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

Example 1 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class ImageConverter method getDoubleData.

/**
	 * Get the data from the image as a double array (include cropping to the ROI). Data is duplicated if the
	 * input already a double array.
	 * <p>
	 * Allows reuse of an existing buffer if provided. This will not be truncated if it is larger than the
	 * ImageProcessor ROI bounds. If smaller then a new buffer will be created.
	 * 
	 * @param oPixels
	 * @param width
	 * @param height
	 * @param bounds
	 * @param buffer
	 * @return The double array data
	 */
public static double[] getDoubleData(final Object oPixels, final int width, final int height, final Rectangle bounds, double[] buffer) {
    if (oPixels == null)
        return null;
    if (oPixels instanceof float[]) {
        float[] pixels = (float[]) oPixels;
        if (bounds != null && (bounds.x != 0 || bounds.y != 0 || bounds.width != width || bounds.height != height)) {
            double[] pixels2 = allocate(buffer, bounds.width * bounds.height);
            for (int ys = bounds.y; ys < bounds.y + bounds.height; ys++) {
                int offset1 = (ys - bounds.y) * bounds.width;
                int offset2 = ys * width + bounds.x;
                for (int xs = 0; xs < bounds.width; xs++) pixels2[offset1++] = pixels[offset2++];
            }
            return pixels2;
        } else {
            double[] pixels2 = allocate(buffer, pixels.length);
            for (int i = 0; i < pixels.length; i++) pixels2[i] = pixels[i];
            return pixels2;
        }
    } else if (oPixels instanceof short[]) {
        short[] pixels = (short[]) oPixels;
        if (bounds != null && (bounds.x != 0 || bounds.y != 0 || bounds.width != width || bounds.height != height)) {
            double[] pixels2 = allocate(buffer, bounds.width * bounds.height);
            for (int ys = bounds.y; ys < bounds.y + bounds.height; ys++) {
                int offset1 = (ys - bounds.y) * bounds.width;
                int offset2 = ys * width + bounds.x;
                for (int xs = 0; xs < bounds.width; xs++) pixels2[offset1++] = pixels[offset2++] & 0xffff;
            }
            return pixels2;
        } else {
            double[] pixels2 = allocate(buffer, pixels.length);
            for (int i = 0; i < pixels.length; i++) pixels2[i] = pixels[i] & 0xffff;
            return pixels2;
        }
    } else if (oPixels instanceof byte[]) {
        byte[] pixels = (byte[]) oPixels;
        if (bounds != null && (bounds.x != 0 || bounds.y != 0 || bounds.width != width || bounds.height != height)) {
            double[] pixels2 = allocate(buffer, bounds.width * bounds.height);
            for (int ys = bounds.y; ys < bounds.y + bounds.height; ys++) {
                int offset1 = (ys - bounds.y) * bounds.width;
                int offset2 = ys * width + bounds.x;
                for (int xs = 0; xs < bounds.width; xs++) pixels2[offset1++] = pixels[offset2++] & 0xff;
            }
            return pixels2;
        } else {
            double[] pixels2 = allocate(buffer, pixels.length);
            for (int i = 0; i < pixels.length; i++) pixels2[i] = pixels[i] & 0xff;
            return pixels2;
        }
    } else if (oPixels instanceof int[]) {
        // The default processing
        ImageProcessor ip = new ColorProcessor(width, height, (int[]) oPixels);
        ip.setRoi(bounds);
        FloatProcessor fp = ip.crop().toFloat(0, null);
        return (double[]) fp.getPixels();
    }
    return null;
}

Example 2 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class DriftCalculator method calculateDriftUsingFrames.

/**
	 * Calculate the drift by aligning N consecutive frames with the overall image. Update the current drift parameters.
	 * 
	 * @param blocks
	 * @param blockT
	 * @param bounds
	 * @param scale
	 * @param dx
	 * @param dy
	 * @param smoothing
	 * @param iterations
	 * @return
	 */
private double calculateDriftUsingFrames(ArrayList<ArrayList<Localisation>> blocks, int[] blockT, Rectangle bounds, float scale, double[] dx, double[] dy, double[] originalDriftTimePoints, double smoothing, int iterations) {
    // Construct images using the current drift
    tracker.status("Constructing images");
    // Built an image for each block of results.
    final ImageProcessor[] images = new ImageProcessor[blocks.size()];
    List<Future<?>> futures = new LinkedList<Future<?>>();
    progressCounter = 0;
    totalCounter = images.length * 2;
    for (int i = 0; i < images.length; i++) {
        futures.add(threadPool.submit(new ImageBuilder(blocks.get(i), images, i, bounds, scale, dx, dy)));
    }
    Utils.waitForCompletion(futures);
    for (int i = 0; i < blocks.size(); i++) {
        tracker.progress(i, blocks.size());
        IJImagePeakResults blockImage = newImage(bounds, scale);
        for (Localisation r : blocks.get(i)) {
            blockImage.add(r.t, (float) (r.x + dx[r.t]), (float) (r.y + dy[r.t]), r.s);
        }
        images[i] = getImage(blockImage);
    }
    // Build an image with all results.
    FloatProcessor allIp = new FloatProcessor(images[0].getWidth(), images[0].getHeight());
    for (ImageProcessor ip : images) allIp.copyBits(ip, 0, 0, Blitter.ADD);
    return calculateDrift(blockT, scale, dx, dy, originalDriftTimePoints, smoothing, iterations, images, allIp, true);
}

Example 3 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method canInterpolateUpInXY.

@Test
public void canInterpolateUpInXY() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 1.75f, 1.75f, 1);
    fp.putPixelValue(1, 1, 0.75f * 0.75f);
    fp.putPixelValue(2, 1, 0.75f * 0.25f);
    fp.putPixelValue(1, 2, 0.75f * 0.25f);
    fp.putPixelValue(2, 2, 0.25f * 0.25f);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}

Example 4 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method canInterpolateInMiddleOfPixel.

@Test
public void canInterpolateInMiddleOfPixel() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 1.5f, 1.5f, 1);
    fp.putPixelValue(1, 1, 1);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}

Example 5 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method canInterpolateDownInXY.

@Test
public void canInterpolateDownInXY() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 1.25f, 1.25f, 1);
    fp.putPixelValue(0, 0, 0.25f * 0.25f);
    fp.putPixelValue(0, 1, 0.75f * 0.25f);
    fp.putPixelValue(1, 0, 0.75f * 0.25f);
    fp.putPixelValue(1, 1, 0.75f * 0.75f);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}