Examples with Shape3D org.scijava.java3d.Shape3D used on opensource projects

Example 1 with Shape3D

use of org.scijava.java3d.Shape3D in project GDSC-SMLM by aherbert.

the class Shape3DHelper method createShape.

/**
 * Creates the shape.
 *
 * @param rendering the rendering
 * @param colorDepth the color depth
 * @return the shape
 */
public static Shape3D createShape(Rendering rendering, int colorDepth) {
    GeometryArray ga;
    final Appearance appearance = new Appearance();
    int vertexFormat = GeometryArray.COORDINATES;
    if (colorDepth == 3) {
        vertexFormat |= GeometryArray.COLOR_3;
    } else if (colorDepth == 4) {
        vertexFormat |= GeometryArray.COLOR_4;
    }
    // Support drawing as points ...
    if (rendering == Rendering.POINT) {
        ga = new PointArray(1, vertexFormat);
        final PointAttributes pa = new PointAttributes();
        pa.setPointAntialiasingEnable(true);
        appearance.setPointAttributes(pa);
    } else {
        ga = createGeometryArray(rendering, colorDepth);
        // // Test using the geometry from a sphere primitive
        // switch (r)
        // {
        // case HIGH_RES_SPHERE:
        // ga = ItemGeometryGroup.createSphere(50);
        // break;
        // case LOW_RES_SPHERE:
        // ga = ItemGeometryGroup.createSphere(16);
        // break;
        // }
        final PolygonAttributes pa = new PolygonAttributes();
        pa.setPolygonMode(PolygonAttributes.POLYGON_FILL);
        if (rendering.is2D()) {
            pa.setCullFace(PolygonAttributes.CULL_NONE);
            pa.setBackFaceNormalFlip(true);
        } else {
            pa.setCullFace(PolygonAttributes.CULL_BACK);
            pa.setBackFaceNormalFlip(false);
        }
        appearance.setPolygonAttributes(pa);
        final ColoringAttributes ca = new ColoringAttributes();
        // if (rendering.isHighResolution() || rendering.is2D())
        // // Smooth across vertices. Required to show 2D surfaces smoothly
        // ca.setShadeModel(ColoringAttributes.SHADE_GOURAUD);
        // else
        // // Faster polygon rendering with flat shading
        // ca.setShadeModel(ColoringAttributes.SHADE_FLAT);
        // For indexed models (with 1 normal per vertex) always use smooth shading
        ca.setShadeModel(ColoringAttributes.SHADE_GOURAUD);
        appearance.setColoringAttributes(ca);
        final Material m = new Material();
        m.setShininess(128f);
        m.setAmbientColor(0.1f, 0.1f, 0.1f);
        if (rendering.isHighResolution()) {
            // Allow shiny highlights on balls
            m.setSpecularColor(0.1f, 0.1f, 0.1f);
        } else {
            // For flat appearance
            m.setSpecularColor(0, 0, 0);
        }
        appearance.setMaterial(m);
    }
    return new Shape3D(ga, appearance);
}

Example 2 with Shape3D

use of org.scijava.java3d.Shape3D in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createItemMesh.

private static ItemMesh createItemMesh(final ImageJ3DResultsViewerSettingsOrBuilder settings, LocalList<Point3f> points, final Point3f[] sphereSize, float transparency, float[] alpha) {
    final Rendering rendering = Rendering.forNumber(settings.getRendering());
    final int colorDepth = (alpha != null) ? 4 : 3;
    final Shape3D shape = Shape3DHelper.createShape(rendering, colorDepth);
    final GeometryArray ga = (GeometryArray) shape.getGeometry();
    final Appearance appearance = shape.getAppearance();
    // Estimate the largest array required for the data.
    // The mesh is created by reference using an array for coords, normals and colors.
    final int singlePointVertexSize = ga.getValidVertexCount();
    int singlePointIndexSize = 0;
    final int stride = Math.max(3, colorDepth);
    if (ga instanceof IndexedGeometryArray) {
        // Indexed arrays may have much larger index array than the vertex array
        singlePointIndexSize = ((IndexedGeometryArray) ga).getIndexCount();
    }
    final int singlePointSize = Math.max(singlePointIndexSize, stride * singlePointVertexSize);
    final long arraySize = (long) points.size() * singlePointSize;
    if (arraySize > CustomContentHelper.MAX_ARRAY_SIZE) {
        final double capacity = (double) arraySize / CustomContentHelper.MAX_ARRAY_SIZE;
        // @formatter:off
        IJ.error(TITLE, TextUtils.wrap(String.format("The results will generate data of %d values. " + "This is amount of data is not supported (%.2fx capacity). " + "Please choose a different dataset with fewer points or " + "different rendering model.", arraySize, capacity), 80));
        // @formatter:on
        return null;
    }
    // Support drawing as points ...
    if (settings.getRendering() == 0) {
        final ItemMesh mesh = new ReferenceItemMesh(points.toArray(new Point3f[0]), ga, appearance, null, null, transparency);
        if (alpha != null) {
            mesh.setItemAlpha(alpha);
        }
        mesh.getAppearance().getPointAttributes().setPointSize(sphereSize[0].x);
        return mesh;
    }
    final int triangles = Shape3DHelper.getNumberOfTriangles(rendering);
    final long size = (long) points.size() * triangles;
    if (size > 10000000L) {
        final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
        egd.addMessage("The results will generate a large mesh of " + size + " triangles.\nThis may take a long time to render and may run out of memory.");
        egd.setOKLabel("Continue");
        egd.showDialog();
        if (egd.wasCanceled()) {
            return null;
        }
    }
    IJ.showStatus("Creating 3D mesh ...");
    final ItemMesh mesh = new ReferenceItemMesh(points.toArray(new Point3f[0]), ga, appearance, sphereSize, null, transparency);
    if (alpha != null) {
        mesh.setItemAlpha(alpha);
    }
    return mesh;
}

Example 3 with Shape3D

use of org.scijava.java3d.Shape3D in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createShape.

@SuppressWarnings("unused")
private static Shape3D createShape(Builder settings) {
    final LocalList<Point3f> points = new LocalList<>(1);
    points.push(new Point3f());
    // We try and match the geometry and appearance of the standard mesh.
    // Do this by creating a mesh with a single point and get the Geometry and Appearance.
    GeometryArray ga;
    CustomMesh mesh;
    final float transparency = getTransparency(settings);
    // Support drawing as points ...
    if (settings.getRendering() == 0) {
        mesh = new TransparentItemPointMesh(points, null, transparency);
        ((ItemPointMesh) mesh).setPointSize((float) settings.getPixelSize());
        updateAppearance(mesh, settings);
        // Assume the TransparentItemPointMesh sets COLOR_4
        ga = (GeometryArray) mesh.getGeometry();
    } else {
        final Rendering r = Rendering.forNumber(settings.getRendering());
        final List<Point3f> point = Shape3DHelper.createLocalisationObject(r);
        final Point3f[] vertices = point.toArray(new Point3f[1]);
        // Correct the direction
        ItemTriangleMesh.checkFacets(vertices);
        final double creaseAngle = (r.isHighResolution()) ? 44 : 0;
        mesh = new ItemTriangleMesh(vertices, points.toArray(new Point3f[1]), null, null, transparency, creaseAngle, null);
        updateAppearance(mesh, settings);
        final int nVertices = vertices.length;
        ga = new TriangleArray(nVertices, GeometryArray.COORDINATES | GeometryArray.NORMALS);
        // Copy the coords and normals. We don't require the vertex colours.
        final float[] coords = new float[nVertices * 3];
        final float[] normals = new float[nVertices * 3];
        final GeometryArray gaToCopy = (GeometryArray) mesh.getGeometry();
        gaToCopy.getCoordinates(0, coords);
        gaToCopy.getNormals(0, normals);
        ga.setCoordinates(0, coords);
        ga.setNormals(0, normals);
        ga.setValidVertexCount(nVertices);
    }
    return new Shape3D(ga, mesh.getAppearance());
}

Example 4 with Shape3D

use of org.scijava.java3d.Shape3D in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createItemGroup.

private static ItemGeometryGroup createItemGroup(final ImageJ3DResultsViewerSettings.Builder settings, final Point3f[] sphereSize, final LocalList<Point3f> points, float[] alpha, float transparency, Color3f[] colors) {
    final Rendering rendering = Rendering.forNumber(settings.getRendering());
    // All objects have colour using the appearance not per vertex colours.
    // The exception is points which do not support colour from appearance.
    final int colorDepth = (rendering == Rendering.POINT) ? 4 : 0;
    final Shape3D shape = Shape3DHelper.createShape(rendering, colorDepth);
    // Use max so that points get a value of 1
    final int triangles = Math.max(Shape3DHelper.getNumberOfTriangles(rendering), 1);
    final GeometryArray ga = (GeometryArray) shape.getGeometry();
    final long size = (long) points.size() * triangles;
    if (size > 10000000L) {
        final String name = (rendering == Rendering.POINT) ? "points" : "triangles";
        final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
        egd.addMessage("The results will generate a large dataset of " + size + " " + name + ".\nThis may take a long time to render and may run out of memory.");
        egd.setOKLabel("Continue");
        egd.showDialog();
        if (egd.wasCanceled()) {
            return null;
        }
    }
    final Appearance appearance = shape.getAppearance();
    final TransparencyAttributes ta = new TransparencyAttributes();
    ta.setTransparency(transparency);
    ta.setTransparencyMode((transparency == 0) ? TransparencyAttributes.NONE : TransparencyAttributes.FASTEST);
    appearance.setTransparencyAttributes(ta);
    if (rendering == Rendering.POINT) {
        appearance.getPointAttributes().setPointSize(sphereSize[0].x);
    }
    if (settings.getSupportDynamicTransparency()) {
        return new ItemGeometryGroup(points.toArray(new Point3f[0]), ga, appearance, sphereSize, colors, alpha);
    }
    return new OrderedItemGeometryGroup(points.toArray(new Point3f[0]), ga, appearance, sphereSize, colors, alpha);
}

Example 5 with Shape3D

use of org.scijava.java3d.Shape3D 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");
}