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

Example 1 with AreaContainer

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

the class Segmentation method magicWand.

public static Bureaucrat magicWand(final AreaWrapper aw, final Layer layer, final Rectangle srcRect, final int x_p_w, final int y_p_w, final List<Runnable> post_tasks, final boolean inverse, final boolean subtract) {
    // Capture pointers before they are set to null
    final AreaContainer ac = (AreaContainer) aw.getSource();
    final AffineTransform source_aff = aw.getSource().getAffineTransform();
    final Rectangle box = new Rectangle(x_p_w - Segmentation.fmp.width / 2, y_p_w - Segmentation.fmp.height / 2, Segmentation.fmp.width, Segmentation.fmp.height);
    Bureaucrat burro = Bureaucrat.create(new Worker.Task("Magic Wand") {

        public void exec() {
            // Capture image as large as the fmp width,height centered on x_p_w,y_p_w
            Utils.log2("fmp box is " + box);
            ImageProcessor ip = Patch.makeFlatImage(ImagePlus.GRAY8, layer, box, 1.0, (Collection) layer.getDisplayables(Patch.class, new Area(box), true), Color.black);
            // Apply wand
            Wand wand = new Wand(ip);
            String smode = WandToolOptions.getMode();
            int mode = Wand.LEGACY_MODE;
            if (null == smode) {
            } else if (smode.startsWith("4"))
                mode = Wand.FOUR_CONNECTED;
            else if (smode.startsWith("8"))
                mode = Wand.EIGHT_CONNECTED;
            // 8-bit image
            wand.autoOutline(ip.getWidth() / 2, ip.getHeight() / 2, WandToolOptions.getTolerance(), mode);
            if (wand.npoints > 0) {
                Area area = M.getArea(new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, PolygonRoi.FREEROI));
                if (inverse) {
                    Area b = new Area(new Rectangle(0, 0, box.width, box.height));
                    b.subtract(area);
                    area = b;
                }
                // Compose an Area that is local to the AreaWrapper's area
                final AffineTransform aff = new AffineTransform(1, 0, 0, 1, box.x, box.y);
                try {
                    aff.preConcatenate(source_aff.createInverse());
                } catch (NoninvertibleTransformException nite) {
                    IJError.print(nite);
                    return;
                }
                area.transform(aff);
                if (subtract)
                    aw.getArea().subtract(area);
                else
                    aw.getArea().add(area);
                ac.calculateBoundingBox(layer);
                Display.repaint(layer);
            }
        }
    }, layer.getProject());
    if (null != post_tasks)
        for (Runnable task : post_tasks) burro.addPostTask(task);
    burro.goHaveBreakfast();
    return burro;
}

Example 2 with AreaContainer

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

the class Segmentation method fastMarching.

public static Bureaucrat fastMarching(final AreaWrapper aw, final Layer layer, final Rectangle srcRect, final int x_p_w, final int y_p_w, final List<Runnable> post_tasks) {
    // Capture pointers before they are set to null
    final AreaContainer ac = (AreaContainer) aw.getSource();
    final AffineTransform source_aff = aw.getSource().getAffineTransform();
    final Rectangle box = new Rectangle(x_p_w - Segmentation.fmp.width / 2, y_p_w - Segmentation.fmp.height / 2, Segmentation.fmp.width, Segmentation.fmp.height);
    Bureaucrat burro = Bureaucrat.create(new Worker.Task("Fast marching") {

        public void exec() {
            // Capture image as large as the fmp width,height centered on x_p_w,y_p_w
            Utils.log2("fmp box is " + box);
            ImagePlus imp = new ImagePlus("", Patch.makeFlatImage(ImagePlus.GRAY8, layer, box, 1.0, (Collection) layer.getDisplayables(Patch.class, new Area(box), true), Color.black));
            // Bandpass filter
            if (fmp.apply_bandpass_filter) {
                IJ.run(imp, "Bandpass Filter...", "filter_large=" + fmp.low_frequency_threshold + " filter_small=" + fmp.high_frequency_threshold + " suppress=None tolerance=5" + (fmp.autoscale_after_filtering ? " autoscale" : "") + (fmp.saturate_when_autoscaling ? " saturate" : ""));
            }
            // Setup seed point
            PointRoi roi = new PointRoi(box.width / 2, box.height / 2);
            imp.setRoi(roi);
            Utils.log2("imp: " + imp);
            Utils.log2("proi: " + imp.getRoi() + "    " + Utils.toString(new int[] { x_p_w - srcRect.x, y_p_w - srcRect.y }));
            // Setup state
            ImageContainer ic = new ImageContainer(imp);
            StateContainer state = new StateContainer();
            state.setROI(roi, ic.getWidth(), ic.getHeight(), ic.getImageCount(), imp.getCurrentSlice());
            state.setExpansionToInside(false);
            // Run FastMarching
            final FastMarching fm = new FastMarching(ic, null, state, true, fmp.fm_grey, fmp.fm_dist, fmp.apply_grey_value_erosion);
            final int max_iterations = fmp.max_iterations;
            final int iter_inc = fmp.iter_inc;
            for (int i = 0; i < max_iterations; i++) {
                if (Thread.currentThread().isInterrupted()) {
                    return;
                }
                if (!fm.step(iter_inc))
                    break;
            }
            // Extract ROI
            setTaskName("Adding area");
            final ArrayList<Coordinate> vc = fm.getStateContainer().getXYZ(false);
            if (0 == vc.size()) {
                Utils.log("No area growth.");
                return;
            }
            final Area area = new Area();
            Coordinate first = vc.remove(0);
            final Rectangle r = new Rectangle(first.x, first.y, 1, 1);
            int count = 0;
            // Scan and add line-wise
            for (final Coordinate c : vc) {
                count++;
                if (c.y == r.y && c.x == r.x + 1) {
                    // same line:
                    r.width += 1;
                    continue;
                } else {
                    // add previous one
                    area.add(new Area(r));
                }
                // start new line:
                r.x = c.x;
                r.y = c.y;
                r.width = 1;
                if (0 == count % 1024 && Thread.currentThread().isInterrupted()) {
                    return;
                }
            }
            // add last:
            area.add(new Area(r));
            /*
			// Trying from the image mask: JUST AS SLOW
			final byte[] b = (byte[]) fm.getStateContainer().getIPMask()[0].getPixels();
			final int w = imp.getWidth();
			for (int i=0; i<b.length; i++) {
				if (0 == b[i]) {
					r.x = i%w;
					r.y = i/w;
					area.add(new Area(r));
				}
			}
			*/
            /* // DOESN'T FILL?
			// Trying to just get the contour, and then filling holes
			for (final Coordinate c : fm.getStateContainer().getXYZ(true)) {
				r.x = c.x;
				r.y = c.y;
				area.add(new Area(r));
			}
			Polygon pol = new Polygon();
			final float[] coords = new float[6];
			for (PathIterator pit = area.getPathIterator(null); !pit.isDone(); ) {
				switch (pit.currentSegment(coords)) {
					case PathIterator.SEG_MOVETO:
					case PathIterator.SEG_LINETO:
						pol.addPoint((int)coords[0], (int)coords[1]);
						break;
					case PathIterator.SEG_CLOSE:
						area.add(new Area(pol));
						// prepare next:
						pol = new Polygon();
						break;
					default:
						Utils.log2("WARNING: unhandled seg type.");
						break;
				}
				pit.next();
				if (pit.isDone()) {
					break;
				}
			}
			*/
            // / FAILS because by now AreaWrapper's source is null
            // aw.add(area, new AffineTransform(1, 0, 0, 1, box.x, box.y));
            // Instead, compose an Area that is local to the AreaWrapper's area
            final AffineTransform aff = new AffineTransform(1, 0, 0, 1, box.x, box.y);
            try {
                aff.preConcatenate(source_aff.createInverse());
            } catch (NoninvertibleTransformException nite) {
                IJError.print(nite);
                return;
            }
            aw.getArea().add(area.createTransformedArea(aff));
            ac.calculateBoundingBox(layer);
            Display.repaint(layer);
        }
    }, layer.getProject());
    if (null != post_tasks)
        for (Runnable task : post_tasks) burro.addPostTask(task);
    burro.goHaveBreakfast();
    return burro;
}

Example 3 with AreaContainer

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

the class ProjectThing method measure.

/**
 * Call on children things, and on itself if it contains a basic data type directly.
 *  All children of the same type report to the same table.
 *  Result tables are returned without ever displaying them.
 */
public HashMap<Class<?>, ResultsTable> measure(HashMap<Class<?>, ResultsTable> ht) {
    if (null == ht)
        ht = new HashMap<Class<?>, ResultsTable>();
    if (null != object && object instanceof Displayable) {
        Displayable d = (Displayable) object;
        if (d.isVisible()) {
            ResultsTable rt = d.measure(ht.get(d.getClass()));
            if (null != rt)
                ht.put(d.getClass(), rt);
            // Areas:
            if (object instanceof AreaContainer) {
                ResultsTable rta = ((AreaContainer) object).measureAreas(ht.get(AreaContainer.class));
                if (null != rta)
                    ht.put(AreaContainer.class, rta);
            }
        } else {
            Utils.log("Measure: skipping hidden object " + d.getProject().getMeaningfulTitle(d));
        }
    }
    if (null == al_children)
        return ht;
    // profile list: always special ...
    if (template.getType().equals("profile_list") && null != al_children) {
        synchronized (al_children) {
            if (al_children.size() > 1) {
                Profile[] p = new Profile[al_children.size()];
                for (int i = 0; i < al_children.size(); i++) p[i] = (Profile) al_children.get(i).object;
                ResultsTable rt = Profile.measure(p, ht.get(Profile.class), this.id);
                if (null != rt)
                    ht.put(Profile_List.class, rt);
            // return ht; // don't return: do each profile separately as well
            }
        }
    }
    synchronized (al_children) {
        for (ProjectThing child : al_children) child.measure(ht);
    }
    return ht;
}