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

Example 1 with Layer

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

the class DBLoader method importStackAsPatches.

/**
 * Returns the last Patch.
 */
protected Patch importStackAsPatches(final Project project, final Layer first_layer, final double x, final double y, final ImagePlus imp_stack, final boolean as_copy, final String filepath) {
    double pos_x = Double.MAX_VALUE != x ? x : first_layer.getLayerWidth() / 2 - imp_stack.getWidth() / 2;
    double pos_y = Double.MAX_VALUE != y ? y : first_layer.getLayerHeight() / 2 - imp_stack.getHeight() / 2;
    final double thickness = first_layer.getThickness();
    final String title = Utils.removeExtension(imp_stack.getTitle()).replace(' ', '_');
    Utils.showProgress(0);
    Patch previous_patch = null;
    final int n = imp_stack.getStackSize();
    for (int i = 1; i <= n; i++) {
        Layer layer = first_layer;
        double z = first_layer.getZ() + (i - 1) * thickness;
        // will create new layer if not found
        if (i > 1)
            layer = first_layer.getParent().getLayer(z, thickness, true);
        if (null == layer) {
            Utils.log("Display.importStack: could not create new layers.");
            return null;
        }
        ImageProcessor ip = imp_stack.getStack().getProcessor(i);
        if (as_copy)
            ip = ip.duplicate();
        ImagePlus imp_patch_i = new ImagePlus(title + "__slice=" + i, ip);
        String label = imp_stack.getStack().getSliceLabel(i);
        if (null == label)
            label = "";
        Patch patch = new Patch(project, label + " " + title + " " + i, pos_x, pos_y, imp_patch_i);
        layer.add(patch);
        if (null != previous_patch)
            patch.link(previous_patch);
        previous_patch = patch;
        Utils.showProgress(i * (1.0 / n));
    }
    Utils.showProgress(1.0);
    // return the last Patch
    return previous_patch;
}

Example 2 with Layer

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

the class DBLoader method unpackLayers.

/**
 * Recursive. Place all Layer (but not LayerSet) objects with a key as Long(id).
 */
private void unpackLayers(LayerThing root, HashMap hs) {
    Object ob = root.getObject();
    if (ob instanceof Layer)
        hs.put(new Long(((DBObject) ob).getId()), ob);
    if (null == root.getChildren())
        return;
    Iterator it = root.getChildren().iterator();
    while (it.hasNext()) {
        LayerThing child = (LayerThing) it.next();
        unpackLayers(child, hs);
    }
}

Example 3 with Layer

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

the class DBLoader method getLayerThing.

private LayerThing getLayerThing(ResultSet r, Project project, HashMap hs_pt, TemplateThing layer_set_tt, TemplateThing layer_tt) throws Exception {
    long id = r.getLong("id");
    String type = r.getString("type");
    // if not a "Layer", then it's a "Layer Set"
    TemplateThing template = type.equals("layer_set") ? layer_set_tt : layer_tt;
    // HERE the order of the arguments layer_set_tt and layer_tt was inverted, and it worked??? There was a compensating bug, incredibly enough, in the type.equals(.. above.
    return new LayerThing(template, project, id, r.getString("title"), getLayerThingObject(project, r.getLong("object_id"), template, hs_pt), getChildrenLayerThing(project, id, hs_pt, layer_set_tt, layer_tt));
}

Example 4 with Layer

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

the class AmiraImporter method importAmiraLabels.

/**
 * Returns the array of AreaList or null if the file dialog is canceled. The xo,yo is the pivot of reference.
 */
public static Collection<AreaList> importAmiraLabels(Layer first_layer, double xo, double yo, final String default_dir) {
    // open file
    OpenDialog od = new OpenDialog("Choose Amira Labels File", default_dir, "");
    String filename = od.getFileName();
    if (null == filename || 0 == filename.length())
        return null;
    String dir = od.getDirectory();
    if (IJ.isWindows())
        dir = dir.replace('\\', '/');
    if (!dir.endsWith("/"))
        dir += "/";
    String path = dir + filename;
    AmiraMeshDecoder dec = new AmiraMeshDecoder();
    if (!dec.open(path)) {
        YesNoDialog yn = new YesNoDialog("Error", "File was not an Amira labels file.\nChoose another one?");
        if (yn.yesPressed())
            return importAmiraLabels(first_layer, xo, yo, default_dir);
        return null;
    }
    ImagePlus imp = null;
    if (dec.isTable()) {
        Utils.showMessage("Select the other file (the labels)!");
        return null;
    } else {
        FileInfo fi = new FileInfo();
        fi.fileName = filename;
        fi.directory = dir;
        imp = new ImagePlus("Amira", dec.getStack());
        dec.parameters.setParameters(imp);
    }
    return extractAmiraLabels(imp, dec.parameters, first_layer, xo, yo);
}

Example 5 with Layer

use of ini.trakem2.display.Layer 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;
}