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

Example 26 with Layer

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

the class MatchIntensities method run.

/**
 * @param layers
 * @param radius
 * @param scale
 * @param numCoefficients
 * @param lambda1
 * @param lambda2
 * @param neighborWeight
 * @param roi
 */
public <M extends Model<M> & Affine1D<M>> void run(final List<Layer> layers, final int radius, final double scale, final int numCoefficients, final double lambda1, final double lambda2, final double neighborWeight, final Rectangle roi) throws InterruptedException, ExecutionException {
    final int firstLayerIndex = layerset.getLayerIndex(layers.get(0).getId());
    final int lastLayerIndex = layerset.getLayerIndex(layers.get(layers.size() - 1).getId());
    // final PointMatchFilter filter = new RansacRegressionFilter();
    final PointMatchFilter filter = new RansacRegressionReduceFilter();
    /* collect patches */
    Utils.log("Collecting patches ... ");
    final ArrayList<Patch> patches = new ArrayList<Patch>();
    for (final Layer layer : layers) patches.addAll((Collection) layer.getDisplayables(Patch.class, roi));
    /* delete existing intensity coefficients */
    Utils.log("Clearing existing intensity maps ... ");
    for (final Patch p : patches) p.clearIntensityMap();
    /* generate coefficient tiles for all patches
		 * TODO consider offering alternative models */
    final HashMap<Patch, ArrayList<Tile<? extends M>>> coefficientsTiles = (HashMap) generateCoefficientsTiles(patches, new InterpolatedAffineModel1D<InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>, IdentityModel>(new InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>(new AffineModel1D(), new TranslationModel1D(), lambda1), new IdentityModel(), lambda2), numCoefficients * numCoefficients);
    /* completed patches */
    final HashSet<Patch> completedPatches = new HashSet<Patch>();
    /* collect patch pairs */
    Utils.log("Collecting patch pairs ... ");
    final ArrayList<ValuePair<Patch, Patch>> patchPairs = new ArrayList<ValuePair<Patch, Patch>>();
    for (final Patch p1 : patches) {
        completedPatches.add(p1);
        final Rectangle box1 = p1.getBoundingBox().intersection(roi);
        final ArrayList<Patch> p2s = new ArrayList<Patch>();
        /* across adjacent layers */
        final int layerIndex = layerset.getLayerIndex(p1.getLayer().getId());
        for (int i = Math.max(firstLayerIndex, layerIndex - radius); i <= Math.min(lastLayerIndex, layerIndex + radius); ++i) {
            final Layer layer = layerset.getLayer(i);
            if (layer != null)
                p2s.addAll((Collection) layer.getDisplayables(Patch.class, box1));
        }
        for (final Patch p2 : p2s) {
            /*
				 * if this patch had been processed earlier, all matches are
				 * already in
				 */
            if (completedPatches.contains(p2))
                continue;
            patchPairs.add(new ValuePair<Patch, Patch>(p1, p2));
        }
    }
    final int numThreads = Integer.parseInt(layerset.getProperty("n_mipmap_threads", Integer.toString(Runtime.getRuntime().availableProcessors())));
    Utils.log("Matching intensities using " + numThreads + " threads ... ");
    final ExecutorService exec = Executors.newFixedThreadPool(numThreads);
    final ArrayList<Future<?>> futures = new ArrayList<Future<?>>();
    for (final ValuePair<Patch, Patch> patchPair : patchPairs) {
        futures.add(exec.submit(new Matcher(roi, patchPair, (HashMap) coefficientsTiles, filter, scale, numCoefficients)));
    }
    for (final Future<?> future : futures) future.get();
    /* connect tiles within patches */
    Utils.log("Connecting coefficient tiles in the same patch  ... ");
    for (final Patch p1 : completedPatches) {
        /* get the coefficient tiles */
        final ArrayList<Tile<? extends M>> p1CoefficientsTiles = coefficientsTiles.get(p1);
        for (int y = 1; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            final int yr1 = yr - numCoefficients;
            for (int x = 0; x < numCoefficients; ++x) {
                identityConnect(p1CoefficientsTiles.get(yr1 + x), p1CoefficientsTiles.get(yr + x), neighborWeight);
            }
        }
        for (int y = 0; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            for (int x = 1; x < numCoefficients; ++x) {
                final int yrx = yr + x;
                identityConnect(p1CoefficientsTiles.get(yrx), p1CoefficientsTiles.get(yrx - 1), neighborWeight);
            }
        }
    }
    /* optimize */
    Utils.log("Optimizing ... ");
    final TileConfiguration tc = new TileConfiguration();
    for (final ArrayList<Tile<? extends M>> coefficients : coefficientsTiles.values()) {
        // for ( final Tile< ? > t : coefficients )
        // if ( t.getMatches().size() == 0 )
        // IJ.log( "bang" );
        tc.addTiles(coefficients);
    }
    try {
        tc.optimize(0.01f, iterations, iterations, 0.75f);
    } catch (final NotEnoughDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (final IllDefinedDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    /* save coefficients */
    final double[] ab = new double[2];
    final FSLoader loader = (FSLoader) layerset.getProject().getLoader();
    final String itsDir = loader.getUNUIdFolder() + "trakem2.its/";
    for (final Entry<Patch, ArrayList<Tile<? extends M>>> entry : coefficientsTiles.entrySet()) {
        final FloatProcessor as = new FloatProcessor(numCoefficients, numCoefficients);
        final FloatProcessor bs = new FloatProcessor(numCoefficients, numCoefficients);
        final Patch p = entry.getKey();
        final double min = p.getMin();
        final double max = p.getMax();
        final ArrayList<Tile<? extends M>> tiles = entry.getValue();
        for (int i = 0; i < numCoefficients * numCoefficients; ++i) {
            final Tile<? extends M> t = tiles.get(i);
            final Affine1D<?> affine = t.getModel();
            affine.toArray(ab);
            /* coefficients mapping into existing [min, max] */
            as.setf(i, (float) ab[0]);
            bs.setf(i, (float) ((max - min) * ab[1] + min - ab[0] * min));
        }
        final ImageStack coefficientsStack = new ImageStack(numCoefficients, numCoefficients);
        coefficientsStack.addSlice(as);
        coefficientsStack.addSlice(bs);
        final String itsPath = itsDir + FSLoader.createIdPath(Long.toString(p.getId()), "it", ".tif");
        new File(itsPath).getParentFile().mkdirs();
        IJ.saveAs(new ImagePlus("", coefficientsStack), "tif", itsPath);
    }
    /* update mipmaps */
    for (final Patch p : patches) p.getProject().getLoader().decacheImagePlus(p.getId());
    final ArrayList<Future<Boolean>> mipmapFutures = new ArrayList<Future<Boolean>>();
    for (final Patch p : patches) mipmapFutures.add(p.updateMipMaps());
    for (final Future<Boolean> f : mipmapFutures) f.get();
    Utils.log("Matching intensities done.");
}

Example 27 with Layer

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

the class Render method main.

public static final void main(final String... args) {
    new ImageJ();
    final double scale = 0.05;
    // final double scale = 1;
    final int numCoefficients = 4;
    final Project project = Project.openFSProject("/home/saalfeld/tmp/bock-lens-correction/subproject.xml", false);
    final Layer layer = project.getRootLayerSet().getLayer(0);
    final ArrayList<Patch> patches = (ArrayList) layer.getDisplayables(Patch.class);
    final Patch patch1 = patches.get(0);
    final Patch patch2 = patches.get(2);
    final Rectangle box = patch1.getBoundingBox().intersection(patch2.getBoundingBox());
    // final Rectangle box = patch1.getBoundingBox();
    final int w = (int) (box.width * scale + 0.5);
    final int h = (int) (box.height * scale + 0.5);
    final FloatProcessor pixels1 = new FloatProcessor(w, h);
    final FloatProcessor weights1 = new FloatProcessor(w, h);
    final ColorProcessor coefficients1 = new ColorProcessor(w, h);
    final FloatProcessor pixels2 = new FloatProcessor(w, h);
    final FloatProcessor weights2 = new FloatProcessor(w, h);
    final ColorProcessor coefficients2 = new ColorProcessor(w, h);
    render(patch1, numCoefficients, numCoefficients, pixels1, weights1, coefficients1, box.x, box.y, scale);
    render(patch2, numCoefficients, numCoefficients, pixels2, weights2, coefficients2, box.x, box.y, scale);
    final ImageStack stack = new ImageStack(w, h);
    stack.addSlice(pixels1);
    stack.addSlice(pixels2);
    stack.addSlice(weights1);
    stack.addSlice(weights2);
    stack.addSlice(coefficients1.convertToFloatProcessor());
    stack.addSlice(coefficients2.convertToFloatProcessor());
    new ImagePlus("", stack).show();
}

Example 28 with Layer

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

the class Display method getPopupMenu.

/**
 * Return a context-sensitive popup menu.
 */
protected JPopupMenu getPopupMenu() {
    // get the job canceling dialog
    if (!canvas.isInputEnabled()) {
        return project.getLoader().getJobsPopup(this);
    }
    // create new
    this.popup = new JPopupMenu();
    JMenuItem item = null;
    JMenu menu = null;
    if (mode instanceof InspectPatchTrianglesMode) {
        item = new JMenuItem("Exit inspection");
        item.addActionListener(this);
        popup.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
        return popup;
    } else if (canvas.isTransforming()) {
        item = new JMenuItem("Apply transform");
        item.addActionListener(this);
        popup.add(item);
        // dummy, for I don't add a MenuKeyListener, but "works" through the normal key listener. It's here to provide a visual cue
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0, true));
        item = new JMenuItem("Apply transform propagating to last layer");
        item.addActionListener(this);
        popup.add(item);
        if (layer.getParent().indexOf(layer) == layer.getParent().size() - 1)
            item.setEnabled(false);
        if (!(getMode().getClass() == AffineTransformMode.class || getMode().getClass() == NonLinearTransformMode.class))
            item.setEnabled(false);
        item = new JMenuItem("Apply transform propagating to first layer");
        item.addActionListener(this);
        popup.add(item);
        if (0 == layer.getParent().indexOf(layer))
            item.setEnabled(false);
        if (!(getMode().getClass() == AffineTransformMode.class || getMode().getClass() == NonLinearTransformMode.class))
            item.setEnabled(false);
        item = new JMenuItem("Cancel transform");
        item.addActionListener(this);
        popup.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
        item = new JMenuItem("Specify transform...");
        item.addActionListener(this);
        popup.add(item);
        if (getMode().getClass() != AffineTransformMode.class)
            item.setEnabled(false);
        if (getMode().getClass() == ManualAlignMode.class) {
            final JMenuItem lexport = new JMenuItem("Export landmarks");
            popup.add(lexport);
            final JMenuItem limport = new JMenuItem("Import landmarks");
            popup.add(limport);
            final ActionListener a = new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent ae) {
                    final ManualAlignMode mam = (ManualAlignMode) getMode();
                    final Object source = ae.getSource();
                    if (lexport == source) {
                        mam.exportLandmarks();
                    } else if (limport == source) {
                        mam.importLandmarks();
                    }
                }
            };
            lexport.addActionListener(a);
            limport.addActionListener(a);
        }
        return popup;
    }
    final Class<?> aclass = null == active ? null : active.getClass();
    if (null != active) {
        if (Profile.class == aclass) {
            item = new JMenuItem("Duplicate, link and send to next layer");
            item.addActionListener(this);
            popup.add(item);
            Layer nl = layer.getParent().next(layer);
            if (nl == layer)
                item.setEnabled(false);
            item = new JMenuItem("Duplicate, link and send to previous layer");
            item.addActionListener(this);
            popup.add(item);
            nl = layer.getParent().previous(layer);
            if (nl == layer)
                item.setEnabled(false);
            menu = new JMenu("Duplicate, link and send to");
            int i = 1;
            for (final Layer la : layer.getParent().getLayers()) {
                // TODO should label which layers contain Profile instances linked to the one being duplicated
                item = new JMenuItem(i + ": z = " + la.getZ());
                // TODO should label which layers contain Profile instances linked to the one being duplicated
                item.addActionListener(this);
                // TODO should label which layers contain Profile instances linked to the one being duplicated
                menu.add(item);
                if (la == this.layer)
                    item.setEnabled(false);
                i++;
            }
            popup.add(menu);
            item = new JMenuItem("Duplicate, link and send to...");
            item.addActionListener(this);
            popup.add(item);
            popup.addSeparator();
            item = new JMenuItem("Unlink from images");
            item.addActionListener(this);
            popup.add(item);
            // isLinked() checks if it's linked to a Patch in its own layer
            if (!active.isLinked())
                item.setEnabled(false);
            item = new JMenuItem("Show in 3D");
            item.addActionListener(this);
            popup.add(item);
            popup.addSeparator();
        } else if (Patch.class == aclass) {
            final JMenu m = new JMenu("Patch");
            item = new JMenuItem("Fill ROI in alpha mask");
            item.addActionListener(this);
            m.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, 0));
            item.setEnabled(null != getRoi());
            item = new JMenuItem("Fill inverse ROI in alpha mask");
            item.addActionListener(this);
            m.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, Event.SHIFT_MASK));
            item.setEnabled(null != getRoi());
            item = new JMenuItem("Remove alpha mask");
            item.addActionListener(this);
            m.add(item);
            if (!((Patch) active).hasAlphaMask())
                item.setEnabled(false);
            item = new JMenuItem("Unlink from images");
            item.addActionListener(this);
            m.add(item);
            if (!active.isLinked(Patch.class))
                item.setEnabled(false);
            if (((Patch) active).isStack()) {
                item = new JMenuItem("Unlink slices");
                item.addActionListener(this);
                m.add(item);
            }
            final int n_sel_patches = selection.getSelected(Patch.class).size();
            item = new JMenuItem("Snap");
            item.addActionListener(this);
            m.add(item);
            item.setEnabled(1 == n_sel_patches);
            item = new JMenuItem("Montage");
            item.addActionListener(this);
            m.add(item);
            item.setEnabled(n_sel_patches > 1);
            item = new JMenuItem("Lens correction");
            item.addActionListener(this);
            m.add(item);
            item.setEnabled(n_sel_patches > 1);
            item = new JMenuItem("Blend");
            item.addActionListener(this);
            m.add(item);
            item.setEnabled(n_sel_patches > 1);
            item = new JMenuItem("Open image");
            item.addActionListener(new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent e) {
                    for (final Patch p : selection.get(Patch.class)) {
                        p.getImagePlus().show();
                    }
                }
            });
            m.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_D, KeyEvent.SHIFT_MASK, true));
            item = new JMenuItem("Open original image");
            item.addActionListener(new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent e) {
                    for (final Patch p : selection.get(Patch.class)) {
                        p.getProject().getLoader().releaseToFit(p.getOWidth(), p.getOHeight(), p.getType(), 5);
                        p.getProject().getLoader().openImagePlus(p.getImageFilePath()).show();
                    }
                }
            });
            item = new JMenuItem("View volume");
            item.addActionListener(this);
            m.add(item);
            final HashSet<Displayable> hs = active.getLinked(Patch.class);
            if (null == hs || 0 == hs.size())
                item.setEnabled(false);
            item = new JMenuItem("View orthoslices");
            item.addActionListener(this);
            m.add(item);
            // if no Patch instances among the directly linked, then it's not a stack
            if (null == hs || 0 == hs.size())
                item.setEnabled(false);
            popup.add(m);
            popup.addSeparator();
        } else {
            item = new JMenuItem("Unlink");
            item.addActionListener(this);
            popup.add(item);
            item = new JMenuItem("Show in 3D");
            item.addActionListener(this);
            popup.add(item);
            popup.addSeparator();
        }
        if (AreaList.class == aclass) {
            final ArrayList<?> al = selection.getSelected();
            int n = 0;
            for (final Iterator<?> it = al.iterator(); it.hasNext(); ) {
                if (it.next().getClass() == AreaList.class)
                    n++;
            }
            item = new JMenuItem("Merge");
            item.addActionListener(this);
            popup.add(item);
            if (n < 2)
                item.setEnabled(false);
            item = new JMenuItem("Split");
            item.addActionListener(this);
            popup.add(item);
            if (n < 1)
                item.setEnabled(false);
            addAreaListAreasMenu(popup, active);
            popup.addSeparator();
        } else if (Pipe.class == aclass) {
            item = new JMenuItem("Reverse point order");
            item.addActionListener(this);
            popup.add(item);
            popup.addSeparator();
        } else if (Treeline.class == aclass || AreaTree.class == aclass) {
            if (AreaTree.class == aclass)
                addAreaTreeAreasMenu(popup, (AreaTree) active);
            item = new JMenuItem("Reroot");
            item.addActionListener(this);
            popup.add(item);
            item = new JMenuItem("Part subtree");
            item.addActionListener(this);
            popup.add(item);
            item = new JMenuItem("Join");
            item.addActionListener(this);
            popup.add(item);
            item = new JMenuItem("Show tabular view");
            item.addActionListener(this);
            popup.add(item);
            final Collection<Tree> trees = selection.get(Tree.class);
            // 
            final JMenu nodeMenu = new JMenu("Nodes");
            item = new JMenuItem("Mark");
            item.addActionListener(this);
            nodeMenu.add(item);
            item = new JMenuItem("Clear marks (selected Trees)");
            item.addActionListener(this);
            nodeMenu.add(item);
            final JMenuItem nodeColor = new JMenuItem("Color...");
            nodeMenu.add(nodeColor);
            nodeColor.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_C, KeyEvent.SHIFT_MASK, true));
            final JMenuItem nodePairColor = new JMenuItem("Color path between two nodes tagged as...");
            nodeMenu.add(nodePairColor);
            final JMenuItem nodeRadius = active instanceof Treeline ? new JMenuItem("Radius...") : null;
            if (null != nodeRadius) {
                nodeMenu.add(nodeRadius);
                nodeRadius.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, 0, true));
            }
            final JMenuItem removeAllTags = new JMenuItem("Drop all tags (selected trees)");
            nodeMenu.add(removeAllTags);
            final JMenuItem removeTag = new JMenuItem("Drop all occurrences of tag...");
            nodeMenu.add(removeTag);
            final JMenuItem colorizeByNodeCentrality = new JMenuItem("Colorize by node betweenness centrality");
            nodeMenu.add(colorizeByNodeCentrality);
            final JMenuItem colorizeByBranchCentrality = new JMenuItem("Colorize by branch betweenness centrality");
            nodeMenu.add(colorizeByBranchCentrality);
            popup.add(nodeMenu);
            final ActionListener ln = new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent ae) {
                    if (null == active) {
                        Utils.showMessage("No tree selected!");
                        return;
                    }
                    if (!(active instanceof Tree)) {
                        Utils.showMessage("The selected object is not a Tree!");
                        return;
                    }
                    final Tree tree = (Tree) active;
                    final Object src = ae.getSource();
                    // 
                    if (src == nodeColor) {
                        final Node nd = tree.getLastVisited();
                        if (null == nd) {
                            Utils.showMessage("Select a node first by clicking on it\nor moving the mouse over it and pushing 'g'.");
                            return;
                        }
                        // sets an undo step
                        tree.adjustNodeColors(nd);
                    } else if (src == nodePairColor) {
                        final TreeMap<String, Tag> sm = getTags(tree);
                        if (null == sm)
                            return;
                        if (1 == sm.size()) {
                            Utils.showMessage("Need at least two different tags in the tree!");
                            return;
                        }
                        final Color color = tree.getColor();
                        final GenericDialog gd = new GenericDialog("Node colors");
                        gd.addSlider("Red: ", 0, 255, color.getRed());
                        gd.addSlider("Green: ", 0, 255, color.getGreen());
                        gd.addSlider("Blue: ", 0, 255, color.getBlue());
                        final String[] stags = asStrings(sm);
                        sm.keySet().toArray(stags);
                        gd.addChoice("Upstream tag:", stags, stags[0]);
                        gd.addChoice("Downstream tag:", stags, stags[1]);
                        gd.showDialog();
                        if (gd.wasCanceled())
                            return;
                        final Color newColor = new Color((int) gd.getNextNumber(), (int) gd.getNextNumber(), (int) gd.getNextNumber());
                        final Tag upstreamTag = sm.get(gd.getNextChoice());
                        final Tag downstreamTag = sm.get(gd.getNextChoice());
                        final List<Tree<?>.NodePath> pairs = tree.findTaggedPairs(upstreamTag, downstreamTag);
                        if (null == pairs || pairs.isEmpty()) {
                            Utils.showMessage("No pairs found for '" + upstreamTag + "' and '" + downstreamTag + "'");
                            return;
                        }
                        getLayerSet().addDataEditStep(tree);
                        for (final Tree<?>.NodePath pair : pairs) {
                            for (final Node<?> nd : pair.path) {
                                nd.setColor(newColor);
                            }
                        }
                        getLayerSet().addDataEditStep(tree);
                        Display.repaint();
                    } else if (src == nodeRadius) {
                        if (!(tree instanceof Treeline))
                            return;
                        final Node nd = tree.getLastVisited();
                        if (null == nd) {
                            Utils.showMessage("Select a node first by clicking on it\nor moving the mouse over it and pushing 'g'.");
                            return;
                        }
                        // sets an undo step
                        ((Treeline) tree).askAdjustRadius(nd);
                    } else if (src == removeAllTags) {
                        if (!Utils.check("Really remove all tags from all selected trees?"))
                            return;
                        final List<Tree> sel = selection.get(Tree.class);
                        getLayerSet().addDataEditStep(new HashSet<Displayable>(sel));
                        try {
                            for (final Tree t : sel) {
                                t.dropAllTags();
                            }
                            // current state
                            getLayerSet().addDataEditStep(new HashSet<Displayable>(sel));
                        } catch (final Exception e) {
                            getLayerSet().undoOneStep();
                            IJError.print(e);
                        }
                        Display.repaint();
                    } else if (src == removeTag) {
                        final TreeMap<String, Tag> tags = getTags(tree);
                        final String[] ts = asStrings(tags);
                        final GenericDialog gd = new GenericDialog("Remove tags");
                        gd.addChoice("Tag:", ts, ts[0]);
                        final String[] c = new String[] { "Active tree", "All selected trees and connectors", "All trees and connectors" };
                        gd.addChoice("From: ", c, c[0]);
                        gd.showDialog();
                        if (gd.wasCanceled())
                            return;
                        final HashSet<Displayable> ds = new HashSet<Displayable>();
                        final Tag tag = tags.get(gd.getNextChoice());
                        switch(gd.getNextChoiceIndex()) {
                            case 0:
                                ds.add(tree);
                                break;
                            case 1:
                                ds.addAll(selection.get(Tree.class));
                            case 2:
                                ds.addAll(getLayerSet().getZDisplayables(Tree.class, true));
                        }
                        getLayerSet().addDataEditStep(ds);
                        try {
                            for (final Displayable d : ds) {
                                final Tree t = (Tree) d;
                                t.removeTag(tag);
                            }
                            getLayerSet().addDataEditStep(ds);
                        } catch (final Exception e) {
                            getLayerSet().undoOneStep();
                            IJError.print(e);
                        }
                        Display.repaint();
                    } else if (src == colorizeByNodeCentrality) {
                        final List<Tree> ts = selection.get(Tree.class);
                        final HashSet<Tree> ds = new HashSet<Tree>(ts);
                        getLayerSet().addDataEditStep(ds);
                        try {
                            for (final Tree t : ts) {
                                t.colorizeByNodeBetweennessCentrality();
                            }
                            getLayerSet().addDataEditStep(ds);
                            Display.repaint();
                        } catch (final Exception e) {
                            getLayerSet().undoOneStep();
                            IJError.print(e);
                        }
                    } else if (src == colorizeByBranchCentrality) {
                        final List<Tree> ts = selection.get(Tree.class);
                        final HashSet<Tree> ds = new HashSet<Tree>(ts);
                        getLayerSet().addDataEditStep(ds);
                        try {
                            for (final Tree t : ts) {
                                t.colorizeByBranchBetweennessCentrality(2);
                            }
                            getLayerSet().addDataEditStep(ds);
                            Display.repaint();
                        } catch (final Exception e) {
                            getLayerSet().undoOneStep();
                            IJError.print(e);
                        }
                    }
                }
            };
            for (final JMenuItem a : new JMenuItem[] { nodeColor, nodePairColor, nodeRadius, removeAllTags, removeTag, colorizeByNodeCentrality, colorizeByBranchCentrality }) {
                if (null == a)
                    continue;
                a.addActionListener(ln);
            }
            // 
            final JMenu review = new JMenu("Review");
            final JMenuItem tgenerate = new JMenuItem("Generate review stacks (selected Trees)");
            review.add(tgenerate);
            tgenerate.setEnabled(trees.size() > 0);
            final JMenuItem tslab = new JMenuItem("Generate review stack for current slab");
            review.add(tslab);
            final JMenuItem tsubtree = new JMenuItem("Generate review stacks for subtree");
            review.add(tsubtree);
            final JMenuItem tremove = new JMenuItem("Remove reviews (selected Trees)");
            review.add(tremove);
            tremove.setEnabled(trees.size() > 0);
            final JMenuItem tconnectors = new JMenuItem("View table of outgoing/incoming connectors");
            review.add(tconnectors);
            final ActionListener l = new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent ae) {
                    if (!Utils.check("Really " + ae.getActionCommand())) {
                        return;
                    }
                    dispatcher.exec(new Runnable() {

                        @Override
                        public void run() {
                            int count = 0;
                            for (final Tree<?> t : trees) {
                                Utils.log("Processing " + (++count) + "/" + trees.size());
                                Bureaucrat bu = null;
                                if (ae.getSource() == tgenerate)
                                    bu = t.generateAllReviewStacks();
                                else if (ae.getSource() == tremove)
                                    bu = t.removeReviews();
                                else if (ae.getSource() == tslab) {
                                    final Point po = canvas.consumeLastPopupPoint();
                                    Utils.log2(po, layer, 1.0);
                                    bu = t.generateReviewStackForSlab(po.x, po.y, Display.this.layer, 1.0);
                                } else if (ae.getSource() == tsubtree) {
                                    final Point po = canvas.consumeLastPopupPoint();
                                    bu = t.generateSubtreeReviewStacks(po.x, po.y, Display.this.layer, 1.0);
                                }
                                if (null != bu)
                                    try {
                                        bu.getWorker().join();
                                    } catch (final InterruptedException ie) {
                                        return;
                                    }
                            }
                        }
                    });
                }
            };
            for (final JMenuItem c : new JMenuItem[] { tgenerate, tslab, tsubtree, tremove }) c.addActionListener(l);
            tconnectors.addActionListener(new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent ae) {
                    for (final Tree<?> t : trees) TreeConnectorsView.create(t);
                }
            });
            popup.add(review);
            final JMenu go = new JMenu("Go");
            item = new JMenuItem("Previous branch node or start");
            item.addActionListener(this);
            go.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_B, 0, true));
            item = new JMenuItem("Next branch node or end");
            item.addActionListener(this);
            go.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, 0, true));
            item = new JMenuItem("Root");
            item.addActionListener(this);
            go.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R, 0, true));
            go.addSeparator();
            item = new JMenuItem("Last added node");
            item.addActionListener(this);
            go.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, 0, true));
            item = new JMenuItem("Last edited node");
            item.addActionListener(this);
            go.add(item);
            item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, 0, true));
            popup.add(go);
            final JMenu tmeasure = new JMenu("Measure");
            final JMenuItem dist_to_root = new JMenuItem("Distance from this node to root");
            tmeasure.add(dist_to_root);
            final JMenuItem dist_to_tag = new JMenuItem("Distance from this node to all nodes tagged as...");
            tmeasure.add(dist_to_tag);
            final JMenuItem dist_to_mark = new JMenuItem("Distance from this node to the marked node");
            tmeasure.add(dist_to_mark);
            final JMenuItem dist_pairs = new JMenuItem("Shortest distances between all pairs of nodes tagged as...");
            tmeasure.add(dist_pairs);
            final ActionListener tma = getTreePathMeasureListener((Tree<?>) active);
            for (final JMenuItem mi : new JMenuItem[] { dist_to_root, dist_to_tag, dist_to_mark, dist_pairs }) {
                mi.addActionListener(tma);
            }
            popup.add(tmeasure);
            final String[] name = new String[] { AreaTree.class.getSimpleName(), Treeline.class.getSimpleName() };
            if (Treeline.class == aclass) {
                final String a = name[0];
                name[0] = name[1];
                name[1] = a;
            }
            item = new JMenuItem("Duplicate " + name[0] + " as " + name[1]);
            item.addActionListener(new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent e) {
                    Bureaucrat.createAndStart(new Worker.Task("Converting") {

                        @Override
                        public void exec() {
                            try {
                                getLayerSet().addChangeTreesStep();
                                final Map<Tree<?>, Tree<?>> m = Tree.duplicateAs(selection.getSelected(), (Class<Tree<?>>) (Treeline.class == aclass ? AreaTree.class : Treeline.class));
                                if (m.isEmpty()) {
                                    getLayerSet().removeLastUndoStep();
                                } else {
                                    getLayerSet().addChangeTreesStep();
                                }
                            } catch (final Exception e) {
                                IJError.print(e);
                            }
                        }
                    }, getProject());
                }
            });
            popup.add(item);
            popup.addSeparator();
        } else if (Connector.class == aclass) {
            item = new JMenuItem("Merge");
            item.addActionListener(new ActionListener() {

                @Override
                public void actionPerformed(final ActionEvent ae) {
                    if (null == getActive() || getActive().getClass() != Connector.class) {
                        Utils.log("Active object must be a Connector!");
                        return;
                    }
                    final List<Connector> col = selection.get(Connector.class);
                    if (col.size() < 2) {
                        Utils.log("Select more than one Connector!");
                        return;
                    }
                    if (col.get(0) != getActive()) {
                        if (col.remove(getActive())) {
                            col.add(0, (Connector) getActive());
                        } else {
                            Utils.log("ERROR: cannot find active object in selection list!");
                            return;
                        }
                    }
                    Bureaucrat.createAndStart(new Worker.Task("Merging connectors") {

                        @Override
                        public void exec() {
                            getLayerSet().addChangeTreesStep();
                            Connector base = null;
                            try {
                                base = Connector.merge(col);
                            } catch (final Exception e) {
                                IJError.print(e);
                            }
                            if (null == base) {
                                Utils.log("ERROR: could not merge connectors!");
                                getLayerSet().undoOneStep();
                            } else {
                                getLayerSet().addChangeTreesStep();
                            }
                            Display.repaint();
                        }
                    }, getProject());
                }
            });
            popup.add(item);
            item.setEnabled(selection.getSelected(Connector.class).size() > 1);
            popup.addSeparator();
        }
        item = new JMenuItem("Duplicate");
        item.addActionListener(this);
        popup.add(item);
        item = new JMenuItem("Color...");
        item.addActionListener(this);
        popup.add(item);
        if (active instanceof LayerSet)
            item.setEnabled(false);
        if (active.isLocked()) {
            item = new JMenuItem("Unlock");
            item.addActionListener(this);
            popup.add(item);
        } else {
            item = new JMenuItem("Lock");
            item.addActionListener(this);
            popup.add(item);
        }
        menu = new JMenu("Move");
        popup.addSeparator();
        final LayerSet ls = layer.getParent();
        item = new JMenuItem("Move to top");
        item.addActionListener(this);
        menu.add(item);
        // this is just to draw the key name by the menu; it does not incur on any event being generated (that I know if), and certainly not any event being listened to by TrakEM2.
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_HOME, 0, true));
        if (ls.isTop(active))
            item.setEnabled(false);
        item = new JMenuItem("Move up");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_PAGE_UP, 0, true));
        if (ls.isTop(active))
            item.setEnabled(false);
        item = new JMenuItem("Move down");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_PAGE_DOWN, 0, true));
        if (ls.isBottom(active))
            item.setEnabled(false);
        item = new JMenuItem("Move to bottom");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_END, 0, true));
        if (ls.isBottom(active))
            item.setEnabled(false);
        popup.add(menu);
        popup.addSeparator();
        item = new JMenuItem("Delete...");
        item.addActionListener(this);
        popup.add(item);
        try {
            if (Patch.class == aclass) {
                if (!active.isOnlyLinkedTo(Patch.class)) {
                    item.setEnabled(false);
                }
            }
        } catch (final Exception e) {
            IJError.print(e);
            item.setEnabled(false);
        }
        if (Patch.class == aclass) {
            item = new JMenuItem("Revert");
            item.addActionListener(this);
            popup.add(item);
            if (null == ((Patch) active).getOriginalPath())
                item.setEnabled(false);
            popup.addSeparator();
        }
        item = new JMenuItem("Properties...");
        item.addActionListener(this);
        popup.add(item);
        item = new JMenuItem("Show centered");
        item.addActionListener(this);
        popup.add(item);
        popup.addSeparator();
        if (!(active instanceof ZDisplayable)) {
            final int i_layer = layer.getParent().indexOf(layer);
            final int n_layers = layer.getParent().size();
            item = new JMenuItem("Send to previous layer");
            item.addActionListener(this);
            popup.add(item);
            if (1 == n_layers || 0 == i_layer || active.isLinked())
                item.setEnabled(false);
            else // check if the active is a profile and contains a link to another profile in the layer it is going to be sent to, or it is linked
            if (active instanceof Profile && !active.canSendTo(layer.getParent().previous(layer)))
                item.setEnabled(false);
            item = new JMenuItem("Send to next layer");
            item.addActionListener(this);
            popup.add(item);
            if (1 == n_layers || n_layers - 1 == i_layer || active.isLinked())
                item.setEnabled(false);
            else if (active instanceof Profile && !active.canSendTo(layer.getParent().next(layer)))
                item.setEnabled(false);
            menu = new JMenu("Send linked group to...");
            if (active.hasLinkedGroupWithinLayer(this.layer)) {
                int i = 1;
                for (final Layer la : ls.getLayers()) {
                    String layer_title = i + ": " + la.getTitle();
                    if (-1 == layer_title.indexOf(' '))
                        layer_title += " ";
                    item = new JMenuItem(layer_title);
                    item.addActionListener(this);
                    menu.add(item);
                    if (la == this.layer)
                        item.setEnabled(false);
                    i++;
                }
                popup.add(menu);
            } else {
                menu.setEnabled(false);
            // Utils.log("Active's linked group not within layer.");
            }
            popup.add(menu);
            popup.addSeparator();
        }
    }
    item = new JMenuItem("Undo");
    item.addActionListener(this);
    popup.add(item);
    if (!layer.getParent().canUndo() || canvas.isTransforming())
        item.setEnabled(false);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Z, Utils.getControlModifier(), true));
    item = new JMenuItem("Redo");
    item.addActionListener(this);
    popup.add(item);
    if (!layer.getParent().canRedo() || canvas.isTransforming())
        item.setEnabled(false);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Z, Event.SHIFT_MASK | Utils.getControlModifier(), true));
    popup.addSeparator();
    try {
        menu = new JMenu("Hide/Unhide");
        item = new JMenuItem("Hide deselected");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.SHIFT_MASK, true));
        boolean none = 0 == selection.getNSelected();
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Hide deselected except images");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.SHIFT_MASK | Event.ALT_MASK, true));
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Hide selected");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, 0, true));
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().containsDisplayable(DLabel.class);
        item = new JMenuItem("Hide all labels");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all labels");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(AreaList.class);
        item = new JMenuItem("Hide all arealists");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all arealists");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.contains(Profile.class);
        item = new JMenuItem("Hide all profiles");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all profiles");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(Pipe.class);
        item = new JMenuItem("Hide all pipes");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all pipes");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(Polyline.class);
        item = new JMenuItem("Hide all polylines");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all polylines");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(Treeline.class);
        item = new JMenuItem("Hide all treelines");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all treelines");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(AreaTree.class);
        item = new JMenuItem("Hide all areatrees");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all areatrees");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(Ball.class);
        item = new JMenuItem("Hide all balls");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all balls");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().contains(Connector.class);
        item = new JMenuItem("Hide all connectors");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all connectors");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        none = !layer.getParent().containsDisplayable(Patch.class);
        item = new JMenuItem("Hide all images");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Unhide all images");
        item.addActionListener(this);
        menu.add(item);
        if (none)
            item.setEnabled(false);
        item = new JMenuItem("Hide all but images");
        item.addActionListener(this);
        menu.add(item);
        item = new JMenuItem("Unhide all");
        item.addActionListener(this);
        menu.add(item);
        item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.ALT_MASK, true));
        popup.add(menu);
    } catch (final Exception e) {
        IJError.print(e);
    }
    // plugins, if any
    Utils.addPlugIns(popup, "Display", project, new Callable<Displayable>() {

        @Override
        public Displayable call() {
            return Display.this.getActive();
        }
    });
    final JMenu align_menu = new JMenu("Align");
    item = new JMenuItem("Align stack slices");
    item.addActionListener(this);
    align_menu.add(item);
    if (selection.isEmpty() || !(getActive().getClass() == Patch.class && ((Patch) getActive()).isStack()))
        item.setEnabled(false);
    item = new JMenuItem("Align layers");
    item.addActionListener(this);
    align_menu.add(item);
    if (1 == layer.getParent().size())
        item.setEnabled(false);
    item = new JMenuItem("Align layers manually with landmarks");
    item.addActionListener(this);
    align_menu.add(item);
    if (1 == layer.getParent().size())
        item.setEnabled(false);
    item = new JMenuItem("Align multi-layer mosaic");
    item.addActionListener(this);
    align_menu.add(item);
    if (1 == layer.getParent().size())
        item.setEnabled(false);
    item = new JMenuItem("Montage all images in this layer");
    item.addActionListener(this);
    align_menu.add(item);
    if (layer.getDisplayables(Patch.class).size() < 2)
        item.setEnabled(false);
    item = new JMenuItem("Montage selected images");
    item.addActionListener(this);
    align_menu.add(item);
    if (selection.getSelected(Patch.class).size() < 2)
        item.setEnabled(false);
    item = new JMenuItem("Montage multiple layers");
    item.addActionListener(this);
    align_menu.add(item);
    popup.add(align_menu);
    final JMenuItem st = new JMenu("Transform");
    final StartTransformMenuListener tml = new StartTransformMenuListener();
    item = new JMenuItem("Transform (affine)");
    item.addActionListener(tml);
    st.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, 0, true));
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Transform (non-linear)");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, Event.SHIFT_MASK, true));
    item = new JMenuItem("Cancel transform");
    st.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
    // just added as a self-documenting cue; no listener
    item.setEnabled(false);
    item = new JMenuItem("Remove rotation, scaling and shear (selected images)");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Remove rotation, scaling and shear layer-wise");
    item.addActionListener(tml);
    st.add(item);
    item = new JMenuItem("Remove coordinate transforms (selected images)");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Remove coordinate transforms layer-wise");
    item.addActionListener(tml);
    st.add(item);
    item = new JMenuItem("Adjust mesh resolution (selected images)");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Adjust mesh resolution layer-wise");
    item.addActionListener(tml);
    st.add(item);
    item = new JMenuItem("Set coordinate transform of selected image to other selected images");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Set coordinate transform of selected image layer-wise");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Set affine transform of selected image to other selected images");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    item = new JMenuItem("Set affine transform of selected image layer-wise");
    item.addActionListener(tml);
    st.add(item);
    if (null == active)
        item.setEnabled(false);
    popup.add(st);
    final JMenu link_menu = new JMenu("Link");
    item = new JMenuItem("Link images...");
    item.addActionListener(this);
    link_menu.add(item);
    item = new JMenuItem("Unlink all selected images");
    item.addActionListener(this);
    link_menu.add(item);
    item.setEnabled(selection.getSelected(Patch.class).size() > 0);
    item = new JMenuItem("Unlink all");
    item.addActionListener(this);
    link_menu.add(item);
    popup.add(link_menu);
    final JMenu adjust_menu = new JMenu("Adjust images");
    item = new JMenuItem("Enhance contrast layer-wise...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Enhance contrast (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Adjust image filters (selected images)");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Set Min and Max layer-wise...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Set Min and Max (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Adjust min and max (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_J, 0));
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Mask image borders (layer-wise)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Mask image borders (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Remove alpha masks (layer-wise)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Remove alpha masks (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Split images under polyline ROI");
    item.addActionListener(this);
    adjust_menu.add(item);
    final Roi roi = canvas.getFakeImagePlus().getRoi();
    if (null == roi || !(roi.getType() == Roi.POLYLINE || roi.getType() == Roi.FREELINE))
        item.setEnabled(false);
    item = new JMenuItem("Blend (layer-wise)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Blend (selected images)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Match intensities (layer-wise)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    item = new JMenuItem("Remove intensity maps (layer-wise)...");
    item.addActionListener(this);
    adjust_menu.add(item);
    popup.add(adjust_menu);
    final JMenu script = new JMenu("Script");
    final MenuScriptListener msl = new MenuScriptListener();
    item = new JMenuItem("Set preprocessor script layer-wise...");
    item.addActionListener(msl);
    script.add(item);
    item = new JMenuItem("Set preprocessor script (selected images)...");
    item.addActionListener(msl);
    script.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    item = new JMenuItem("Remove preprocessor script layer-wise...");
    item.addActionListener(msl);
    script.add(item);
    item = new JMenuItem("Remove preprocessor script (selected images)...");
    item.addActionListener(msl);
    script.add(item);
    if (selection.isEmpty())
        item.setEnabled(false);
    popup.add(script);
    menu = new JMenu("Import");
    item = new JMenuItem("Import image");
    item.addActionListener(this);
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, Event.ALT_MASK & Event.SHIFT_MASK, true));
    item = new JMenuItem("Import stack...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Import stack with landmarks...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Import grid...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Import sequence as grid...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Import from text file...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Import labels as arealists...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Tags ...");
    item.addActionListener(this);
    menu.add(item);
    popup.add(menu);
    menu = new JMenu("Export");
    final boolean has_arealists = layer.getParent().contains(AreaList.class);
    item = new JMenuItem("Make flat image...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Arealists as labels (tif)");
    item.addActionListener(this);
    menu.add(item);
    item.setEnabled(has_arealists);
    item = new JMenuItem("Arealists as labels (amira)");
    item.addActionListener(this);
    menu.add(item);
    item.setEnabled(has_arealists);
    item = new JMenuItem("Image stack under selected Arealist");
    item.addActionListener(this);
    menu.add(item);
    item.setEnabled(null != active && AreaList.class == active.getClass());
    item = new JMenuItem("Fly through selected Treeline/AreaTree");
    item.addActionListener(this);
    menu.add(item);
    item.setEnabled(null != active && Tree.class.isInstance(active));
    item = new JMenuItem("Tags...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Connectivity graph...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("NeuroML...");
    item.addActionListener(this);
    menu.add(item);
    popup.add(menu);
    menu = new JMenu("Display");
    item = new JMenuItem("Resize canvas/LayerSet...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Autoresize canvas/LayerSet");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Resize canvas/LayerSet to ROI");
    item.addActionListener(this);
    menu.add(item);
    item.setEnabled(null != canvas.getFakeImagePlus().getRoi());
    item = new JMenuItem("Properties ...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Calibration...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Grid overlay...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Adjust snapping parameters...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Adjust fast-marching parameters...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Adjust arealist paint parameters...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Show current 2D position in 3D");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Show layers as orthoslices in 3D");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Inspect image mesh triangles");
    item.addActionListener(this);
    menu.add(item);
    popup.add(menu);
    menu = new JMenu("Project");
    this.project.getLoader().setupMenuItems(menu, this.getProject());
    item = new JMenuItem("Project properties...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Create subproject");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Create sibling project with retiled layers");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Release memory...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Flush image cache");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Regenerate all mipmaps");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Regenerate mipmaps (selected images)");
    item.addActionListener(this);
    menu.add(item);
    menu.addSeparator();
    item = new JMenuItem("Measurement options...");
    item.addActionListener(this);
    menu.add(item);
    popup.add(menu);
    menu = new JMenu("Selection");
    item = new JMenuItem("Select all");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Select all visible");
    item.addActionListener(this);
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, Utils.getControlModifier(), true));
    if (0 == layer.getDisplayableList().size() && 0 == layer.getParent().getDisplayableList().size())
        item.setEnabled(false);
    item = new JMenuItem("Select all that match...");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Select none");
    item.addActionListener(this);
    menu.add(item);
    if (0 == selection.getNSelected())
        item.setEnabled(false);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
    final JMenu bytype = new JMenu("Select all by type");
    item = new JMenuItem("AreaList");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("AreaTree");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Ball");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Connector");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Dissector");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Image");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Pipe");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Polyline");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Profile");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Text");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    item = new JMenuItem("Treeline");
    item.addActionListener(bytypelistener);
    bytype.add(item);
    menu.add(bytype);
    item = new JMenuItem("Restore selection");
    item.addActionListener(this);
    menu.add(item);
    item = new JMenuItem("Select under ROI");
    item.addActionListener(this);
    menu.add(item);
    if (canvas.getFakeImagePlus().getRoi() == null)
        item.setEnabled(false);
    final JMenu graph = new JMenu("Graph");
    final GraphMenuListener gl = new GraphMenuListener();
    item = new JMenuItem("Select outgoing Connectors");
    item.addActionListener(gl);
    graph.add(item);
    item = new JMenuItem("Select incoming Connectors");
    item.addActionListener(gl);
    graph.add(item);
    item = new JMenuItem("Select downstream targets");
    item.addActionListener(gl);
    graph.add(item);
    item = new JMenuItem("Select upstream targets");
    item.addActionListener(gl);
    graph.add(item);
    graph.setEnabled(!selection.isEmpty());
    menu.add(graph);
    item = new JMenuItem("Measure");
    item.addActionListener(this);
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, 0, true));
    item.setEnabled(!selection.isEmpty());
    popup.add(menu);
    menu = new JMenu("Tool");
    item = new JMenuItem("Rectangular ROI");
    item.addActionListener(new SetToolListener(Toolbar.RECTANGLE));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F1, 0, true));
    item = new JMenuItem("Polygon ROI");
    item.addActionListener(new SetToolListener(Toolbar.POLYGON));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F2, 0, true));
    item = new JMenuItem("Freehand ROI");
    item.addActionListener(new SetToolListener(Toolbar.FREEROI));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F3, 0, true));
    item = new JMenuItem("Text");
    item.addActionListener(new SetToolListener(Toolbar.TEXT));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F4, 0, true));
    item = new JMenuItem("Magnifier glass");
    item.addActionListener(new SetToolListener(Toolbar.MAGNIFIER));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F5, 0, true));
    item = new JMenuItem("Hand");
    item.addActionListener(new SetToolListener(Toolbar.HAND));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F6, 0, true));
    item = new JMenuItem("Select");
    item.addActionListener(new SetToolListener(ProjectToolbar.SELECT));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F9, 0, true));
    item = new JMenuItem("Pencil");
    item.addActionListener(new SetToolListener(ProjectToolbar.PENCIL));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F10, 0, true));
    item = new JMenuItem("Pen");
    item.addActionListener(new SetToolListener(ProjectToolbar.PEN));
    menu.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F11, 0, true));
    popup.add(menu);
    item = new JMenuItem("Search...");
    item.addActionListener(this);
    popup.add(item);
    item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, Utils.getControlModifier(), true));
    // canvas.add(popup);
    return popup;
}

Example 29 with Layer

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

the class Display method createColumnScreenshots.

/**
 * Only for DefaultMode.
 */
private final void createColumnScreenshots() {
    final int n;
    try {
        if (mode.getClass() == DefaultMode.class) {
            int ahead = project.getProperty("look_ahead_cache", 0);
            if (ahead < 0)
                ahead = 0;
            if (0 == ahead)
                return;
            n = ahead;
        } else
            return;
    } catch (final Exception e) {
        IJError.print(e);
        return;
    }
    project.getLoader().doLater(new Callable<Object>() {

        @Override
        public Object call() {
            final Layer current = Display.this.layer;
            // 1 - Create DisplayCanvas.Screenshot instances for the next 5 and previous 5 layers
            final ArrayList<DisplayCanvas.Screenshot> s = new ArrayList<DisplayCanvas.Screenshot>();
            Layer now = current;
            Layer prev = now.getParent().previous(now);
            int i = 0;
            Layer next = now.getParent().next(now);
            while (now != next && i < n) {
                s.add(canvas.createScreenshot(next));
                now = next;
                next = now.getParent().next(now);
                i++;
            }
            now = current;
            i = 0;
            while (now != prev && i < n) {
                s.add(0, canvas.createScreenshot(prev));
                now = prev;
                prev = now.getParent().previous(now);
                i++;
            }
            // Store them all into the LayerSet offscreens hashmap, but trigger image creation in parallel threads.
            for (final DisplayCanvas.Screenshot sc : s) {
                if (!current.getParent().containsScreenshot(sc)) {
                    sc.init();
                    current.getParent().storeScreenshot(sc);
                    project.getLoader().doLater(new Callable<Object>() {

                        @Override
                        public Object call() {
                            sc.createImage();
                            return null;
                        }
                    });
                }
            }
            current.getParent().trimScreenshots();
            return null;
        }
    });
}

Example 30 with Layer

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

the class Display method importImage.

protected Bureaucrat importImage() {
    final Worker worker = new // / all this verbosity is what happens when functions are not first class citizens. I could abstract it away by passing a string name "importImage" and invoking it with reflection, but that is an even bigger PAIN
    Worker(// / all this verbosity is what happens when functions are not first class citizens. I could abstract it away by passing a string name "importImage" and invoking it with reflection, but that is an even bigger PAIN
    "Import image") {

        @Override
        public void run() {
            startedWorking();
            try {
                // /
                final Rectangle srcRect = canvas.getSrcRect();
                final int x = srcRect.x + srcRect.width / 2;
                final int y = srcRect.y + srcRect.height / 2;
                final Patch p = project.getLoader().importImage(project, x, y);
                if (null == p) {
                    finishedWorking();
                    Utils.showMessage("Could not open the image.");
                    return;
                }
                Display.this.getLayerSet().addLayerContentStep(layer);
                // will add it to the proper Displays
                layer.add(p);
                Display.this.getLayerSet().addLayerContentStep(layer);
            // /
            } catch (final Exception e) {
                IJError.print(e);
            }
            finishedWorking();
        }
    };
    return Bureaucrat.createAndStart(worker, getProject());
}