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

Example 1 with Connector

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

the class NeuroML method exportNeuroML.

/**
 * Export to NeuroML 1.8.3, with synapses.
 * Every {@link Tree} is represented by a <cell>, and an instance of that <cell>
 * is represented by a <population> of one single cell.
 */
public static final void exportNeuroML(final Set<Tree<?>> trees, final Writer w) throws Exception {
    if (trees.isEmpty())
        return;
    // Header
    w.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<!-- Exported from TrakEM2 '" + Utils.version + "' at " + new Date() + "\nTrakEM2 software by Albert Cardona, Institute of Neuroinformatics of the University of Zurich and ETH Zurich -->\n" + "<neuroml xmlns=\"http://morphml.org/neuroml/schema\"\n" + " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" + " xmlns:net=\"http://morphml.org/networkml/schema\"\n" + " xmlns:mml=\"http://morphml.org/morphml/schema\"\n" + " xmlns:meta=\"http://morphml.org/metadata/schema\"\n" + " xmlns:bio=\"http://morphml.org/biophysics/schema\"\n" + " xmlns:cml=\"http://morphml.org/channelml/schema\"\n" + " xsi:schemaLocation=\"http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd\"\n" + " length_units=\"micrometer\">\n");
    final List<HalfSynapse> presynaptic = new ArrayList<HalfSynapse>();
    final List<HalfSynapse> postsynaptic = new ArrayList<HalfSynapse>();
    // Scale units to micrometers
    final Calibration cal = trees.iterator().next().getLayerSet().getCalibration();
    final double scale = scaleToMicrometers(cal);
    final AffineTransform scale2d = new AffineTransform(cal.pixelWidth * scale, 0, 0, cal.pixelHeight * scale, 0, 0);
    // not pixelDepth
    final double zScale = cal.pixelWidth * scale;
    w.write("<cells>\n");
    // Each Tree is a cell
    for (final Tree<?> t : trees) {
        if (null == t.getRoot())
            continue;
        exportMorphMLCell(w, t, trees, presynaptic, postsynaptic, scale2d, zScale);
    }
    w.write("</cells>\n");
    // Write a a population of cell for every Tree, where each population has only one cell at 0,0,0.
    // If the id=10, then the name is p10 and the type is t10.
    w.write("<populations xmlns=\"http://morphml.org/networkml/schema\">\n");
    for (final Tree<?> t : trees) {
        w.write(" <population name=\"p");
        final String sid = Long.toString(t.getId());
        w.write(sid);
        w.write("\" cell_type=\"t");
        w.write(sid);
        w.write("\">\n  <instances size=\"1\">\n   <instance id=\"0\"><location x=\"0\" y=\"0\" z=\"0\"/></instance>\n  </instances>\n </population>\n");
    }
    w.write("</populations>\n");
    // Write a project group with all the synapses among the members of the set of trees.
    w.write("<projections units=\"Physiological Units\" xmlns=\"http://morphml.org/networkml/schema\">\n");
    // Figure out which pre connect to which post: the Connector instance is shared, so use it as key
    final Map<Connector, HalfSynapse> cpre = new HashMap<Connector, HalfSynapse>();
    for (final HalfSynapse syn : presynaptic) {
        cpre.put(syn.c, syn);
    }
    final Map<TreePair, List<Synapse>> pairs = new HashMap<TreePair, List<Synapse>>();
    for (final HalfSynapse post : postsynaptic) {
        final HalfSynapse pre = cpre.get(post.c);
        // Does not originate within the set of trees
        if (null == pre)
            continue;
        // pre and post share the same Connector
        final TreePair pair = new TreePair(pre.t, post.t);
        List<Synapse> ls = pairs.get(pair);
        if (null == ls) {
            ls = new ArrayList<Synapse>();
            pairs.put(pair, ls);
        }
        ls.add(new Synapse(pre, post));
    }
    for (final Map.Entry<TreePair, List<Synapse>> e : pairs.entrySet()) {
        // Write synapse between pre and post
        final TreePair pair = e.getKey();
        w.write("  <projection name=\"NetworkConnection\" source=\"p");
        w.write(Long.toString(pair.source.getId()));
        w.write("\" target=\"p");
        w.write(Long.toString(pair.target.getId()));
        w.write("\">\n");
        w.write("   <synapse_props synapse_type=\"DoubExpSynA\" internal_delay=\"5\" weight=\"1\" threshold=\"-20\"/>\n");
        w.write("   <connections size=\"");
        final List<Synapse> ls = e.getValue();
        w.write(Integer.toString(ls.size()));
        w.write("\">\n");
        int cid = 0;
        for (final Synapse syn : ls) {
            w.write("    <connection id=\"");
            w.write(Integer.toString(cid));
            w.write("\" pre_cell_id=\"0\" pre_segment_id=\"");
            w.write(Long.toString(syn.pre.segmentId));
            w.write("\" pre_fraction_along=\"0.5\" post_cell_id=\"0\" post_segment_id=\"");
            w.write(Long.toString(syn.post.segmentId));
            w.write("\"/>\n");
            cid += 1;
        }
        w.write("   </connections>\n");
        w.write("  </projection>\n");
    }
    w.write(" </projections>\n");
    w.write("</neuroml>\n");
}

Example 2 with Connector

use of ini.trakem2.display.Connector 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 3 with Connector

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

the class ProjectTree method tryAddNewConnector.

/**
 * If the parent node of {@code active} can accept a Connector or has a direct child
 * node that can accept a {@link Connector}, add a new {@link Connector} and return it.
 *
 * @param d The {@link Displayable} that serves as reference, to decide which node to add the new {@link Connector}.
 * @param selectNode Whether to select the new node containing the {@link Connector} in the ProjectTree.
 *
 * @return The newly created {@link Connector}.
 */
public Connector tryAddNewConnector(final Displayable d, final boolean selectNode) {
    ProjectThing pt = project.findProjectThing(d);
    ProjectThing parent = (ProjectThing) pt.getParent();
    TemplateThing connectorType = project.getTemplateThing("connector");
    boolean add = false;
    if (parent.canHaveAsChild(connectorType)) {
        // Add as a sibling of pt
        add = true;
    } else {
        // Inspect if any of the sibling nodes can have it as child
        for (final ProjectThing child : parent.getChildren()) {
            if (child.canHaveAsChild(connectorType)) {
                parent = child;
                add = true;
                break;
            }
        }
    }
    Connector c = null;
    DefaultMutableTreeNode node = null;
    if (add) {
        // reuse same String instance
        c = new Connector(project, connectorType.getType());
        node = addChild(parent, connectorType.getType(), c);
    }
    if (null != node) {
        d.getLayerSet().add(c);
        if (selectNode)
            setSelectionPath(new TreePath(node.getPath()));
        return c;
    }
    Utils.logAll("Could not add a new Connector related to " + d);
    return null;
}

Example 4 with Connector

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

the class Merger method compare.

/**
 * Take two projects and find out what is different among them,
 *  independent of id.
 */
public static final void compare(final Project p1, final Project p2) {
    Utils.log("Be warned: only Treeline, AreaTree and Connector are considered at the moment.");
    final LayerSet ls1 = p1.getRootLayerSet(), ls2 = p2.getRootLayerSet();
    final Collection<ZDisplayable> zds1 = ls1.getZDisplayables(), zds2 = ls2.getZDisplayables();
    final HashSet<Class<?>> accepted = new HashSet<Class<?>>();
    accepted.add(Treeline.class);
    accepted.add(AreaTree.class);
    accepted.add(Connector.class);
    final HashMap<Displayable, List<Change>> matched = new HashMap<Displayable, List<Change>>();
    final HashSet<ZDisplayable> empty1 = new HashSet<ZDisplayable>(), empty2 = new HashSet<ZDisplayable>();
    final HashSet<ZDisplayable> unmatched1 = new HashSet<ZDisplayable>(), unmatched2 = new HashSet<ZDisplayable>(zds2);
    // Remove instances of classes not accepted
    for (final Iterator<ZDisplayable> it = unmatched2.iterator(); it.hasNext(); ) {
        ZDisplayable zd = it.next();
        if (!accepted.contains(zd.getClass())) {
            it.remove();
            continue;
        }
        if (zd.isDeletable()) {
            it.remove();
            empty2.add(zd);
        }
    }
    zds2.removeAll(empty2);
    final AtomicInteger counter = new AtomicInteger(0);
    // or at least one or more that are similar in that they have some nodes in common.
    try {
        ini.trakem2.parallel.Process.unbound(zds1, new TaskFactory<ZDisplayable, Object>() {

            @Override
            public Object process(final ZDisplayable zd1) {
                Utils.showProgress(counter.getAndIncrement() / (float) zds1.size());
                if (!accepted.contains(zd1.getClass())) {
                    Utils.log("Ignoring: [A] " + zd1);
                    return null;
                }
                if (zd1.isDeletable()) {
                    synchronized (empty1) {
                        empty1.add(zd1);
                    }
                    return null;
                }
                final List<Change> cs = new ArrayList<Change>();
                for (final ZDisplayable zd2 : zds2) {
                    // Same class?
                    if (zd1.getClass() != zd2.getClass())
                        continue;
                    if (zd1 instanceof Tree<?> && zd2 instanceof Tree<?>) {
                        Change c = compareTrees(zd1, zd2);
                        if (c.hasSimilarNodes()) {
                            cs.add(c);
                            if (1 == cs.size()) {
                                synchronized (matched) {
                                    matched.put(zd1, cs);
                                }
                            }
                            synchronized (unmatched2) {
                                unmatched2.remove(zd2);
                            }
                        }
                        // debug
                        if (zd1.getId() == zd2.getId()) {
                            Utils.log("zd1 #" + zd1.getId() + " is similar to #" + zd2.getId() + ": " + c.hasSimilarNodes());
                        }
                    }
                }
                if (cs.isEmpty()) {
                    synchronized (unmatched1) {
                        unmatched1.add(zd1);
                    }
                }
                return null;
            }
        });
    } catch (Exception e) {
        IJError.print(e);
    }
    // reset
    Utils.showProgress(1);
    Utils.log("matched.size(): " + matched.size());
    makeGUI(p1, p2, empty1, empty2, matched, unmatched1, unmatched2);
}

Example 5 with Connector

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

the class Graph method extractAndShowGraph.

/**
 * Shows a dialog to pick which classes is one interested in.
 */
public static final void extractAndShowGraph(final LayerSet ls) {
    GenericDialog gd = new GenericDialog("Graph elements");
    Class<Displayable>[] c = new Class[] { AreaList.class, AreaTree.class, Ball.class, Connector.class, Patch.class, Pipe.class, Polyline.class, Profile.class, DLabel.class, Treeline.class };
    String[] types = new String[] { "AreaList", "AreaTree", "Ball", "Connector", "Image", "Pipe", "Polyline", "Profile", "Text", "Treeline" };
    boolean[] states = new boolean[] { true, true, false, false, false, false, true, true, false, true };
    assert (c.length == types.length && types.length == states.length);
    for (int i = 0; i < c.length; i++) {
        if (ZDisplayable.class.isAssignableFrom(c[i])) {
            if (!ls.contains(c[i]))
                states[i] = false;
        } else if (!ls.containsDisplayable(c[i]))
            states[i] = false;
    }
    gd.addCheckboxGroup(types.length, 1, types, states, new String[] { "Include only:" });
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    HashSet<Class<Displayable>> only = new HashSet<Class<Displayable>>();
    for (int i = 0; i < types.length; i++) {
        if (gd.getNextBoolean())
            only.add(c[i]);
    }
    Graph.extractAndShowGraph(ls, only);
}