Examples with Rendering uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering used on opensource projects

Example 1 with Rendering

use of uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method getPoints.

/**
 * Gets the points.
 *
 * @param results the results
 * @param settings the settings
 * @return the points
 */
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
    final LocalList<Point3f> points = new LocalList<>(results.size());
    if (results.is3D()) {
        results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
            points.push(new Point3f(x, y, z));
        });
    } else {
        results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
            points.push(new Point3f(x, y, 0));
        });
        final double range = settings.getDepthRange();
        if (range > 0 && results.size() > 1) {
            final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
            final double min = -settings.getDepthRange() / 2;
            switch(mode) {
                case DITHER:
                    final SplitMix r = SplitMix.new64(settings.getDitherSeed());
                    for (int i = points.size(); i-- > 0; ) {
                        points.unsafeGet(i).z += (min + r.nextDouble() * range);
                    }
                    break;
                case INTENSITY:
                    // Rank by intensity, highest first
                    final StandardResultProcedure p = new StandardResultProcedure(results);
                    p.getI();
                    final int[] indices = SimpleArrayUtils.natural(results.size());
                    SortUtils.sortIndices(indices, p.intensity, true);
                    final double inc = range / indices.length;
                    for (int i = 0; i < indices.length; i++) {
                        // The standard rendering has +z going away so put the highest rank at min
                        points.unsafeGet(indices[i]).z += (min + i * inc);
                    }
                    break;
                case NONE:
                    break;
                default:
                    throw new IllegalStateException("Unknown depth mode: " + mode);
            }
        }
    }
    return points;
}

Example 2 with Rendering

use of uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createMesh.

@SuppressWarnings("unused")
private static CustomMesh createMesh(final ImageJ3DResultsViewerSettingsOrBuilder settings, LocalList<Point3f> points, final Point3f[] sphereSize, float transparency, float[] alpha) {
    // Coordinates + color
    int stride = 3 + 3;
    if (alpha != null) {
        // add color alpha
        stride++;
    }
    // Support drawing as points ...
    if (settings.getRendering() == 0) {
        final long arraySize = (long) points.size() * stride;
        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.", arraySize, capacity), 80));
            // @formatter:on
            return null;
        }
        CustomPointMesh mesh;
        if (alpha != null) {
            final TransparentItemPointMesh mesh2 = new TransparentItemPointMesh(points, null, transparency);
            mesh = mesh2;
            mesh2.setItemAlpha(alpha);
        } else {
            mesh = new ItemPointMesh(points, null, transparency);
        }
        mesh.setPointSize(sphereSize[0].x);
        return mesh;
    }
    final Rendering r = Rendering.forNumber(settings.getRendering());
    // Repeated mesh creation is much faster as the normals are cached.
    // There does not appear to be a difference in the speed the image responds
    // to user interaction between indexed or standard triangles.
    // Currently the RepeatedIndexedTriangleMesh computes the normals a different way to
    // the super class to preserve the orientation of the normals. So if the coordinates
    // are modified through the mesh then the appearance will change. For now just use
    // the RepeatedTriangleMesh.
    // TODO - check this. It may not be true if the shading mode is flat...
    // Also the IndexedTriangleMesh has one normal per vertex and this causes a colour fall-off
    // on the triangle plane towards the edges. The TriangleMesh colours the entire surface
    // of each triangle the same which looks 'normal'.
    final List<Point3f> point = Shape3DHelper.createLocalisationObject(r);
    // + normals
    stride += 3;
    final int singlePointSize = point.size();
    final long size = (long) points.size() * singlePointSize;
    final long arraySize = size * stride;
    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 rendering model with fewer vertices.", arraySize, capacity), 80));
        // @formatter:on
        return null;
    }
    if (size > 10000000L) {
        final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
        egd.addMessage("The results will generate a large mesh of " + size + " vertices.\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 double creaseAngle = (r.isHighResolution()) ? 44 : 0;
    // Used for debugging construction time
    final ImageJTrackProgress progress = null;
    if (alpha != null) {
        final TransparentItemTriangleMesh mesh = new TransparentItemTriangleMesh(point.toArray(new Point3f[singlePointSize]), points.toArray(new Point3f[0]), sphereSize, null, transparency, creaseAngle, progress);
        mesh.setItemAlpha(alpha);
        return mesh;
    }
    return new ItemTriangleMesh(point.toArray(new Point3f[singlePointSize]), points.toArray(new Point3f[0]), sphereSize, null, transparency, creaseAngle, progress);
}

Example 3 with Rendering

use of uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering 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 4 with Rendering

use of uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method updateAppearance.

private static void updateAppearance(CustomMesh mesh, final ImageJ3DResultsViewerSettingsOrBuilder settings) {
    mesh.setShaded(settings.getShaded());
    final Appearance appearance = mesh.getAppearance();
    final PolygonAttributes pa = appearance.getPolygonAttributes();
    // For all 3D polygons we want to support a true face orientation so transparency works
    final Rendering r = Rendering.forNumber(settings.getRendering());
    if (r.is2D()) {
        pa.setCullFace(PolygonAttributes.CULL_NONE);
        pa.setBackFaceNormalFlip(true);
    } else {
        pa.setCullFace(PolygonAttributes.CULL_BACK);
        pa.setBackFaceNormalFlip(false);
    }
    // TransparencyAttributes ta = appearance.getTransparencyAttributes();
    // ta.setSrcBlendFunction(TransparencyAttributes.BLEND_SRC_ALPHA);
    // ta.setDstBlendFunction(TransparencyAttributes.BLEND_ONE);
    // ta.setDstBlendFunction(TransparencyAttributes.BLEND_ONE_MINUS_SRC_ALPHA); // Default
    ItemTriangleMesh.setTransparencyMode(TransparencyAttributes.FASTEST);
    // ItemTriangleMesh.setTransparencyMode(TransparencyAttributes.SCREEN_DOOR);
    // ItemTriangleMesh.setTransparencyMode(TransparencyAttributes.BLENDED);
    final ColoringAttributes ca = appearance.getColoringAttributes();
    if (r.isHighResolution() || r.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);
    }
}

Example 5 with Rendering

use of uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering 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());
}