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

Example 31 with ImageProcessor

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

the class YeastMask method createMask.

private void createMask() {
    // Create the dimensions
    final int hw = (int) Math.ceil(radius * 1000 / nmPerPixel);
    final int hd = (int) Math.ceil(radius * 1000 / nmPerSlice);
    final int width = 2 * hw + 1;
    final int depth = 2 * hd + 1;
    ImageStack stack = createHemiSphere(width, depth);
    // Extend the centre circle of the sphere into a tube of the required length
    final int h = (int) Math.ceil(length * 1000 / nmPerPixel);
    if (h > 0) {
        ImageStack newStack = new ImageStack(width, stack.getHeight() + h, stack.getSize());
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            byte[] pixels = (byte[]) stack.getPixels(slice);
            byte[] newPixels = new byte[width * newStack.getHeight()];
            newStack.setPixels(newPixels, slice);
            System.arraycopy(pixels, 0, newPixels, 0, pixels.length);
            // Get the final strip to be extended
            final int offset = pixels.length - width;
            int target = pixels.length;
            for (int i = 0; i < h; i++) {
                System.arraycopy(pixels, offset, newPixels, target, width);
                target += width;
            }
        }
        stack = newStack;
    }
    // Copy the hemi-sphere onto the end
    ImageStack newStack = new ImageStack(width, stack.getHeight() + hw, stack.getSize());
    for (int slice = 1; slice <= stack.getSize(); slice++) {
        byte[] pixels = (byte[]) stack.getPixels(slice);
        byte[] newPixels = new byte[width * newStack.getHeight()];
        newStack.setPixels(newPixels, slice);
        System.arraycopy(pixels, 0, newPixels, 0, pixels.length);
        // Copy the hemi-sphere
        int source = 0;
        int target = newPixels.length - width;
        for (int i = 0; i < hw; i++) {
            System.arraycopy(pixels, source, newPixels, target, width);
            target -= width;
            source += width;
        }
    }
    stack = newStack;
    if (excludeNucleus) {
        ImageStack stack2 = createNucleusSphere(width, depth);
        int xloc = (stack.getWidth() - stack2.getWidth()) / 2;
        int yloc = (stack.getHeight() - stack2.getHeight()) / 2;
        int offset = (stack.getSize() - stack2.getSize()) / 2;
        for (int slice = 1; slice <= stack2.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice + offset);
            ImageProcessor ip2 = stack2.getProcessor(slice);
            ip.copyBits(ip2, xloc, yloc, Blitter.SUBTRACT);
        }
    }
    if (squareOutput && stack.getWidth() != stack.getHeight()) {
        ImageStack stack2 = new ImageStack(stack.getHeight(), stack.getHeight());
        int end = stack.getHeight() - stack.getWidth();
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice);
            ImageProcessor ip2 = new ByteProcessor(stack2.getWidth(), stack2.getHeight());
            stack2.addSlice(ip2);
            for (int xloc = 0; xloc <= end; xloc += stack.getWidth()) {
                ip2.insert(ip, xloc, 0);
            }
        }
        stack = stack2;
    }
    if (border > 0) {
        ImageStack stack2 = new ImageStack(stack.getWidth() + 2 * border, stack.getHeight() + 2 * border);
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice);
            ImageProcessor ip2 = new ByteProcessor(stack2.getWidth(), stack2.getHeight());
            stack2.addSlice(ip2);
            ip2.insert(ip, border, border);
        }
        stack = stack2;
    }
    ImagePlus imp;
    if (is2D) {
        // TODO - Remove this laziness since we should really just do a 2D image
        int centre = stack.getSize() / 2;
        imp = Utils.display(TITLE, stack.getProcessor(centre));
    } else {
        imp = Utils.display(TITLE, stack);
    }
    // Calibrate
    Calibration cal = new Calibration();
    cal.setUnit("um");
    cal.pixelWidth = cal.pixelHeight = nmPerPixel / 1000;
    cal.pixelDepth = nmPerSlice / 1000;
    imp.setCalibration(cal);
}

Example 32 with ImageProcessor

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

the class PCPALMAnalysis method displayCorrelation.

private void displayCorrelation(FloatProcessor correlation, String title, Rectangle crop) {
    correlation.setRoi(crop);
    ImageProcessor ip = correlation.crop();
    ip.resetMinAndMax();
    Utils.display(title, ip);
}

Example 33 with ImageProcessor

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

the class PCPALMAnalysis method padImage.

/**
	 * Pad the image by the specified number of pixels
	 * 
	 * @param im
	 * @param pad
	 * @return
	 */
private ImageProcessor padImage(ImageProcessor im, int pad) {
    // int newW = pad * 2 + im.getWidth();
    // int newH = pad * 2 + im.getHeight();
    int newW = pad + im.getWidth();
    int newH = pad + im.getHeight();
    ImageProcessor im2 = im.createProcessor(newW, newH);
    // im2.insert(im, pad, pad);
    im2.insert(im, 0, 0);
    return im2;
}