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

Example 6 with Layer

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

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

the class Blending method blendLayerWise.

public static final void blendLayerWise(final List<Layer> layers, final boolean respect_current_mask, final Filter<Patch> filter) {
    for (final Layer layer : layers) {
        final List<Patch> patches = layer.getAll(Patch.class);
        final Set<Patch> s = new HashSet<Patch>();
        if (null == filter) {
            s.addAll(patches);
        } else {
            for (final Iterator<Patch> it = patches.iterator(); it.hasNext(); ) {
                final Patch p = it.next();
                if (filter.accept(p))
                    s.add(p);
            }
        }
        blendPatches(s, respect_current_mask);
    }
}

Example 8 with Layer

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

the class Blending method blendPatches.

public static final void blendPatches(final Set<Patch> patches, final boolean respect_current_mask) {
    ExecutorService exe = null;
    try {
        if (null == patches || patches.size() < 2)
            return;
        final Layer layer = patches.iterator().next().getLayer();
        for (final Patch p : patches) {
            if (null != p.getCoordinateTransform()) {
                Utils.log("CANNOT blend: at least one image has a coordinate transform.\nBlending of coordinate-transformed images will be enabled in the near future.");
                return;
            }
            if (p.getLayer() != layer) {
                Utils.log("CANNOT blend: all images must belong to the same layer!\n  Otherwise the overlap cannot be computed.");
                return;
            }
        }
        final HashMap<Patch, TransformMesh> meshes = new HashMap<Patch, TransformMesh>();
        for (final Patch p : patches) {
            meshes.put(p, null == p.getCoordinateTransform() ? null : new TransformMesh(p.getCoordinateTransform(), p.getMeshResolution(), p.getOWidth(), p.getOHeight()));
        }
        exe = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
        final List<Future<?>> futures = Collections.synchronizedList(new ArrayList<Future<?>>());
        final List<Future<?>> futures2 = Collections.synchronizedList(new ArrayList<Future<?>>());
        // Cache the indices that determine overlap order within the layer
        final HashMap<Patch, Integer> indices = new HashMap<Patch, Integer>();
        int i = 0;
        for (final Displayable d : layer.getDisplayables()) {
            if (d.getClass() == Patch.class && patches.contains((Patch) d)) {
                indices.put((Patch) d, i);
            }
            i += 1;
        }
        for (final Patch p : patches) {
            if (Thread.currentThread().isInterrupted())
                break;
            futures.add(exe.submit(new Runnable() {

                @Override
                public void run() {
                    final int pLayerIndex = indices.get(p);
                    final Set<Patch> overlapping = new HashSet<Patch>();
                    for (final Patch op : patches) {
                        if (indices.get(op) < pLayerIndex)
                            overlapping.add(op);
                    }
                    if (setBlendingMask(p, overlapping, meshes, respect_current_mask)) {
                        futures2.add(p.updateMipMaps());
                    }
                }
            }, null));
        }
        // join all:
        Utils.waitIfAlive(futures, false);
        Utils.waitIfAlive(futures2, false);
    } catch (final Exception e) {
        IJError.print(e);
    } finally {
        if (null != exe)
            exe.shutdown();
        Display.repaint();
    }
}

Example 9 with Layer

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

the class LayerStack method getProcessor.

/**
 * Returns an ImageProcessor for the specified slice,
 *		where {@code 1<=n<=nslices}. Returns null if the stack is empty.
 */
@Override
public ImageProcessor getProcessor(int n) {
    if (n < 1 || n > layers.size())
        return null;
    // Create a flat image on the fly with everything on it, and return its processor.
    final Layer layer = layers.get(n - 1);
    final Loader loader = layer.getProject().getLoader();
    Long cid;
    synchronized (id_cache) {
        cid = id_cache.get(layer.getId());
        if (null == cid) {
            cid = loader.getNextTempId();
            id_cache.put(layer.getId(), cid);
        }
    }
    ImageProcessor ip;
    synchronized (cid) {
        ImagePlus imp = loader.getCachedImagePlus(cid);
        if (null == imp || null == imp.getProcessor() || null == imp.getProcessor().getPixels()) {
            ip = loader.getFlatImage(layer, this.roi, this.scale, this.c_alphas, this.type, this.clazz, null).getProcessor();
            if (invert)
                ip.invert();
            loader.cacheImagePlus(cid, new ImagePlus("", ip));
        } else
            ip = imp.getProcessor();
    }
    return ip;
}

Example 10 with Layer

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

the class FilterEditor method GUI.

public static final void GUI(final Collection<Patch> patches, final Patch reference) {
    final ArrayList<FilterWrapper> filters = new ArrayList<FilterWrapper>();
    // Find out if all images have the exact same filters
    final StringBuilder sb = new StringBuilder();
    final Patch ref = (null == reference ? patches.iterator().next() : reference);
    final IFilter[] refFilters = ref.getFilters();
    if (null != refFilters) {
        // makes a copy of the IFilter
        for (final IFilter f : refFilters) filters.add(new FilterWrapper(f));
    }
    // 
    for (final Patch p : patches) {
        if (ref == p)
            continue;
        final IFilter[] fs = p.getFilters();
        // ok
        if (null == fs && null == refFilters)
            continue;
        if ((null != refFilters && null == fs) || (null == refFilters && null != fs) || (null != refFilters && null != fs && fs.length != refFilters.length)) {
            sb.append("WARNING: patch #" + p.getId() + " has a different number of filters than reference patch #" + ref.getId());
            continue;
        }
        // Compare each
        for (int i = 0; i < refFilters.length; ++i) {
            if (fs[i].getClass() != refFilters[i].getClass()) {
                sb.append("WARNING: patch #" + p.getId() + " has a different filters than reference patch #" + ref.getId());
                break;
            }
            // Does the filter have the same parameters?
            if (!filters.get(i).sameParameterValues(new FilterWrapper(fs[i]))) {
                sb.append("WARNING: patch #" + p.getId() + " has filter '" + fs[i].getClass().getSimpleName() + "' with different parameters than the reference patch #" + ref.getId());
            }
        }
    }
    if (sb.length() > 0) {
        final GenericDialog gd = new GenericDialog("WARNING", null == Display.getFront() ? IJ.getInstance() : Display.getFront().getFrame());
        gd.addMessage("Filters are not all the same for all images:");
        gd.addTextAreas(sb.toString(), null, 20, 30);
        final String[] s = new String[] { "Use the filters of the reference image", "Start from an empty list of filters" };
        gd.addChoice("Do:", s, s[0]);
        gd.showDialog();
        if (gd.wasCanceled())
            return;
        if (1 == gd.getNextChoiceIndex())
            filters.clear();
    }
    final TableChosenFilters tcf = new TableChosenFilters(filters);
    final TableParameters tp = new TableParameters(tcf);
    tcf.setupListener(tp);
    final TableAvailableFilters taf = new TableAvailableFilters(tcf);
    if (filters.size() > 0) {
        tcf.getSelectionModel().setSelectionInterval(0, 0);
    }
    final JFrame frame = new JFrame("Image filters");
    final JButton set = new JButton("Set");
    final JComboBox pulldown = new JComboBox(new String[] { "Selected images (" + patches.size() + ")", "All images in layer " + (ref.getLayer().getParent().indexOf(ref.getLayer()) + 1), "All images in layer range..." });
    final Component[] cs = new Component[] { set, pulldown, tcf, tp, taf };
    set.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(final ActionEvent e) {
            if (check(frame, filters)) {
                final ArrayList<Patch> ps = new ArrayList<Patch>();
                switch(pulldown.getSelectedIndex()) {
                    case 0:
                        ps.addAll(patches);
                        break;
                    case 1:
                        for (final Displayable d : ref.getLayer().getDisplayables(Patch.class)) {
                            ps.add((Patch) d);
                        }
                        break;
                    case 2:
                        final GenericDialog gd = new GenericDialog("Apply filters");
                        Utils.addLayerRangeChoices(ref.getLayer(), gd);
                        gd.addStringField("Image title matches:", "", 30);
                        gd.addCheckbox("Visible images only", true);
                        gd.showDialog();
                        if (gd.wasCanceled())
                            return;
                        final String regex = gd.getNextString();
                        final boolean visible_only = gd.getNextBoolean();
                        Pattern pattern = null;
                        if (0 != regex.length()) {
                            pattern = Pattern.compile(regex);
                        }
                        for (final Layer l : ref.getLayer().getParent().getLayers(gd.getNextChoiceIndex(), gd.getNextChoiceIndex())) {
                            for (final Displayable d : l.getDisplayables(Patch.class, visible_only)) {
                                if (null != pattern && !pattern.matcher(d.getTitle()).matches()) {
                                    continue;
                                }
                                ps.add((Patch) d);
                            }
                        }
                }
                apply(ps, filters, cs, false);
            }
        }
    });
    final JPanel buttons = new JPanel();
    final JLabel label = new JLabel("Push F1 for help");
    final GridBagConstraints c2 = new GridBagConstraints();
    final GridBagLayout gb2 = new GridBagLayout();
    buttons.setLayout(gb2);
    c2.anchor = GridBagConstraints.WEST;
    c2.gridx = 0;
    gb2.setConstraints(label, c2);
    buttons.add(label);
    c2.gridx = 1;
    c2.weightx = 1;
    final JPanel empty = new JPanel();
    gb2.setConstraints(empty, c2);
    buttons.add(empty);
    c2.gridx = 2;
    c2.weightx = 0;
    c2.anchor = GridBagConstraints.EAST;
    final JLabel a = new JLabel("Apply to:");
    gb2.setConstraints(a, c2);
    buttons.add(a);
    c2.gridx = 3;
    c2.insets = new Insets(4, 10, 4, 0);
    gb2.setConstraints(pulldown, c2);
    buttons.add(pulldown);
    c2.gridx = 4;
    gb2.setConstraints(set, c2);
    buttons.add(set);
    // 
    taf.setPreferredSize(new Dimension(350, 500));
    tcf.setPreferredSize(new Dimension(350, 250));
    tp.setPreferredSize(new Dimension(350, 250));
    // 
    final GridBagLayout gb = new GridBagLayout();
    final GridBagConstraints c = new GridBagConstraints();
    final JPanel all = new JPanel();
    all.setBackground(Color.white);
    all.setPreferredSize(new Dimension(700, 500));
    all.setLayout(gb);
    c.gridx = 0;
    c.gridy = 0;
    c.anchor = GridBagConstraints.NORTHWEST;
    c.fill = GridBagConstraints.BOTH;
    c.gridheight = 2;
    c.weightx = 0.5;
    final JScrollPane p1 = new JScrollPane(taf);
    p1.setPreferredSize(taf.getPreferredSize());
    gb.setConstraints(p1, c);
    all.add(p1);
    c.gridx = 1;
    c.gridy = 0;
    c.gridheight = 1;
    c.weighty = 0.7;
    final JScrollPane p2 = new JScrollPane(tcf);
    p2.setPreferredSize(tcf.getPreferredSize());
    gb.setConstraints(p2, c);
    all.add(p2);
    c.gridx = 1;
    c.gridy = 1;
    c.weighty = 0.3;
    final JScrollPane p3 = new JScrollPane(tp);
    p3.setPreferredSize(tp.getPreferredSize());
    gb.setConstraints(p3, c);
    all.add(p3);
    c.gridx = 0;
    c.gridy = 2;
    c.gridwidth = 2;
    c.weightx = 1;
    c.weighty = 0;
    gb.setConstraints(buttons, c);
    all.add(buttons);
    final KeyAdapter help = new KeyAdapter() {

        @Override
        public void keyPressed(final KeyEvent ke) {
            if (ke.getKeyCode() == KeyEvent.VK_F1) {
                final GenericDialog gd = new GenericDialog("Help :: image filters");
                gd.addMessage("In the table 'Available Filters':\n" + " - double-click a filter to add it to the table of 'Chosen Filters'\n \n" + "In the table 'Chosen Filters':\n" + " - double-click a filter to remove it.\n" + " - PAGE UP/DOWN keys move the filter up/down in the list.\n" + " - 'Delete' key removes the selected filter.\n \n" + "In the table of parameter names and values:\n" + " - double-click a value to edit it. Then push enter to set the new value.\n \n" + "What you need to know:\n" + " - filters are set and applied in order, so order matters.\n" + " - filters with parameters for which you entered a value of zero\nwill result in a warning message.\n" + " - when applying the filters, if you choose 'Selected images', these are the images\nthat were selected when the filter editor was opened.\n" + " - when applying the filters, if you want to filter for a regular expression pattern\nin the image name, use the 'All images in layer range...' option,\nwhere a range of one single layer is also possible.");
                gd.hideCancelButton();
                gd.setModal(false);
                gd.showDialog();
            }
        }
    };
    taf.addKeyListener(help);
    tcf.addKeyListener(help);
    tp.addKeyListener(help);
    all.addKeyListener(help);
    buttons.addKeyListener(help);
    empty.addKeyListener(help);
    a.addKeyListener(help);
    frame.getContentPane().add(all);
    frame.pack();
    frame.setVisible(true);
}