable
            if (null != last_displayable) {
                last_displayable.setProperty(ht_attributes.get("key"), ht_attributes.get("value"));
            }
        } else if (type.equals("linked_prop")) {
            // Add linked property to last created Displayable. Has to wait until the Displayable ids have been resolved to instances.
            if (null != last_displayable) {
                putLinkedProperty(last_displayable, ht_attributes);
            }
        } else {
            Utils.log2("TMLHandler Unknown type: " + type);
        }
    } catch (Exception e) {
        IJError.print(e);
    }
    // default:
    return null;
}

Example 69 with Displayable

use of ini.trakem2.display.Displayable in project TrakEM2 by trakem2.

the class TMLHandler method startElement.

public void startElement(String namespace_URI, String local_name, String qualified_name, Attributes attributes) throws SAXException {
    if (null == loader)
        return;
    // Utils.log2("startElement: " + qualified_name);
    this.counter++;
    if (0 == counter % 100) {
        // davi-experimenting: don't talk so much when you have > 600,000 patches to load!
        Utils.showStatus("Loading " + counter, false);
    }
    try {
        // failsafe:
        qualified_name = qualified_name.toLowerCase();
        final HashMap<String, String> ht_attributes = new HashMap<String, String>();
        for (int i = attributes.getLength() - 1; i > -1; i--) {
            ht_attributes.put(attributes.getQName(i).toLowerCase(), attributes.getValue(i));
        }
        // get the id, which whenever possible it's the id of the encapsulating Thing object. The encapsulated object id is the oid
        // The type is specified by the qualified_name
        Thing thing = null;
        if (0 == qualified_name.indexOf("t2_")) {
            if (qualified_name.equals("t2_display")) {
                // store for later, until the layers exist
                if (open_displays)
                    al_displays.add(ht_attributes);
            } else {
                // a Layer, LayerSet or Displayable object
                thing = makeLayerThing(qualified_name, ht_attributes);
                if (null != thing) {
                    if (null == root_lt && thing.getObject() instanceof LayerSet) {
                        root_lt = (LayerThing) thing;
                    }
                }
            }
        } else if (qualified_name.equals("project")) {
            if (null != this.root_pt) {
                Utils.log("WARNING: more than one project definitions.");
                return;
            }
            // Create the project
            this.project = new Project(Long.parseLong(ht_attributes.remove("id")), ht_attributes.remove("title"));
            // temp, but will be the same anyway
            this.project.setTempLoader(this.loader);
            this.project.parseXMLOptions(ht_attributes);
            // register id
            this.project.addToDatabase();
            String title = ht_attributes.get("title");
            if (null != title)
                this.project.setTitle(title);
            // Add all unique TemplateThing types to the project
            for (Iterator<TemplateThing> it = root_tt.getUniqueTypes(new HashMap<String, TemplateThing>()).values().iterator(); it.hasNext(); ) {
                this.project.addUniqueType(it.next());
            }
            this.project.addUniqueType(this.project_tt);
            this.root_pt = new ProjectThing(this.project_tt, this.project, this.project);
            // Add a project pointer to all template things
            this.root_tt.addToDatabase(this.project);
            thing = root_pt;
        } else if (qualified_name.startsWith("ict_transform") || qualified_name.startsWith("iict_transform")) {
            makeCoordinateTransform(qualified_name, ht_attributes);
        } else if (!qualified_name.equals("trakem2")) {
            // Any abstract object
            thing = makeProjectThing(qualified_name, ht_attributes);
        }
        if (null != thing) {
            // get the previously open thing and add this new_thing to it as a child
            int size = al_open.size();
            if (size > 0) {
                Thing parent = al_open.get(size - 1);
                parent.addChild(thing);
            // Utils.log2("Adding child " + thing + " to parent " + parent);
            }
            // add the new thing as open
            al_open.add(thing);
        }
    } catch (Exception e) {
        IJError.print(e);
        skip = true;
    }
}

Example 70 with Displayable

use of ini.trakem2.display.Displayable in project TrakEM2 by trakem2.

the class LayerTree method actionPerformed.

public void actionPerformed(ActionEvent ae) {
    try {
        String command = ae.getActionCommand();
        // commands for multiple selections:
        TreePath[] paths = this.getSelectionPaths();
        if (null != paths && paths.length > 1) {
            if (command.equals("Reverse layer Z coords")) {
                // check that all layers belong to the same layer set
                // just do it
                Layer[] layer = new Layer[paths.length];
                LayerSet ls = null;
                for (int i = 0; i < paths.length; i++) {
                    layer[i] = (Layer) ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getObject();
                    if (null == ls)
                        ls = layer[i].getParent();
                    else if (!ls.equals(layer[i].getParent())) {
                        Utils.showMessage("To reverse, all layers must belong to the same layer set");
                        return;
                    }
                }
                final ArrayList<Layer> al = new ArrayList<Layer>();
                for (int i = 0; i < layer.length; i++) al.add(layer[i]);
                ls.addLayerEditedStep(al);
                // ASSSUMING layers are already Z ordered! CHECK
                for (int i = 0, j = layer.length - 1; i < layer.length / 2; i++, j--) {
                    double z = layer[i].getZ();
                    layer[i].setZ(layer[j].getZ());
                    layer[j].setZ(z);
                }
                updateList(ls);
                ls.addLayerEditedStep(al);
                Display.updateLayerScroller(ls);
            } else if (command.equals("Translate layers in Z...")) {
                GenericDialog gd = ControlWindow.makeGenericDialog("Range");
                gd.addMessage("Translate selected range in the Z axis:");
                gd.addNumericField("by: ", 0, 4);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                // else, displace
                double dz = gd.getNextNumber();
                if (Double.isNaN(dz)) {
                    Utils.showMessage("Invalid number");
                    return;
                }
                HashSet<LayerSet> hs_parents = new HashSet<LayerSet>();
                for (int i = 0; i < paths.length; i++) {
                    Layer layer = (Layer) ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getObject();
                    layer.setZ(layer.getZ() + dz);
                    hs_parents.add(layer.getParent());
                }
                for (LayerSet ls : hs_parents) {
                    updateList(ls);
                }
                // now update all profile's Z ordering in the ProjectTree
                ProjectThing root_pt = project.getRootProjectThing();
                for (final ProjectThing pt : root_pt.findChildrenOfType("profile_list")) {
                    pt.fixZOrdering();
                    project.getProjectTree().updateList(pt);
                }
                project.getProjectTree().updateUILater();
            // Display.updateLayerScroller((LayerSet)((DefaultMutableTreeNode)getModel().getRoot()).getUserObject());
            } else if (command.equals("Delete...")) {
                if (!Utils.check("Really remove all selected layers?"))
                    return;
                for (int i = 0; i < paths.length; i++) {
                    DefaultMutableTreeNode lnode = (DefaultMutableTreeNode) paths[i].getLastPathComponent();
                    LayerThing lt = (LayerThing) lnode.getUserObject();
                    Layer layer = (Layer) lt.getObject();
                    if (!layer.remove(false)) {
                        Utils.showMessage("Could not delete layer " + layer);
                        this.updateUILater();
                        return;
                    }
                    if (lt.remove(false)) {
                        ((DefaultTreeModel) this.getModel()).removeNodeFromParent(lnode);
                    }
                }
                this.updateUILater();
            } else if (command.equals("Scale Z and thickness...")) {
                GenericDialog gd = new GenericDialog("Scale Z");
                gd.addNumericField("scale: ", 1.0, 2);
                gd.showDialog();
                double scale = gd.getNextNumber();
                if (Double.isNaN(scale) || 0 == scale) {
                    Utils.showMessage("Imvalid scaling factor: " + scale);
                    return;
                }
                for (int i = 0; i < paths.length; i++) {
                    DefaultMutableTreeNode lnode = (DefaultMutableTreeNode) paths[i].getLastPathComponent();
                    LayerThing lt = (LayerThing) lnode.getUserObject();
                    Layer layer = (Layer) lt.getObject();
                    layer.setZ(layer.getZ() * scale);
                    layer.setThickness(layer.getThickness() * scale);
                }
                this.updateUILater();
            } else {
                Utils.showMessage("Don't know what to do with command " + command + " for multiple selected nodes");
            }
            return;
        }
        // commands for single selection:
        if (null == selected_node)
            return;
        LayerThing thing = (LayerThing) selected_node.getUserObject();
        LayerThing new_thing = null;
        TemplateThing tt = null;
        Object ob = null;
        int i_position = -1;
        if (command.startsWith("new ")) {
            String name = command.substring(4).toLowerCase();
            if (name.equals("layer")) {
                // Create new Layer and add it to the selected node
                LayerSet set = (LayerSet) thing.getObject();
                Layer new_layer = Layer.create(thing.getProject(), set);
                if (null == new_layer)
                    return;
                tt = thing.getChildTemplate("layer");
                ob = new_layer;
                Display.updateTitle(set);
            } else if (name.equals("layer set")) {
                // with space in the middle
                // Create a new LayerSet and add it in the middle
                Layer layer = (Layer) thing.getObject();
                LayerSet new_set = layer.getParent().create(layer);
                if (null == new_set)
                    return;
                layer.add(new_set);
                // add it at the end of the list
                // with space, not underscore
                tt = thing.getChildTemplate("layer set");
                ob = new_set;
                i_position = selected_node.getChildCount();
                Display.update(layer);
            } else {
                Utils.log("LayerTree.actionPerformed: don't know what to do with the command: " + command);
                return;
            }
        } else if (command.equals("many new layers...")) {
            LayerSet set = (LayerSet) thing.getObject();
            List<Layer> layers = Layer.createMany(set.getProject(), set);
            // add them to the tree as LayerThing
            if (null == layers)
                return;
            for (Layer la : layers) {
                // null layers will be skipped
                addLayer(set, la);
            }
            Display.updateTitle(set);
            return;
        } else if (command.equals("Show")) {
            // create a new Display
            DBObject dbo = (DBObject) thing.getObject();
            // the top level LayerSet
            if (thing.getType().equals("layer_set") && null == ((LayerSet) dbo).getParent())
                return;
            Display.createDisplay(dbo.getProject(), thing.getType().equals("layer") ? (Layer) dbo : ((LayerSet) dbo).getParent());
            return;
        } else if (command.equals("Show centered in Display")) {
            LayerSet ls = (LayerSet) thing.getObject();
            Display.showCentered(ls.getParent(), ls, false, false);
        } else if (command.equals("Delete...")) {
            remove(true, thing, selected_node);
            return;
        } else if (command.equals("Import stack...")) {
            if (thing.getObject() instanceof LayerSet) {
                LayerSet set = (LayerSet) thing.getObject();
                Layer layer = null;
                if (0 == set.getLayers().size()) {
                    layer = Layer.create(set.getProject(), set);
                    if (null == layer)
                        return;
                    tt = thing.getChildTemplate("Layer");
                    ob = layer;
                } else
                    // click on a desired, existing layer.
                    return;
                layer.getProject().getLoader().importStack(layer, null, true);
            } else if (thing.getObject() instanceof Layer) {
                Layer layer = (Layer) thing.getObject();
                layer.getProject().getLoader().importStack(layer, null, true);
                return;
            }
        } else if (command.equals("Import grid...")) {
            if (thing.getObject() instanceof Layer) {
                Layer layer = (Layer) thing.getObject();
                layer.getProject().getLoader().importGrid(layer);
            }
        } else if (command.equals("Import sequence as grid...")) {
            if (thing.getObject() instanceof Layer) {
                Layer layer = (Layer) thing.getObject();
                layer.getProject().getLoader().importSequenceAsGrid(layer);
            }
        } else if (command.equals("Import from text file...")) {
            if (thing.getObject() instanceof Layer) {
                Layer layer = (Layer) thing.getObject();
                layer.getProject().getLoader().importImages(layer);
            }
        } else if (command.equals("Resize LayerSet...")) {
            if (thing.getObject() instanceof LayerSet) {
                LayerSet ls = (LayerSet) thing.getObject();
                ij.gui.GenericDialog gd = ControlWindow.makeGenericDialog("Resize LayerSet");
                gd.addNumericField("new width: ", ls.getLayerWidth(), 3);
                gd.addNumericField("new height: ", ls.getLayerHeight(), 3);
                gd.addChoice("Anchor: ", LayerSet.ANCHORS, LayerSet.ANCHORS[0]);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                float new_width = (float) gd.getNextNumber(), new_height = (float) gd.getNextNumber();
                // will complain and prevent cropping existing Displayable objects
                ls.setDimensions(new_width, new_height, gd.getNextChoiceIndex());
            }
        } else if (command.equals("Autoresize LayerSet")) {
            if (thing.getObject() instanceof LayerSet) {
                LayerSet ls = (LayerSet) thing.getObject();
                ls.setMinimumDimensions();
            }
        } else if (command.equals("Adjust...")) {
            if (thing.getObject() instanceof Layer) {
                Layer layer = (Layer) thing.getObject();
                ij.gui.GenericDialog gd = ControlWindow.makeGenericDialog("Adjust Layer");
                gd.addNumericField("new z: ", layer.getZ(), 4);
                gd.addNumericField("new thickness: ", layer.getThickness(), 4);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                double new_z = gd.getNextNumber();
                layer.setThickness(gd.getNextNumber());
                if (new_z != layer.getZ()) {
                    layer.setZ(new_z);
                    // move in the tree
                    /*
						DefaultMutableTreeNode child = findNode(thing, this);
						DefaultMutableTreeNode parent = (DefaultMutableTreeNode)child.getParent();
						parent.remove(child);
						// reinsert
						int n = parent.getChildCount();
						int i = 0;
						for (; i < n; i++) {
							DefaultMutableTreeNode child_node = (DefaultMutableTreeNode)parent.getChildAt(i);
							LayerThing child_thing = (LayerThing)child_node.getUserObject();
							if (!child_thing.getType().equals("Layer")) continue;
							double iz = ((Layer)child_thing.getObject()).getZ();
							if (iz < new_z) continue;
							// else, add the layer here, after this one
							break;
						}
						((DefaultTreeModel)this.getModel()).insertNodeInto(child, parent, i);
						*/
                    // fix tree crappiness (empty slot ?!?)
                    /* // the fix doesn't work. ARGH TODO
						Enumeration e = parent.children();
						parent.removeAllChildren();
						i = 0;
						while (e.hasMoreElements()) {
							//parent.add((DefaultMutableTreeNode)e.nextElement());
							((DefaultTreeModel)this.getModel()).insertNodeInto(child, parent, i);
							i++;
						}*/
                    // easier and correct: overkill
                    updateList(layer.getParent());
                    // set selected
                    DefaultMutableTreeNode child = findNode(thing, this);
                    TreePath treePath = new TreePath(child.getPath());
                    this.scrollPathToVisible(treePath);
                    this.setSelectionPath(treePath);
                }
            }
            return;
        } else if (command.equals("Rename...")) {
            GenericDialog gd = ControlWindow.makeGenericDialog("Rename");
            gd.addStringField("new name: ", thing.getTitle());
            gd.showDialog();
            if (gd.wasCanceled())
                return;
            project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
            thing.setTitle(gd.getNextString());
            project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
        } else if (command.equals("Translate layers in Z...")) {
            // / TODO: this method should use multiple selections directly on the tree
            if (thing.getObject() instanceof LayerSet) {
                LayerSet ls = (LayerSet) thing.getObject();
                ArrayList<Layer> al_layers = ls.getLayers();
                String[] layer_names = new String[al_layers.size()];
                for (int i = 0; i < layer_names.length; i++) {
                    layer_names[i] = ls.getProject().findLayerThing(al_layers.get(i)).toString();
                }
                GenericDialog gd = ControlWindow.makeGenericDialog("Range");
                gd.addMessage("Translate selected range in the Z axis:");
                gd.addChoice("from: ", layer_names, layer_names[0]);
                gd.addChoice("to: ", layer_names, layer_names[layer_names.length - 1]);
                gd.addNumericField("by: ", 0, 4);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                // else, displace
                double dz = gd.getNextNumber();
                if (Double.isNaN(dz)) {
                    Utils.showMessage("Invalid number");
                    return;
                }
                int i_start = gd.getNextChoiceIndex();
                int i_end = gd.getNextChoiceIndex();
                for (int i = i_start; i <= i_end; i++) {
                    Layer layer = (Layer) al_layers.get(i);
                    layer.setZ(layer.getZ() + dz);
                }
                // update node labels and position
                updateList(ls);
            }
        } else if (command.equals("Reverse layer Z coords...")) {
            // / TODO: this method should use multiple selections directly on the tree
            if (thing.getObject() instanceof LayerSet) {
                LayerSet ls = (LayerSet) thing.getObject();
                ArrayList<Layer> al_layers = ls.getLayers();
                String[] layer_names = new String[al_layers.size()];
                for (int i = 0; i < layer_names.length; i++) {
                    layer_names[i] = ls.getProject().findLayerThing(al_layers.get(i)).toString();
                }
                GenericDialog gd = ControlWindow.makeGenericDialog("Range");
                gd.addMessage("Reverse Z coordinates of selected range:");
                gd.addChoice("from: ", layer_names, layer_names[0]);
                gd.addChoice("to: ", layer_names, layer_names[layer_names.length - 1]);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                int i_start = gd.getNextChoiceIndex();
                int i_end = gd.getNextChoiceIndex();
                for (int i = i_start, j = i_end; i < i_end / 2; i++, j--) {
                    Layer layer1 = (Layer) al_layers.get(i);
                    double z1 = layer1.getZ();
                    Layer layer2 = (Layer) al_layers.get(j);
                    layer1.setZ(layer2.getZ());
                    layer2.setZ(z1);
                }
                // update node labels and position
                updateList(ls);
            }
        } else if (command.equals("Search...")) {
            Search.showWindow();
        } else if (command.equals("Reset layer Z and thickness")) {
            LayerSet ls = ((LayerSet) thing.getObject());
            List<Layer> layers = ls.getLayers();
            ls.addLayerEditedStep(layers);
            int i = 0;
            for (final Layer la : ls.getLayers()) {
                la.setZ(i++);
                la.setThickness(1);
            }
            ls.addLayerEditedStep(layers);
        } else {
            Utils.log("LayerTree.actionPerformed: don't know what to do with the command: " + command);
            return;
        }
        if (null == tt)
            return;
        new_thing = new LayerThing(tt, thing.getProject(), ob);
        if (-1 == i_position && new_thing.getType().equals("layer")) {
            // find the node whose 'z' is larger than z, and add the Layer before that.
            // (just because there could be objects other than LayerThing with a Layer in it in the future, so set.getLayers().indexOf(layer) may not be useful)
            double z = ((Layer) ob).getZ();
            int n = selected_node.getChildCount();
            int i = 0;
            for (; i < n; i++) {
                DefaultMutableTreeNode child_node = (DefaultMutableTreeNode) selected_node.getChildAt(i);
                LayerThing child_thing = (LayerThing) child_node.getUserObject();
                if (!child_thing.getType().equals("layer")) {
                    continue;
                }
                double iz = ((Layer) child_thing.getObject()).getZ();
                if (iz < z) {
                    continue;
                }
                // else, add the layer here, after this one
                break;
            }
            i_position = i;
        }
        thing.addChild(new_thing);
        DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
        ((DefaultTreeModel) this.getModel()).insertNodeInto(new_node, selected_node, i_position);
        TreePath treePath = new TreePath(new_node.getPath());
        this.scrollPathToVisible(treePath);
        this.setSelectionPath(treePath);
        if (new_thing.getType().equals("layer set")) {
            // add the first layer to it, and open it in a Display
            LayerSet newls = (LayerSet) new_thing.getObject();
            Layer la = new Layer(newls.getProject(), 0, 1, newls);
            addLayer(newls, la);
            new Display(newls.getProject(), la);
        }
    } catch (Exception e) {
        IJError.print(e);
    }
}