Examples with ReconstructArea ini.trakem2.utils.ReconstructArea used on opensource projects

Example 1 with ReconstructArea

use of ini.trakem2.utils.ReconstructArea 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;
}