Examples with ContentInstant ij3d.ContentInstant used on opensource projects

Example 1 with ContentInstant

use of ij3d.ContentInstant in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createImage3DUniverse.

/**
 * Creates the image 3D universe with a unique name.
 *
 * @param title the title
 * @param titleList the title list (of titles to ignore)
 * @return the image 3D universe
 */
private Image3DUniverse createImage3DUniverse(String title, List<String> titleList) {
    // Get a unique name by appending numbers to the end
    String title2 = title;
    int counter = 2;
    while (titleList.contains(title2)) {
        title2 = title + " " + (counter++);
    }
    final Image3DUniverse universe = new Image3DUniverse();
    universe.addUniverseListener(new LocalUniverseListener());
    universe.setShowBoundingBoxUponSelection(false);
    universe.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
    // Capture a canvas mouse click/region and identify the coordinates.
    final ImageCanvas3D canvas = (ImageCanvas3D) universe.getCanvas();
    final BranchGroup scene = universe.getScene();
    final MouseListener mouseListener = new MouseAdapter() {

        @Override
        public void mouseClicked(final MouseEvent event) {
            if (!consumeEvent(event)) {
                return;
            }
            // Consume the event
            event.consume();
            // This finds the vertex indices of the rendered object.
            final Pair<Content, IntersectionInfo> pair = getPickedContent(canvas, scene, event.getX(), event.getY());
            if (pair == null) {
                // Do the same as the mouseClicked in Image3DUniverse
                universe.select(null);
                return;
            }
            // Only process content added from localisations
            final Content c = pair.getKey();
            if (!(c.getUserData() instanceof ResultsMetaData)) {
                // Do the same as the mouseClicked in Image3DUniverse
                universe.select(c);
                return;
            }
            final ResultsMetaData data = (ResultsMetaData) c.getUserData();
            final MemoryPeakResults results = data.results;
            // Look up the localisation from the clicked vertex
            final ContentInstant content = c.getCurrent();
            int index = -1;
            if (content.getContent() instanceof CustomMeshNode) {
                final CustomMeshNode node = (CustomMeshNode) content.getContent();
                final CustomMesh mesh = node.getMesh();
                int vertexCount;
                final GeometryArray ga = (GeometryArray) mesh.getGeometry();
                // Default to the number of vertices
                vertexCount = ga.getValidVertexCount();
                final int countPerLocalisation = vertexCount / results.size();
                // Determine the localisation
                final int vertexIndex = pair.getValue().getVertexIndices()[0];
                index = vertexIndex / countPerLocalisation;
            } else if (content.getContent() instanceof ItemGroupNode) {
                // All shapes have the index as the user data
                final Object o = pair.getValue().getGeometry().getUserData();
                if (o instanceof Integer) {
                    index = (Integer) pair.getValue().getGeometry().getUserData();
                }
            }
            if (index == -1) {
                return;
            }
            final PeakResult result = results.get(index);
            if (event.getClickCount() > 1) {
                // Centre on the localisation
                final Point3d coordinate = new Point3d();
                coordinate.set(data.points.get(index));
                // Handle the local transform of the content ...
                final Transform3D vWorldToLocal = getVworldToLocal(content);
                vWorldToLocal.transform(coordinate);
                universe.centerAt(coordinate);
            } else if (event.isShiftDown()) {
                // Ctrl+Shift held down to remove selected
                data.removeFromSelectionModel(result);
            } else {
                // Ctrl held down to set selection
                data.addToSelectionModel(result);
            }
        }

        private boolean consumeEvent(final MouseEvent event) {
            if (event.isConsumed() || event.getButton() != MouseEvent.BUTTON1 || !(event.isControlDown())) {
                return false;
            }
            if (event.getClickCount() == 1) {
                return true;
            }
            return (event.getClickCount() == 2);
        }
    };
    // 0 = ImageCanvas3D
    // 1 = DefaultUniverse
    // 2 = Image3DUniverse
    final MouseListener[] l = canvas.getMouseListeners();
    for (int i = 0; i < l.length; i++) {
        if (l[i].getClass().getName().contains("Image3DUniverse")) {
            // We want to be before the Image3DUniverse to allow consuming the click event.
            // Only allow the click event.
            // This disables the right-click pop-up menu.
            // It doesn't have anything of use for localisations anyway.
            canvas.removeMouseListener(l[i]);
            canvas.addMouseListener(mouseListener);
            canvas.addMouseListener(new MouseListenerWrapper(l[i], MouseListenerWrapper.MOUSE_CLICKED));
        }
    }
    // 0 = ImageCanvas3D
    // 1 = DefaultUniverse
    // 2 = Image3DUniverse
    // 3 = EventCatcher (from scijava)
    final MouseMotionListener[] ml = canvas.getMouseMotionListeners();
    for (int i = 0; i < ml.length; i++) {
        if (ml[i].getClass().getName().contains("Image3DUniverse")) {
            // Ignore this as it just shows the name in the IJ status bar
            canvas.removeMouseMotionListener(ml[i]);
        }
    }
    // Finally display the window
    universe.show();
    final ImageWindow3D window = universe.getWindow();
    GUI.center(window);
    window.setTitle(title2);
    WindowManager.addWindow(window);
    window.addWindowListener(new WindowAdapter() {

        @Override
        public void windowClosing(WindowEvent event) {
            WindowManager.removeWindow(window);
        }
    });
    // Add a new menu for SMLM functionality
    createSmlmMenuBar(universe);
    return universe;
}

Example 2 with ContentInstant

use of ij3d.ContentInstant in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method getTotalTransparentObjects.

private static long getTotalTransparentObjects(Image3DUniverse univ, String ignoreName) {
    long size = 0;
    for (final Iterator<Content> it = univ.contents(); it.hasNext(); ) {
        final Content c = it.next();
        if (ignoreName.equals(c.getName())) {
            continue;
        }
        if (!(c.getUserData() instanceof ResultsMetaData)) {
            return 0;
        }
        final ContentInstant content = c.getCurrent();
        if (content.getContent() instanceof ItemGroupNode) {
            final ItemGroupNode node = (ItemGroupNode) content.getContent();
            final ItemGroup g = node.getItemGroup();
            if (g instanceof ItemGeometryGroup) {
                size += g.size();
            }
        }
    }
    return size;
}

Example 3 with ContentInstant

use of ij3d.ContentInstant in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewerDemo method run.

@Override
public void run(String arg) {
    if (ImageJ3DViewerUtils.JAVA_3D_VERSION == null) {
        IJ.error(TITLE, "Java 3D is not available");
        return;
    }
    final boolean renderingTest = true;
    if (renderingTest) {
        // Put all the shapes from rendering on a view and see how they look.
        final Image3DUniverse univ = new Image3DUniverse();
        univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
        univ.show();
        final ImageWindow3D w = univ.getWindow();
        GUI.center(w);
        // Test how many vertices a primitive sphere has
        float x = 0;
        final float y = 0;
        final float space = 2.5f;
        for (final Rendering rendering : Rendering.values()) {
            final Shape3D shape = Shape3DHelper.createShape(rendering, 3);
            final Appearance a = shape.getAppearance();
            final ItemMesh mesh = new ReferenceItemMesh(new Point3f[] { new Point3f(x, y, 0) }, (GeometryArray) shape.getGeometry(), a, null, null, 0f);
            ImageJUtils.log("R=%s %s  Vc=%d  V=%d  T=%d", rendering, shape.getGeometry().getClass().getSimpleName(), mesh.getVerticesCountPerItem(), mesh.getVerticesPerItem(), Shape3DHelper.getNumberOfTriangles(rendering));
            if (rendering == Rendering.POINT) {
                a.getPointAttributes().setPointSize(10);
            }
            univ.addCustomMesh(mesh, x + "," + y);
            x += space;
        }
        return;
    }
    final boolean sphereTest = true;
    if (sphereTest) {
        // Sphere test
        // Put lots of spheres on a view and see how they look.
        // Is it worth supporting an ItemTriangleStripMesh so we can control
        // the sphere better than the icosahedron?
        final Image3DUniverse univ = new Image3DUniverse();
        univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
        univ.show();
        final ImageWindow3D w = univ.getWindow();
        GUI.center(w);
        // Test how many vertices a primitive sphere has
        float x = 0;
        float y = 0;
        final float space = 2.5f;
        Appearance app = null;
        for (int d = 0; d < 4; d++) {
            final List<Point3f> points = customnode.MeshMaker.createIcosahedron(d, 1f);
            final Pair<Point3f[], int[]> p = CustomContentHelper.createIndexedObject(points);
            final int v = points.size();
            final int t = v / 3;
            ImageJUtils.log("Icosahedron divisions = %d, V=%d, T=%d, Vi=%d (%.2f), i=%d", d, v, t, p.getKey().length, v / (double) p.getKey().length, p.getValue().length);
            CustomMesh mesh = new ItemTriangleMesh(points.toArray(new Point3f[0]), new Point3f[] { new Point3f(x, y, 0) }, null, null, 0);
            app = mesh.getAppearance();
            univ.addCustomMesh(mesh, x + "," + y + "," + t);
            final float y2 = y + space;
            mesh = new ItemIndexedTriangleMesh(p.getKey(), p.getValue(), new Point3f[] { new Point3f(x, y2, 0) }, null, null, 0);
            univ.addCustomMesh(mesh, x + "," + y2 + "," + t);
            x += space;
        }
        // Avoid null pointer warnings
        if (app == null) {
            throw new NullPointerException();
        }
        // The T=800 sphere looks about the same as the Icosahedron(div=3) T=1280
        // This may be a better super-high resolution option.
        x = 0;
        y += 2 * space;
        app = (Appearance) app.cloneNodeComponent(true);
        // a.getColoringAttributes().setColor(0, 1, 0);
        app.getMaterial().setDiffuseColor(0, 1, 0);
        for (int d = 4; d < 50; d += 4) {
            // This is a triangle strip array so is more space efficient
            final Sphere s = new Sphere(1, Primitive.GENERATE_NORMALS, d);
            final int t = s.getNumTriangles();
            ImageJUtils.log("Sphere divisions = %d, V=%d, T=%d", d, s.getNumVertices(), t);
            final ItemGeometryGroup g = new ItemGeometryGroup(new Point3f[] { new Point3f(x, y, 0) }, (GeometryArray) s.getShape().getGeometry(), app, null, null, null);
            final String name = x + "," + y + "," + t;
            final CustomContent content = new CustomContent(name, true);
            content.getCurrent().display(new ItemGroupNode(g));
            univ.addContent(content);
            x += space;
        }
        return;
    }
    LocalList<Point3f> pointList;
    float scale;
    if (MemoryPeakResults.isMemoryEmpty()) {
        pointList = new LocalList<>();
        int range;
        // 9 points
        range = 1;
        // range = 49; // 99^3 = 970299 points
        for (int x = -range; x <= range; x++) {
            for (int y = -range; y <= range; y++) {
                for (int z = -range; z <= range; z++) {
                    pointList.add(new Point3f(x, y, z));
                }
            }
        }
        scale = 0.25f;
    } else {
        final ImageJ3DResultsViewerSettings.Builder settings = SettingsManager.readImageJ3DResultsViewerSettings(0).toBuilder();
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Select a dataset to display");
        ResultsManager.addInput(gd, settings.getInputOption(), InputSource.MEMORY);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
        final String name = ResultsManager.getInputSource(gd);
        settings.setInputOption(name);
        SettingsManager.writeSettings(settings);
        final MemoryPeakResults results = ResultsManager.loadInputResults(name, false, null, null);
        if (MemoryPeakResults.isEmpty(results)) {
            IJ.error(TITLE, "No results could be loaded");
            IJ.showStatus("");
            return;
        }
        pointList = ImageJ3DResultsViewer.getPoints(results, settings);
        if (pointList == null) {
            return;
        }
        scale = 10f;
    }
    final Image3DUniverse univ = new Image3DUniverse();
    univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
    univ.show();
    final ImageWindow3D w = univ.getWindow();
    GUI.center(w);
    final View view = univ.getViewer().getView();
    view.setTransparencySortingPolicy(View.TRANSPARENCY_SORT_GEOMETRY);
    // I am not sure if this is required if objects are sorted.
    // view.setDepthBufferFreezeTransparent(false)
    IJ.showStatus("Creating points ...");
    final Point3f[] points = pointList.toArray(new Point3f[0]);
    final Point3f[] sizes = new Point3f[] { new Point3f(scale, scale, scale) };
    final Appearance appearance = new Appearance();
    final TransparencyAttributes ta = new TransparencyAttributes();
    ta.setTransparency(0.5f);
    ta.setTransparencyMode(TransparencyAttributes.FASTEST);
    appearance.setTransparencyAttributes(ta);
    final ItemGeometryGroup pointGroup = new ItemGeometryGroup(points, null, appearance, sizes, null, null);
    // pointGroup = new OrderedItemGeometryGroup(points, null, appearance, sizes, null, null);
    // // This supports transparency sorting
    // BranchGroup bg = new BranchGroup();
    // bg.addChild(pointGroup);
    // bg.compile();
    // univ.getScene().addChild(bg);
    // // This does not since ContentInstant uses an OrderedPath to show:
    // // the content; the object bounding box, coordinate system and point list
    // final Content c = new Content("Test");
    // final ContentInstant content = c.getCurrent();
    // content.display(new PointGroupNode(pointGroup));
    // univ.addContent(c);
    // This does since ItemGeometryNode uses a Group to show the points as individual shapes
    // and the CustomContentInstant uses a group not an ordered group so show all the adornments.
    IJ.showStatus("Displaying points ...");
    final CustomContent c = new CustomContent("Test", false);
    final ContentInstant content = c.getCurrent();
    content.display(new ItemGroupNode(pointGroup));
    univ.addContent(c);
    IJ.showStatus("Done");
}