Examples with ByteProcessor ij.process.ByteProcessor used on opensource projects

Example 16 with ByteProcessor

use of ij.process.ByteProcessor in project TrakEM2 by trakem2.

the class ExportBestFlatImage method makeFlatFloatGrayImageAndAlpha.

/**
 * While the data is in the 8-bit range, the format is as a FloatProcessor.
 */
public Pair<FloatProcessor, FloatProcessor> makeFlatFloatGrayImageAndAlpha() {
    printInfo();
    if (canUseAWTImage()) {
        // In color to preserve the alpha channel present in mipmaps
        final Image img = createAWTImage(ImagePlus.COLOR_RGB);
        final int width = img.getWidth(null);
        final int height = img.getHeight(null);
        final int[] pixels = new int[width * height];
        PixelGrabber pg = new PixelGrabber(img, 0, 0, width, height, pixels, 0, width);
        try {
            pg.grabPixels();
        } catch (InterruptedException e) {
        }
        ;
        final float[] grey = new float[pixels.length];
        final float[] alpha = new float[pixels.length];
        for (int i = 0; i < pixels.length; ++i) {
            final int p = pixels[i];
            alpha[i] = ((p & 0xff000000) >> 24);
            grey[i] = (((p & 0x00ff0000) >> 16) + ((p & 0x0000ff00) >> 8) + (p & 0x000000ff)) / 3f;
        }
        return new Pair<FloatProcessor, FloatProcessor>(new FloatProcessor(width, height, grey, null), new FloatProcessor(width, height, alpha, null));
    }
    if (!isSmallerThan2GB()) {
        Utils.log("Cannot create an image larger than 2 GB.");
        return null;
    }
    if (loader.isMipMapsRegenerationEnabled()) {
        // Use mipmaps directly: they are already Gaussian-downsampled
        final Pair<ByteProcessor, ByteProcessor> pair = ExportUnsignedByte.makeFlatImageFromMipMaps(patches, finalBox, 0, scale);
        return new Pair<FloatProcessor, FloatProcessor>(pair.a.convertToFloatProcessor(), pair.b.convertToFloatProcessor());
    }
    // Else: no mipmaps
    loader.releaseAll();
    // Use originals and Gaussian-downsample them, then map them onto the target image
    final Pair<ByteProcessor, ByteProcessor> pair = ExportUnsignedByte.makeFlatImageFromOriginals(patches, finalBox, 0, scale);
    return new Pair<FloatProcessor, FloatProcessor>(pair.a.convertToFloatProcessor(), pair.b.convertToFloatProcessor());
}

Example 17 with ByteProcessor

use of ij.process.ByteProcessor in project TrakEM2 by trakem2.

the class TransformMeshMappingWithMasks method map.

public final void map(final ImageProcessorWithMasks source, final ImageProcessorWithMasks target, final int numThreads) {
    target.outside = new ByteProcessor(target.getWidth(), target.getHeight());
    final HashMap<AffineModel2D, ArrayList<PointMatch>> av = transform.getAV();
    if (numThreads > 1) {
        final ArrayList<AffineModel2D> triangles = new ArrayList<AffineModel2D>(av.keySet());
        final AtomicInteger i = new AtomicInteger(0);
        final ArrayList<Thread> threads = new ArrayList<Thread>(numThreads);
        for (int k = 0; k < numThreads; ++k) {
            final Thread mtt = new MapTriangleThread(i, triangles, transform, source, target);
            threads.add(mtt);
            mtt.start();
        }
        for (final Thread mtt : threads) {
            try {
                mtt.join();
            } catch (final InterruptedException e) {
            }
        }
    } else if (source.mask == null) {
        for (final AffineModel2D triangle : av.keySet()) {
            mapTriangle(transform, triangle, source.ip, target.ip, target.outside);
        }
    } else {
        for (final AffineModel2D triangle : av.keySet()) {
            mapTriangle(transform, triangle, source.ip, source.mask, target.ip, target.mask, target.outside);
        }
    }
}

Example 18 with ByteProcessor

use of ij.process.ByteProcessor in project TrakEM2 by trakem2.

the class TransformMeshMappingWithMasks method mapInterpolated.

public final void mapInterpolated(final ImageProcessorWithMasks source, final ImageProcessorWithMasks target, final int numThreads) {
    target.outside = new ByteProcessor(target.getWidth(), target.getHeight());
    source.ip.setInterpolationMethod(ImageProcessor.BILINEAR);
    if (source.mask != null) {
        source.mask.setInterpolationMethod(ImageProcessor.BILINEAR);
    }
    final HashMap<AffineModel2D, ArrayList<PointMatch>> av = transform.getAV();
    if (numThreads > 1) {
        final ArrayList<AffineModel2D> triangles = new ArrayList<AffineModel2D>(av.keySet());
        final AtomicInteger i = new AtomicInteger(0);
        final ArrayList<Thread> threads = new ArrayList<Thread>(numThreads);
        for (int k = 0; k < numThreads; ++k) {
            final Thread mtt = new MapTriangleInterpolatedThread(i, triangles, transform, source, target);
            threads.add(mtt);
            mtt.start();
        }
        for (final Thread mtt : threads) {
            try {
                mtt.join();
            } catch (final InterruptedException e) {
            }
        }
    } else if (source.mask == null) {
        for (final AffineModel2D triangle : av.keySet()) {
            mapTriangleInterpolated(transform, triangle, source.ip, target.ip, target.outside);
        }
    } else {
        for (final AffineModel2D triangle : av.keySet()) {
            mapTriangleInterpolated(transform, triangle, source.ip, source.mask, target.ip, target.mask, target.outside);
        }
    }
}

Example 19 with ByteProcessor

use of ij.process.ByteProcessor in project TrakEM2 by trakem2.

the class Downsampler method downsampleOutside.

/**
 * Downsample and outside mask.  Those pixels not fully covered in the
 * outside mask are set to 0, all others to 255.
 *
 * @param aOutside
 * @return
 */
public static final ByteProcessor downsampleOutside(final ByteProcessor aOutside) {
    final int wa = aOutside.getWidth();
    final int ha = aOutside.getHeight();
    final int wa2 = wa + wa;
    final int wb = wa / 2;
    final int hb = ha / 2;
    final int nb = hb * wb;
    final ByteProcessor bOutside = new ByteProcessor(wb, hb);
    final byte[] aOutsidePixels = (byte[]) aOutside.getPixels();
    final byte[] bOutsidePixels = (byte[]) bOutside.getPixels();
    for (int ya = 0, yb = 0; yb < nb; ya += wa2, yb += wb) {
        final int ya1 = ya + wa;
        for (int xa = 0, xb = 0; xb < wb; xa += 2, ++xb) {
            final int xa1 = xa + 1;
            final int sOutside = andByte(ya + xa, ya + xa1, ya1 + xa, ya1 + xa1, aOutsidePixels);
            if (sOutside == 0xff)
                bOutsidePixels[yb + xb] = -1;
            else
                bOutsidePixels[yb + xb] = 0;
        }
    }
    return bOutside;
}

Example 20 with ByteProcessor

use of ij.process.ByteProcessor in project TrakEM2 by trakem2.

the class DisplayCanvas method paintWithFiltering.

private final void paintWithFiltering(final Graphics2D g, final ArrayList<Displayable> al_paint, final Collection<? extends Paintable> paintables, final int first_non_patch, final int g_width, final int g_height, final Displayable active, final int c_alphas, final Layer layer, final List<Layer> layers, final boolean paint_non_images) {
    // Determine the type of the image: if any Patch is of type COLOR_RGB or COLOR_256, use RGB
    int type = BufferedImage.TYPE_BYTE_GRAY;
    search: for (final Displayable d : al_paint) {
        if (d.getClass() == Patch.class) {
            switch(((Patch) d).getType()) {
                case ImagePlus.COLOR_256:
                case ImagePlus.COLOR_RGB:
                    type = BufferedImage.TYPE_INT_ARGB;
                    break search;
            }
        }
    }
    // Paint all patches to an image
    final BufferedImage bi = new BufferedImage(g_width, g_height, type);
    final Graphics2D gpre = bi.createGraphics();
    gpre.setTransform(atc);
    int i = 0;
    for (final Paintable p : paintables) {
        if (i == first_non_patch)
            break;
        p.paint(gpre, srcRect, magnification, p == active, c_alphas, layer, layers);
        i++;
    }
    gpre.dispose();
    final ImagePlus imp = new ImagePlus("filtered", type == BufferedImage.TYPE_BYTE_GRAY ? new ByteProcessor(bi) : new ColorProcessor(bi));
    bi.flush();
    display.applyFilters(imp);
    // Paint the filtered image
    final AffineTransform aff = g.getTransform();
    // reset
    g.setTransform(new AffineTransform());
    g.drawImage(imp.getProcessor().createImage(), 0, 0, null);
    // Paint the remaining elements if any
    if (paint_non_images && first_non_patch != paintables.size()) {
        // restore srcRect and magnification
        g.setTransform(aff);
        // to smooth edges of the images
        g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
        g.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
        g.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
        i = 0;
        for (final Paintable p : paintables) {
            if (i < first_non_patch) {
                i++;
                continue;
            }
            p.paint(g, srcRect, magnification, p == active, c_alphas, layer, layers);
            i++;
        }
    }
}