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

Example 6 with AreaTree

use of ini.trakem2.display.AreaTree 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 7 with AreaTree

use of ini.trakem2.display.AreaTree 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 8 with AreaTree

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

the class TMLHandler method makeLayerThing.

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

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

Example 9 with AreaTree

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

the class ProjectTree method insertSegmentations.

/* // makes no sense, because there may be multiple projects open and thus the viewport and position may interfere with each other across multiple projects. Saving the collapsed node state suffices.
	public void exportXML(final StringBuffer sb_body, String indent, JScrollPane jsp) {
		Point p = jsp.getViewport().getViewPosition();
		Dimension d = jsp.getSize(null);
		sb_body.append(indent).append("<t2_tree")
		       .append(" width=\"").append(d.width).append('\"')
		       .append(" height=\"").append(d.height).append('\"')
		       .append(" viewport_x=\"").append(p.e).append('\"')
		       .append(" viewport_y=\"").append(p.y).append('\"')
		;
		sb_body.append("\n").append(indent).append("</t2_tree>\n");
	}
	*/
/**
 * Creates a new node of basic type for each AreaList, Ball, Pipe or Polyline present in the ArrayList. Other elements are ignored.
 */
public void insertSegmentations(final Collection<? extends Displayable> al) {
    final TemplateThing tt_root = (TemplateThing) project.getTemplateTree().getRoot().getUserObject();
    // create a new abstract node called "imported_segmentations", if not there
    final String imported_labels = "imported_labels";
    if (!project.typeExists(imported_labels)) {
        // create it
        // yes I know I should check for the project of each Displayable in the ArrayList
        TemplateThing tet = new TemplateThing(imported_labels, project);
        project.addUniqueType(tet);
        DefaultMutableTreeNode root = project.getTemplateTree().getRoot();
        tt_root.addChild(tet);
        DefaultMutableTreeNode child_node = addChild(tet, root);
        DNDTree.expandNode(project.getTemplateTree(), child_node);
    // JTree is serious pain
    }
    // it's the same as 'tet' above, unless it existed
    TemplateThing tt_is = project.getTemplateThing(imported_labels);
    // create a project node from "imported_segmentations" template under a new top node
    final DefaultMutableTreeNode project_node = project.getProjectTree().getRoot();
    ProjectThing project_pt = (ProjectThing) project_node.getUserObject();
    final ProjectThing ct = project_pt.createChild(tt_root.getType());
    ProjectThing pt_is = ct.createChild(imported_labels);
    // addChild(pt_is, ctn);
    final DefaultMutableTreeNode node_pt_is = new DefaultMutableTreeNode(pt_is);
    final HashMap<Class<?>, String> types = new HashMap<Class<?>, String>();
    types.put(AreaList.class, "area_list");
    types.put(Pipe.class, "pipe");
    types.put(Polyline.class, "polyline");
    types.put(Ball.class, "ball");
    types.put(Treeline.class, "treeline");
    types.put(AreaTree.class, "areatree");
    types.put(Connector.class, "connector");
    // now, insert a new ProjectThing if of type AreaList, Ball and/or Pipe under node_child
    for (final Displayable d : al) {
        final String type = types.get(d.getClass());
        if (null == type) {
            Utils.log("insertSegmentations: ignoring " + d);
            continue;
        }
        try {
            final TemplateThing tt = getOrCreateChildTemplateThing(tt_is, type);
            ProjectThing one = new ProjectThing(tt, project, d);
            pt_is.addChild(one);
            // addChild(one, node_pt_is);
            // at the end
            node_pt_is.add(new DefaultMutableTreeNode(one));
        // Utils.log2("one parent : " + one.getParent());
        } catch (Exception e) {
            IJError.print(e);
        }
    }
    javax.swing.SwingUtilities.invokeLater(new Runnable() {

        public void run() {
            DefaultMutableTreeNode ctn = addChild(ct, project_node);
            ctn.add(node_pt_is);
            try {
                ProjectTree.this.scrollPathToVisible(new TreePath(node_pt_is.getPath()));
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    });
    DNDTree.expandNode(this, node_pt_is);
}