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

Example 6 with Treeline

use of ini.trakem2.display.Treeline 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);
}

Example 7 with Treeline

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

the class Display method adjustProperties.

public void adjustProperties() {
    final GenericDialog gd = new GenericDialog("Properties", Display.this.frame);
    // gd.addNumericField("layer_scroll_step: ", this.scroll_step, 0);
    gd.addSlider("layer_scroll_step: ", 1, layer.getParent().size(), Display.this.scroll_step);
    gd.addChoice("snapshots_mode", LayerSet.snapshot_modes, LayerSet.snapshot_modes[layer.getParent().getSnapshotsMode()]);
    gd.addCheckbox("prefer_snapshots_quality", layer.getParent().snapshotsQuality());
    final Loader lo = getProject().getLoader();
    final boolean using_mipmaps = lo.isMipMapsRegenerationEnabled();
    gd.addCheckbox("enable_mipmaps", using_mipmaps);
    gd.addCheckbox("enable_layer_pixels virtualization", layer.getParent().isPixelsVirtualizationEnabled());
    final double max = layer.getParent().getLayerWidth() < layer.getParent().getLayerHeight() ? layer.getParent().getLayerWidth() : layer.getParent().getLayerHeight();
    gd.addSlider("max_dimension of virtualized layer pixels: ", 0, max, layer.getParent().getPixelsMaxDimension());
    gd.addCheckbox("Show arrow heads in Treeline/AreaTree", layer.getParent().paint_arrows);
    gd.addCheckbox("Show edge confidence boxes in Treeline/AreaTree", layer.getParent().paint_edge_confidence_boxes);
    gd.addSlider("Stroke width (Treeline, AreaTree, Ball)", 1.0, 10.0, DisplayCanvas.DEFAULT_STROKE.getLineWidth());
    gd.addCheckbox("Show color cues", layer.getParent().color_cues);
    gd.addSlider("+/- layers to color cue", 0, 10, layer.getParent().n_layers_color_cue);
    gd.addCheckbox("Show color cues for areas", layer.getParent().area_color_cues);
    gd.addCheckbox("Use red/blue for color cues", layer.getParent().use_color_cue_colors);
    gd.addCheckbox("Prepaint images", layer.getParent().prepaint);
    gd.addSlider("Preload ahead from sections: ", 0, layer.getParent().size(), layer.getParent().preload_ahead);
    // --------
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    // --------
    int sc = (int) gd.getNextNumber();
    if (sc < 1)
        sc = 1;
    Display.this.scroll_step = sc;
    updateInDatabase("scroll_step");
    // 
    layer.getParent().setSnapshotsMode(gd.getNextChoiceIndex());
    layer.getParent().setSnapshotsQuality(gd.getNextBoolean());
    // 
    final boolean using_mipmaps2 = gd.getNextBoolean();
    if (using_mipmaps2 == using_mipmaps) {
    // Nothing changed
    } else if (!using_mipmaps2 && using_mipmaps) {
        // Desactivate mipmaps
        lo.setMipMapsRegeneration(false);
        lo.flushMipMaps(true);
    } else if (using_mipmaps2 && !using_mipmaps) {
        // Reactivate mipmaps
        lo.setMipMapsRegeneration(true);
        lo.generateMipMaps(layer.getParent().getDisplayables(Patch.class));
    }
    // 
    layer.getParent().setPixelsVirtualizationEnabled(gd.getNextBoolean());
    layer.getParent().setPixelsMaxDimension((int) gd.getNextNumber());
    layer.getParent().paint_arrows = gd.getNextBoolean();
    layer.getParent().paint_edge_confidence_boxes = gd.getNextBoolean();
    DisplayCanvas.DEFAULT_STROKE = new BasicStroke((float) Math.max(1, gd.getNextNumber()), BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
    layer.getParent().color_cues = gd.getNextBoolean();
    layer.getParent().n_layers_color_cue = (int) gd.getNextNumber();
    layer.getParent().area_color_cues = gd.getNextBoolean();
    layer.getParent().use_color_cue_colors = gd.getNextBoolean();
    layer.getParent().prepaint = gd.getNextBoolean();
    layer.getParent().preload_ahead = (int) Math.min(gd.getNextNumber(), layer.getParent().size());
    Display.repaint(layer.getParent());
}

Example 8 with Treeline

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

the class Project method getUniqueTypes.

/**
 * Returns a list of existing unique types in the template tree
 * (thus the 'project' type is not included, nor the label).
 * The basic types are guaranteed to be present even if there are no instances in the template tree.
 * As a side effect, this method populates the HashMap of unique TemplateThing types.
 */
public String[] getUniqueTypes() {
    synchronized (ht_unique_tt) {
        // ensure the basic types (pipe, ball, profile, profile_list) are present
        if (!ht_unique_tt.containsKey("profile"))
            ht_unique_tt.put("profile", new TemplateThing("profile"));
        if (!ht_unique_tt.containsKey("profile_list")) {
            TemplateThing tpl = new TemplateThing("profile_list");
            tpl.addChild((TemplateThing) ht_unique_tt.get("profile"));
            ht_unique_tt.put("profile_list", tpl);
        }
        if (!ht_unique_tt.containsKey("pipe"))
            ht_unique_tt.put("pipe", new TemplateThing("pipe"));
        if (!ht_unique_tt.containsKey("polyline"))
            ht_unique_tt.put("polyline", new TemplateThing("polyline"));
        if (!ht_unique_tt.containsKey("treeline"))
            ht_unique_tt.put("treeline", new TemplateThing("treeline"));
        if (!ht_unique_tt.containsKey("areatree"))
            ht_unique_tt.put("areatree", new TemplateThing("areatree"));
        if (!ht_unique_tt.containsKey("connector"))
            ht_unique_tt.put("connector", new TemplateThing("connector"));
        if (!ht_unique_tt.containsKey("ball"))
            ht_unique_tt.put("ball", new TemplateThing("ball"));
        if (!ht_unique_tt.containsKey("area_list"))
            ht_unique_tt.put("area_list", new TemplateThing("area_list"));
        if (!ht_unique_tt.containsKey("dissector"))
            ht_unique_tt.put("dissector", new TemplateThing("dissector"));
        // this should be done automagically by querying the classes in the package ... but java can't do that without peeking into the .jar .class files. Buh.
        TemplateThing project_tt = ht_unique_tt.remove("project");
        /* // debug
		for (Iterator it = ht_unique_tt.keySet().iterator(); it.hasNext(); ) {
			Utils.log2("class: " + it.next().getClass().getName());
		} */
        final String[] ut = new String[ht_unique_tt.size()];
        ht_unique_tt.keySet().toArray(ut);
        ht_unique_tt.put("project", project_tt);
        Arrays.sort(ut);
        return ut;
    }
}

Example 9 with Treeline

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

the class TreelineGraphEditor method invoke.

public Object invoke(Object... args) {
    if (null == args || args.length < 1 || null == args[0] || !(args[0] instanceof Treeline))
        return null;
    try {
        Class RT = Class.forName("clojure.lang.RT");
        Method var = RT.getDeclaredMethod("var", new Class[] { String.class, String.class });
        Object fn = var.invoke(null, new Object[] { "treeline.graph_editor", "as-graph" });
        return Class.forName("clojure.lang.Var").getDeclaredMethod("invoke", new Class[] { Object.class }).invoke(fn, new Object[] { args[0] });
    } catch (Throwable e) {
        IJError.print(e);
    }
    return null;
}

Example 10 with Treeline

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

the class TMLHandler method makeLayerThing.

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

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