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

Example 26 with GeometryArray

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

the class ItemGeometryGroup method setItemAlpha.

/**
 * Sets the item alpha and the global transparency in one operation.
 *
 * @param alpha the alpha
 * @param transparency the transparency
 * @throws IllegalArgumentException the illegal argument exception
 * @see #setItemAlpha(float[])
 */
public void setItemAlpha(float[] alpha, float transparency) {
    if (alpha != null) {
        final int size = size();
        if (alpha.length != size) {
            throw new IllegalArgumentException("list of size " + size + " expected");
        }
        this.alphas = alpha.clone();
    } else {
        this.alphas = null;
    }
    if (isPointArray) {
        // PointArray alpha must be updated
        if (alpha != null) {
            for (int i = 0; i < geometryArray.length; i++) {
                final GeometryArray ga = geometryArray[i];
                ga.getColors(0, pointArrayColorUpdater.pointColor);
                pointArrayColorUpdater.getColors(alpha[i]);
                ga.setColors(0, pointArrayColorUpdater.pointColor);
            }
        } else {
            for (int i = 0; i < geometryArray.length; i++) {
                final GeometryArray ga = geometryArray[i];
                ga.getColors(0, pointArrayColorUpdater.pointColor);
                pointArrayColorUpdater.getColors(1f);
                ga.setColors(0, pointArrayColorUpdater.pointColor);
            }
        }
    }
    setTransparency(transparency);
}

Example 27 with GeometryArray

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

the class ItemGeometryGroup method setItemAlpha.

@Override
public void setItemAlpha(float[] alpha) {
    if (alpha != null) {
        final int size = size();
        if (alpha.length != size) {
            throw new IllegalArgumentException("list of size " + size + " expected");
        }
        this.alphas = alpha.clone();
    } else {
        this.alphas = null;
    }
    if (isPointArray) {
        // PointArray alpha must be updated
        if (alpha != null) {
            for (int i = 0; i < geometryArray.length; i++) {
                final GeometryArray ga = geometryArray[i];
                ga.getColors(0, pointArrayColorUpdater.pointColor);
                pointArrayColorUpdater.getColors(alpha[i]);
                ga.setColors(0, pointArrayColorUpdater.pointColor);
            }
        } else {
            for (int i = 0; i < geometryArray.length; i++) {
                final GeometryArray ga = geometryArray[i];
                ga.getColors(0, pointArrayColorUpdater.pointColor);
                pointArrayColorUpdater.getColors(1f);
                ga.setColors(0, pointArrayColorUpdater.pointColor);
            }
        }
    } else {
        // Global transparency is merged with alpha
        setTransparency(this.transparency);
    }
}

Example 28 with GeometryArray

use of org.scijava.java3d.GeometryArray 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 29 with GeometryArray

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

the class ReferenceItemMesh method setItemColor.

@Override
public void setItemColor(Color3f color) {
    if (color == null) {
        color = DEFAULT_COLOR;
    }
    this.color = color;
    if (!hasColor()) {
        if (isColorByMaterial) {
            getAppearance().getMaterial().setDiffuseColor(color);
        } else {
            getAppearance().getColoringAttributes().setColor(color);
        }
        return;
    }
    final GeometryArray ga = (GeometryArray) getGeometry();
    if (ga == null) {
        return;
    }
    final float[] colors;
    if (hasColor3()) {
        colors = new float[size() * colorUpdater.size()];
        final float[] tmp = new float[3];
        color.get(tmp);
        duplicate(tmp, 0, 3, colors.length / 3, colors, 0);
    } else {
        // Preserve alpha
        colors = ga.getColorRefFloat().clone();
        for (int i = 0; i < colors.length; i += 4) {
            colors[i] = color.x;
            colors[i + 1] = color.y;
            colors[i + 2] = color.z;
        }
    }
    ga.setColorRefFloat(colors);
    changed = true;
}

Example 30 with GeometryArray

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

the class ReferenceItemMesh method createGeometry.

@Override
protected GeometryArray createGeometry(float[] coords, GeometryArray sourceGa) {
    final GeometryArray ga = createGeometryArray(sourceGa, GeometryArray.BY_REFERENCE);
    ga.setCoordRefFloat(coords);
    ga.setCapability(GeometryArray.ALLOW_REF_DATA_READ);
    ga.setCapability(GeometryArray.ALLOW_REF_DATA_WRITE);
    // Handle indexed array
    if (isIndexGeometryArray()) {
        final IndexedGeometryArray sourceIga = (IndexedGeometryArray) sourceGa;
        final IndexedGeometryArray iga = (IndexedGeometryArray) ga;
        final int objectIndexCount = sourceIga.getValidIndexCount();
        final int[] objectIndices = new int[objectIndexCount];
        final int[] allIndices = new int[objectIndices.length * points.length];
        sourceIga.getCoordinateIndices(0, objectIndices);
        duplicateIndices(objectIndices, allIndices);
        iga.setCoordinateIndices(0, allIndices);
        // Check if we need the color and normal indices
        if ((vertexFormat & GeometryArray.USE_COORD_INDEX_ONLY) == 0) {
            // Duplicate the other indices
            if (hasNormals()) {
                sourceIga.getNormalIndices(0, objectIndices);
                duplicateIndices(objectIndices, allIndices);
                iga.setNormalIndices(0, allIndices);
            }
            if (hasColor()) {
                sourceIga.getColorIndices(0, objectIndices);
                duplicateIndices(objectIndices, allIndices);
                iga.setColorIndices(0, allIndices);
            }
        }
    }
    // Handle normals
    if (hasNormals()) {
        final float[] objectNormals = new float[vertexCount * 3];
        sourceGa.getNormals(0, objectNormals);
        final float[] allNormals = new float[objectNormals.length * points.length];
        duplicate(objectNormals, 0, objectNormals.length, points.length, allNormals, 0);
        ga.setNormalRefFloat(allNormals);
    }
    // Handle colors
    if (hasColor()) {
        colorUpdater = ArrayColorUpdater.create(vertexCount, hasColor4());
        ga.setColorRefFloat(new float[colorUpdater.size() * size()]);
    }
    return ga;
}