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

Example 71 with ByteProcessor

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

the class Patch method addAlphaMaskLocal.

/**
 * Add the given area, in local coordinates, to the alpha mask, using the given fill value.
 */
public void addAlphaMaskLocal(final Area aLocal, int value) {
    if (value < 0)
        value = 0;
    if (value > 255)
        value = 255;
    // 
    CoordinateTransform ct = null;
    if (hasCoordinateTransform() && null == (ct = getCT())) {
        return;
    }
    // When the area is larger than the image, sometimes the area fails to be set at all
    // Also, intersection accelerates calls to contains(x,y) for complex polygons
    final Area a = new Area(new Rectangle(0, 0, (int) (width + 1), (int) (height + 1)));
    a.intersect(aLocal);
    if (M.isEmpty(a)) {
        Utils.log("ROI does not intersect the active image!");
        return;
    }
    ByteProcessor mask = getAlphaMask();
    // Use imglib to bypass all the problems with ShapeROI
    // Create a Shape image with background and the Area on it with 'value'
    final int background = (null != mask && 255 == value) ? 0 : 255;
    final ShapeList<UnsignedByteType> shapeList = new ShapeList<UnsignedByteType>(new int[] { (int) width, (int) height, 1 }, new UnsignedByteType(background));
    shapeList.addShape(a, new UnsignedByteType(value), new int[] { 0 });
    final mpicbg.imglib.image.Image<UnsignedByteType> shapeListImage = new mpicbg.imglib.image.Image<UnsignedByteType>(shapeList, shapeList.getBackground(), "mask");
    ByteProcessor rmask = (ByteProcessor) ImageJFunctions.copyToImagePlus(shapeListImage, ImagePlus.GRAY8).getProcessor();
    if (hasCoordinateTransform()) {
        // inverse the coordinate transform
        final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
        final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
        rmask = (ByteProcessor) mapping.createInverseMappedImageInterpolated(rmask);
    }
    if (null == mask) {
        // There wasn't a mask, hence just set it
        mask = rmask;
    } else {
        final byte[] b1 = (byte[]) mask.getPixels();
        final byte[] b2 = (byte[]) rmask.getPixels();
        // Whatever is not background in the new mask gets set on the old mask
        for (int i = 0; i < b1.length; i++) {
            // background pixel in new mask
            if (background == (b2[i] & 0xff))
                continue;
            // replace old pixel with new pixel
            b1[i] = b2[i];
        }
    }
    setAlphaMask(mask);
}

Example 72 with ByteProcessor

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

the class Patch method getAlphaMask.

/**
 * Return a new {@link ByteProcessor} representing the alpha mask, if any, over the pixel data.
 * @return null if there isn't one, or if the mask image could not be loaded.
 */
public synchronized ByteProcessor getAlphaMask() {
    if (0 == alpha_mask_id)
        return null;
    final String path = createAlphaMaskFilePath(alpha_mask_id);
    // Expects a zip file containing one single TIFF file entry
    ZipInputStream zis = null;
    try {
        zis = new ZipInputStream(new FileInputStream(path));
        // prepares the entry for reading
        final ZipEntry ze = zis.getNextEntry();
        // Assume the first entry is the mask
        final ImageProcessor mask = new FileOpener(new TiffDecoder(zis, ze.getName()).getTiffInfo()[0]).open(false).getProcessor();
        if (mask.getWidth() != o_width || mask.getHeight() != o_height) {
            Utils.log2("Mask has improper dimensions: " + mask.getWidth() + " x " + mask.getHeight() + " for patch #" + this.id + " which is of " + o_width + " x " + o_height);
            return null;
        }
        return (ByteProcessor) (mask.getClass() == ByteProcessor.class ? mask : mask.convertToByte(false));
    } catch (final Throwable t) {
        Utils.log2("Could not load alpha mask for patch #" + this.id + " from file " + path);
        IJError.print(t);
        return null;
    } finally {
        try {
            if (null != zis)
                zis.close();
        } catch (final Exception e) {
            IJError.print(e);
        }
    }
}

Example 73 with ByteProcessor

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

the class Blending method setBlendingMask.

/**
 * Returns true if a new mask has been set to Patch p.
 */
private static boolean setBlendingMask(final Patch p, Set<Patch> overlapping, final Map<Patch, TransformMesh> meshes, final boolean respect_current_mask) {
    Utils.log2("Blending " + p);
    if (overlapping.contains(p)) {
        overlapping = new HashSet<Patch>(overlapping);
        overlapping.remove(p);
    }
    final AffineTransform at = p.getAffineTransform();
    final TransformMesh mesh = meshes.get(p);
    ByteProcessor mask = null;
    if (respect_current_mask) {
        mask = p.getAlphaMask();
    }
    if (null == mask) {
        mask = new ByteProcessor(p.getOWidth(), p.getOHeight());
        mask.setValue(255);
        mask.fill();
    }
    final byte[] pix = (byte[]) mask.getPixels();
    final Point2D.Double po = new Point2D.Double();
    final double[] fo = new double[2];
    final int p_o_width = p.getOWidth();
    final int p_o_height = p.getOHeight();
    int next = 0;
    // the self as well
    final double[] weights = new double[overlapping.size() + 1];
    int masked = 0;
    for (int y = 0; y < p_o_height; y++) {
        if (Thread.currentThread().isInterrupted())
            return false;
        for (int x = 0; x < p_o_width; x++) {
            // transform x,y to world coords
            if (null != mesh) {
                fo[0] = x;
                fo[1] = y;
                mesh.applyInPlace(fo);
                po.x = fo[0];
                po.y = fo[1];
            } else {
                po.x = x;
                po.y = y;
            }
            at.transform(po, po);
            fo[0] = po.x;
            fo[1] = po.y;
            // debug:
            if (0 == x && 0 == y) {
                Utils.log2("point 0,0 goes to " + fo[0] + ", " + fo[1]);
            }
            // check if it intersects any Patch
            next = 0;
            for (final Patch other : overlapping) {
                final double weight = intersects(fo, other, meshes.get(other));
                if (weight > 0)
                    weights[next++] = weight;
            }
            final int i = y * p_o_width + x;
            if (respect_current_mask) {
                // Don't compute if no overlap or if current mask value is zero
                if (next > 0 && pix[i] != 0) {
                    // the weight of Patch p, added last
                    weights[next++] = computeWeight(x, y, p_o_width, p_o_height);
                    double sum = 0;
                    for (int f = 0; f < next; f++) sum += weights[f];
                    pix[i] = (byte) ((int) (255 * (weights[next - 1] / sum) * ((pix[i] & 0xff) / 255.0f)));
                    masked++;
                }
            // else leave current value untouched
            } else if (next > 0) {
                // Overwritting current mask
                // the weight of Patch p, added last
                weights[next++] = computeWeight(x, y, p_o_width, p_o_height);
                double sum = 0;
                for (int f = 0; f < next; f++) sum += weights[f];
                pix[i] = (byte) ((int) (255 * (weights[next - 1] / sum)));
                masked++;
            }
        }
    }
    Utils.log2("Masked = " + masked + " for " + p);
    if (masked > 0) {
        p.setAlphaMask(mask);
        return true;
    }
    Utils.log("Nothing to blend in image " + p);
    return false;
}

Example 74 with ByteProcessor

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

the class Utils method fireLUT.

/**
 * Returns a byte[3][256] containing the colors of the fire LUT.
 */
public static final IndexColorModel fireLUT() {
    final ImagePlus imp = new ImagePlus("fire", new ByteProcessor(1, 1));
    IJ.run(imp, "Fire", "");
    return (IndexColorModel) imp.getProcessor().getColorModel();
}

Example 75 with ByteProcessor

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

the class NonLinearTransform method visualize.

// FIXME this takes way too much memory
public void visualize() {
    final int density = Math.max(width, height) / 32;
    final int border = Math.max(width, height) / 8;
    final double[][] orig = new double[width * height][2];
    final double[][] trans = new double[height * width][2];
    final double[][] gridOrigVert = new double[width * height][2];
    final double[][] gridTransVert = new double[width * height][2];
    final double[][] gridOrigHor = new double[width * height][2];
    final double[][] gridTransHor = new double[width * height][2];
    final FloatProcessor magnitude = new FloatProcessor(width, height);
    final FloatProcessor angle = new FloatProcessor(width, height);
    final ColorProcessor quiver = new ColorProcessor(width, height);
    final ByteProcessor empty = new ByteProcessor(width + 2 * border, height + 2 * border);
    quiver.setLineWidth(1);
    quiver.setColor(Color.green);
    final GeneralPath quiverField = new GeneralPath();
    float minM = 1000, maxM = 0;
    float minArc = 5, maxArc = -6;
    int countVert = 0, countHor = 0, countHorWhole = 0;
    for (int i = 0; i < width; i++) {
        countHor = 0;
        for (int j = 0; j < height; j++) {
            final double[] position = { (double) i, (double) j };
            final double[] posExpanded = kernelExpand(position);
            final double[] newPosition = multiply(beta, posExpanded);
            orig[i * j][0] = position[0];
            orig[i * j][1] = position[1];
            trans[i * j][0] = newPosition[0];
            trans[i * j][1] = newPosition[1];
            double m = (position[0] - newPosition[0]) * (position[0] - newPosition[0]);
            m += (position[1] - newPosition[1]) * (position[1] - newPosition[1]);
            m = Math.sqrt(m);
            magnitude.setf(i, j, (float) m);
            minM = Math.min(minM, (float) m);
            maxM = Math.max(maxM, (float) m);
            final double a = Math.atan2(position[0] - newPosition[0], position[1] - newPosition[1]);
            minArc = Math.min(minArc, (float) a);
            maxArc = Math.max(maxArc, (float) a);
            angle.setf(i, j, (float) a);
            if (i % density == 0 && j % density == 0)
                drawQuiverField(quiverField, position[0], position[1], newPosition[0], newPosition[1]);
            if (i % density == 0) {
                gridOrigVert[countVert][0] = position[0] + border;
                gridOrigVert[countVert][1] = position[1] + border;
                gridTransVert[countVert][0] = newPosition[0] + border;
                gridTransVert[countVert][1] = newPosition[1] + border;
                countVert++;
            }
            if (j % density == 0) {
                gridOrigHor[countHor * width + i][0] = position[0] + border;
                gridOrigHor[countHor * width + i][1] = position[1] + border;
                gridTransHor[countHor * width + i][0] = newPosition[0] + border;
                gridTransHor[countHor * width + i][1] = newPosition[1] + border;
                countHor++;
                countHorWhole++;
            }
        }
    }
    magnitude.setMinAndMax(minM, maxM);
    angle.setMinAndMax(minArc, maxArc);
    // System.out.println(" " + minArc + " " + maxArc);
    final ImagePlus magImg = new ImagePlus("Magnitude of Distortion Field", magnitude);
    magImg.show();
    // ImagePlus angleImg = new ImagePlus("Angle of Distortion Field Vectors", angle);
    // angleImg.show();
    final ImagePlus quiverImg = new ImagePlus("Quiver Plot of Distortion Field", magnitude);
    quiverImg.show();
    quiverImg.getCanvas().setDisplayList(quiverField, Color.green, null);
    quiverImg.updateAndDraw();
    // GeneralPath gridOrig = new GeneralPath();
    // drawGrid(gridOrig, gridOrigVert, countVert, height);
    // drawGrid(gridOrig, gridOrigHor, countHorWhole, width);
    // ImagePlus gridImgOrig = new ImagePlus("Distortion Grid", empty);
    // gridImgOrig.show();
    // gridImgOrig.getCanvas().setDisplayList(gridOrig, Color.green, null );
    // gridImgOrig.updateAndDraw();
    final GeneralPath gridTrans = new GeneralPath();
    drawGrid(gridTrans, gridTransVert, countVert, height);
    drawGrid(gridTrans, gridTransHor, countHorWhole, width);
    final ImagePlus gridImgTrans = new ImagePlus("Distortion Grid", empty);
    gridImgTrans.show();
    gridImgTrans.getCanvas().setDisplayList(gridTrans, Color.green, null);
    gridImgTrans.updateAndDraw();
    // new FileSaver(quiverImg.getCanvas().imp).saveAsTiff("QuiverCanvas.tif");
    new FileSaver(quiverImg).saveAsTiff("QuiverImPs.tif");
    System.out.println("FINISHED");
}