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

Example 11 with Selection

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

the class Compare method scoreAllToAll.

/**
 * Returns the half matrix of scores, with values copied from one half matrix to the other, and a diagonal of zeros.
 * @param distance_type ranges from 0 to 5, and includes: 0=Levenshtein, 1=Dissimilarity, 2=Average physical distance, 3=Median physical distance, 4=Cummulative physical distance and 5=Standard deviation.
 */
public static float[][] scoreAllToAll(final VectorString3D[] vs, final int distance_type, final double delta, final boolean skip_ends, final int max_mut, final float min_chunk, final boolean direct, final boolean substring_matching, final Worker worker) {
    final float[][] scores = new float[vs.length][vs.length];
    final AtomicInteger ai = new AtomicInteger(0);
    final Thread[] threads = MultiThreading.newThreads();
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                for (int i = ai.getAndIncrement(); i < vs.length; i = ai.getAndIncrement()) {
                    final VectorString3D vs1 = vs[i];
                    for (int j = i + 1; j < vs.length; j++) {
                        if (null != worker && worker.hasQuitted())
                            return;
                        // TODO should add 'distance_type' as well for the selection of the best match when not direct.
                        final Object[] ob = findBestMatch(vs[i], vs[j], delta, skip_ends, max_mut, min_chunk, distance_type, direct, substring_matching);
                        /*
				switch (distance_type) {
					case 0: // Levenshtein
						scores[i][j] = (float)((Editions)ob[0]).getDistance();
						break;
					case 1: // dissimilarity
						scores[i][j] = (float)((Double)ob[1]).doubleValue();
						break;
					case 2: // average physical distance between mutation pairs
						scores[i][j] = (float)((Editions)ob[0]).getPhysicalDistance(skip_ends, max_mut, min_chunk, true);
						break;
					case 3: // median physical distance between mutation pairs
						scores[i][j] = (float)((Editions)ob[0]).getStatistics(skip_ends, max_mut, min_chunk, false)[3]; // 3 is median
						break;
					case 4: // cummulative physical distance between mutation pairs
						scores[i][j] = (float)((Editions)ob[0]).getPhysicalDistance(skip_ends, max_mut, min_chunk, false);
						break;
					case 5: // stdDev of distances between mutation pairs
						scores[i][j] = (float)((Editions)ob[0]).getStdDev(skip_ends, max_mut, min_chunk);
						break;
				}
				*/
                        final Editions ed = (Editions) ob[0];
                        scores[i][j] = (float) getScore(ed, skip_ends, max_mut, min_chunk, distance_type);
                        // mirror value
                        scores[j][i] = scores[i][j];
                    }
                }
            // //
            }
        };
    }
    MultiThreading.startAndJoin(threads);
    if (null != worker && worker.hasQuitted())
        return null;
    return scores;
}

Example 12 with Selection

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

the class LayerTree method mousePressed.

public void mousePressed(MouseEvent me) {
    Object source = me.getSource();
    if (!source.equals(this) || !project.isInputEnabled()) {
        return;
    }
    // ignore if doing multiple selection
    if (!Utils.isPopupTrigger(me) && (me.isShiftDown() || (!ij.IJ.isMacOSX() && me.isControlDown()))) {
        return;
    }
    int x = me.getX();
    int y = me.getY();
    // check if there is a multiple selection
    TreePath[] paths = this.getSelectionPaths();
    if (null != paths && paths.length > 1) {
        if (Utils.isPopupTrigger(me)) {
            // check that all items are of the same type
            String type_first = ((LayerThing) ((DefaultMutableTreeNode) paths[0].getLastPathComponent()).getUserObject()).getType();
            for (int i = 1; i < paths.length; i++) {
                String type = ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getType();
                if (!type.equals(type_first)) {
                    Utils.showMessage("All selected items must be of the same type for operations on multiple items.");
                    return;
                }
            }
            // prepare popup menu
            JPopupMenu popup = new JPopupMenu();
            JMenuItem item = null;
            if (type_first.equals("layer")) {
                item = new JMenuItem("Reverse layer Z coords");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Translate layers in Z...");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Scale Z and thickness...");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Delete...");
                item.addActionListener(this);
                popup.add(item);
            }
            if (popup.getSubElements().length > 0) {
                popup.show(this, x, y);
            }
        }
        // disable commands depending upon a single node being selected
        selected_node = null;
        return;
    }
    // find the node and set it selected
    TreePath path = getPathForLocation(x, y);
    if (null == path) {
        return;
    }
    setSelectionPath(path);
    selected_node = (DefaultMutableTreeNode) path.getLastPathComponent();
    if (2 == me.getClickCount() && !Utils.isPopupTrigger(me) && MouseEvent.BUTTON1 == me.getButton()) {
        // create a new Display
        LayerThing thing = (LayerThing) selected_node.getUserObject();
        DBObject ob = (DBObject) thing.getObject();
        if (thing.getType().toLowerCase().replace('_', ' ').equals("layer set") && null == ((LayerSet) ob).getParent()) {
            // the top level LayerSet
            return;
        }
        // new Display(ob.getProject(), thing.getType().toLowerCase().equals("layer") ? (Layer)ob : ((LayerSet)ob).getParent());
        Display.createDisplay(ob.getProject(), thing.getType().toLowerCase().equals("layer") ? (Layer) ob : ((LayerSet) ob).getParent());
        return;
    } else if (Utils.isPopupTrigger(me)) {
        JPopupMenu popup = getPopupMenu(selected_node);
        if (null == popup)
            return;
        popup.show(this, x, y);
        return;
    }
}

Example 13 with Selection

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

the class LayerTree method actionPerformed.

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

Example 14 with Selection

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

the class DistortionCorrectionTask method correctDistortionFromSelection.

public static final Bureaucrat correctDistortionFromSelection(final Selection selection) {
    final List<Patch> patches = new ArrayList<Patch>();
    for (final Displayable d : Display.getFront().getSelection().getSelected()) if (d instanceof Patch)
        patches.add((Patch) d);
    if (patches.size() < 2) {
        Utils.log("No images in the selection.");
        return null;
    }
    final Worker worker = new Worker("Lens correction") {

        @Override
        public final void run() {
            try {
                startedWorking();
                if (!correctDistortionFromSelectionParam.setup(selection))
                    return;
                DistortionCorrectionTask.run(correctDistortionFromSelectionParam.clone(), patches, selection.getActive(), selection.getLayer(), null);
                Display.repaint();
            } catch (final Exception e) {
                IJError.print(e);
            } finally {
                finishedWorking();
            }
        }
    };
    return Bureaucrat.createAndStart(worker, selection.getProject());
}

Example 15 with Selection

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

the class DistortionCorrectionTask method correctDistortionFromSelectionTask.

public static final Bureaucrat correctDistortionFromSelectionTask(final Selection selection) {
    final Worker worker = new Worker("Distortion Correction", false, true) {

        @Override
        public void run() {
            startedWorking();
            try {
                correctDistortionFromSelection(selection);
                Display.repaint(selection.getLayer());
            } catch (final Throwable e) {
                IJError.print(e);
            } finally {
                finishedWorking();
            }
        }

        @Override
        public void cleanup() {
            if (!selection.isEmpty())
                selection.getLayer().getParent().undoOneStep();
        }
    };
    return Bureaucrat.createAndStart(worker, selection.getProject());
}