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

Example 16 with AreaList

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

the class AmiraImporter method extractAreaLists.

/**
 * Returns a map of label vs AreaList.
 */
public static Map<Float, AreaList> extractAreaLists(final ImagePlus imp, final Layer first_layer, final double base_x, final double base_y, final float alpha, final boolean add_background) {
    try {
        final HashMap<Integer, HashMap<Float, Area>> map = new HashMap<Integer, HashMap<Float, Area>>();
        // works even for images that are not stacks: it creates one
        final ImageStack stack = imp.getStack();
        final AtomicInteger ai = new AtomicInteger(1);
        final AtomicInteger completed_slices = new AtomicInteger(0);
        final int n_slices = imp.getNSlices();
        final Thread parent = Thread.currentThread();
        final Thread[] threads = MultiThreading.newThreads();
        for (int ithread = 0; ithread < threads.length; ithread++) {
            threads[ithread] = new Thread() {

                public void run() {
                    final Rectangle box = new Rectangle(0, 0, 1, 1);
                    for (int i = ai.getAndIncrement(); i <= n_slices; i = ai.getAndIncrement()) {
                        final ImageProcessor ip;
                        synchronized (map) {
                            ip = stack.getProcessor(i);
                        }
                        if (parent.isInterrupted())
                            return;
                        final HashMap<Float, Area> layer_map = new HashMap<Float, Area>();
                        synchronized (map) {
                            map.put(i, layer_map);
                        }
                        AreaUtils.extractAreas(ip, layer_map, add_background, box, parent, true);
                        Utils.showProgress(completed_slices.incrementAndGet() / (float) n_slices);
                    }
                }
            };
        }
        MultiThreading.startAndJoin(threads);
        Utils.showProgress(1);
        if (parent.isInterrupted())
            return null;
        final HashMap<Float, AreaList> alis = new HashMap<Float, AreaList>();
        Utils.log2("Recreating arealists...");
        Utils.log2("map.size() = " + map.size());
        final double thickness = first_layer.getThickness();
        final double first_z = first_layer.getZ();
        // Recreate AreaLists
        for (final Map.Entry<Integer, HashMap<Float, Area>> e : map.entrySet()) {
            final int slice_index = e.getKey();
            final HashMap<Float, Area> layer_map = e.getValue();
            for (final Map.Entry<Float, Area> fa : layer_map.entrySet()) {
                Float label = fa.getKey();
                AreaList ali = alis.get(label);
                if (null == ali) {
                    ali = new AreaList(first_layer.getProject(), "Label " + label.intValue(), base_x, base_y);
                    alis.put(label, ali);
                }
                double z = first_z + (slice_index - 1) * thickness;
                Layer layer = first_layer.getParent().getLayer(z, thickness, true);
                ali.setArea(layer.getId(), fa.getValue());
            }
        }
        Utils.log2("Done recreating.");
        first_layer.getParent().addAll(alis.values());
        Utils.log2("Done adding all to LayerSet");
        float hue = 0;
        for (final Map.Entry<Float, AreaList> e : alis.entrySet()) {
            final AreaList ali = e.getValue();
            ali.setProperty("label", Integer.toString(e.getKey().intValue()));
            ali.calculateBoundingBox(null);
            ali.setColor(Color.getHSBColor(hue, 1, 1));
            ali.setAlpha(alpha);
            // golden angle
            hue += 0.38197f;
            if (hue > 1)
                hue = hue - 1;
        }
        Utils.log2("Done setting properties");
        return alis;
    } catch (Exception e) {
        IJError.print(e);
    }
    return null;
}

Example 17 with AreaList

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

the class AmiraImporter method extractAmiraLabels.

/**
 * Returns an ArrayList containing all AreaList objects. The xo,yo is the pivot of reference.
 */
public static Collection<AreaList> extractAmiraLabels(final ImagePlus labels, final AmiraParameters ap, final Layer first_layer, final double xo, final double yo) {
    final String[] materials = ap.getMaterialList();
    // extract labels as ArrayList of Area
    final Map<Float, AreaList> alis = extractAreaLists(labels, first_layer, xo, yo, 0.4f, false);
    for (int i = 0; i < materials.length; i++) {
        final int id = ap.getMaterialID(materials[i]);
        final double[] color = ap.getMaterialColor(id);
        final String name = ap.getMaterialName(id);
        if (name.equals("Exterior")) {
            Utils.log("Ignoring Amira's \"Exterior\" label");
            continue;
        }
        final AreaList ali = alis.get(new Float(id));
        if (null == ali) {
            Utils.log("ERROR: no AreaList for label id " + id);
            continue;
        }
        ali.setColor(new Color((float) color[0], (float) color[1], (float) color[2]));
        ali.setTitle(name);
    }
    return alis.values();
}