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

Example 16 with FloatProcessor

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

the class PCPALMAnalysis method pad.

/**
	 * Pads the image to the next power of two
	 * 
	 * @param ip
	 * @return padded image
	 */
private FloatProcessor pad(ImageProcessor ip) {
    // Pad to a power of 2
    final int size = FastMath.max(ip.getWidth(), ip.getHeight());
    int newSize = nextPowerOfTwo(size);
    if (size > newSize)
        // Error
        return null;
    FloatProcessor im2 = new FloatProcessor(newSize, newSize);
    // If the binary processor has a min and max this breaks the conversion to float
    // since values are mapped from 0-255 using the min-max look-up calibration table
    ip.resetMinAndMax();
    im2.insert(ip, 0, 0);
    return im2;
}

Example 17 with FloatProcessor

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

the class TraceMolecules method createNNPlot.

private FloatProcessor createNNPlot(List<double[]> results, int w, int h) {
    FloatProcessor fp = new FloatProcessor(w, h);
    // Create lookup table that map the tested threshold values to a position in the image
    int[] xLookup = createLookup(tThresholds, settings.minTimeThreshold, w);
    int[] yLookup = createLookup(dThresholds, settings.minDistanceThreshold, h);
    origX = (settings.minTimeThreshold != 0) ? xLookup[1] : 0;
    origY = (settings.minDistanceThreshold != 0) ? yLookup[1] : 0;
    int gridWidth = tThresholds.length;
    int gridHeight = dThresholds.length;
    for (int y = 0, i = 0; y < gridHeight; y++) {
        for (int x = 0; x < gridWidth; x++, i++) {
            int x1 = xLookup[x];
            int x2 = xLookup[x + 1];
            int y1 = yLookup[y];
            int y2 = yLookup[y + 1];
            double[] result = results.get(i);
            fp.setValue(Math.abs(result[2]));
            fp.setRoi(x1, y1, x2 - x1, y2 - y1);
            fp.fill();
        }
    }
    return fp;
}

Example 18 with FloatProcessor

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

the class PCPALMAnalysis method createWeightImage.

/**
	 * Create a weight image of the same size. All pixels corresponding to the original image area
	 * are set to 1. A window function is optionally applied.
	 * 
	 * @param im
	 * @param applyWindow
	 * @return The weight image
	 */
private ImageProcessor createWeightImage(ImageProcessor im, boolean applyWindow) {
    float[] data = new float[im.getWidth() * im.getHeight()];
    Arrays.fill(data, 1);
    ImageProcessor w = new FloatProcessor(im.getWidth(), im.getHeight(), data, null);
    if (applyWindow) {
        w = applyWindow(w, imageWindow);
    }
    return w;
}

Example 19 with FloatProcessor

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

the class PCPALMAnalysis method computeAutoCorrelationCurveFFT.

/**
	 * Compute the auto-correlation curve using FFT. Computes the correlation image and then samples
	 * the image at radii up to the specified length to get the average correlation at a given
	 * radius.
	 * 
	 * @param im
	 * @param w
	 * @param maxRadius
	 * @param nmPerPixel
	 * @return { distances[], gr[], gr_se[] }
	 */
private double[][] computeAutoCorrelationCurveFFT(ImageProcessor im, ImageProcessor w, int maxRadius, double nmPerPixel, double density) {
    log("Performing FFT correlation");
    FloatProcessor corrIm = computeAutoCorrelationFFT(im);
    FloatProcessor corrW = computeAutoCorrelationFFT(w);
    if (corrIm == null || corrW == null) {
        error("Unable to perform Fourier transform");
        return null;
    }
    final int centre = corrIm.getHeight() / 2;
    Rectangle crop = new Rectangle(centre - maxRadius, centre - maxRadius, maxRadius * 2, maxRadius * 2);
    if (showCorrelationImages) {
        displayCorrelation(corrIm, "Image correlation FFT", crop);
        displayCorrelation(corrW, "Window correlation FFT", crop);
    }
    log("  Normalising correlation");
    FloatProcessor correlation = normaliseCorrelation(corrIm, corrW, density);
    if (showCorrelationImages)
        displayCorrelation(correlation, "Normalised correlation FFT", crop);
    return computeRadialAverage(maxRadius, nmPerPixel, correlation);
}

Example 20 with FloatProcessor

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

the class PCPALMAnalysis method padToFHT2.

/**
	 * Pads the image to the next power of two and transforms into the frequency domain
	 * 
	 * @param ip
	 * @return An FHT2 image in the frequency domain
	 */
private FHT2 padToFHT2(ImageProcessor ip) {
    FloatProcessor im2 = pad(ip);
    if (im2 == null)
        return null;
    FHT2 FHT2 = new FHT2(im2);
    FHT2.setShowProgress(false);
    FHT2.transform();
    return FHT2;
}