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

Example 11 with ImageProcessor

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

the class ImageBackground method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
	 */
public void run(ImageProcessor ip) {
    ImageProcessor median = getProjection();
    //Utils.display("Median", median);
    ImageProcessor background = applyBlur(median);
    subtractBias(background);
    Utils.display("Background", background);
    // Q. Is there a better way to do the thresholding for foreground pixels. 
    // Ideally we want to outline cell shapes. 
    ImageProcessor mask = median.convertToByte(true);
    mask.autoThreshold();
    Utils.display("Mask", mask);
}

Example 12 with ImageProcessor

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

the class ImageBackground method getProjection.

private ImageProcessor getProjection() {
    // Get median intensity projection
    ZProjector p = new ZProjector(imp);
    p.setMethod(ZProjector.MEDIAN_METHOD);
    p.doProjection();
    ImageProcessor median = p.getProjection().getProcessor();
    return median;
}

Example 13 with ImageProcessor

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

the class BinaryDisplay method setup.

/* (non-Javadoc)
	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
	 */
public int setup(String arg, ImagePlus imp) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (imp == null)
        return DONE;
    if (arg.equals("reset")) {
        ImageProcessor ip = imp.getProcessor();
        ip.reset();
        imp.setProcessor(ip);
        imp.resetDisplayRange();
        imp.updateAndDraw();
        return DONE;
    }
    this.imp = imp;
    return DOES_ALL;
}

Example 14 with ImageProcessor

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

the class PCPALMAnalysis method analyse.

/**
	 * Perform the PC Analysis
	 * 
	 * @param molecules
	 */
private void analyse(ArrayList<Molecule> molecules) {
    // Check if the plots are currently shown
    String spatialPlotTitle = TITLE + " molecules/um^2";
    String frequencyDomainTitle = TITLE + " g(r)";
    boolean noPlots;
    String topPlotTitle;
    long start = System.nanoTime();
    if (spatialDomain) {
        // -----------------
        // Analysis in the spatial domain
        // -----------------
        log("---");
        log("Spatial domain analysis");
        log("Computing density histogram");
        // Compute all-vs-all distance matrix.
        // Create histogram of distances at different radii.
        final int nBins = (int) (correlationDistance / correlationInterval) + 1;
        final double maxDistance2 = correlationDistance * correlationDistance;
        int[] H = new int[nBins];
        // TODO - Update this using a grid with a resolution of maxDistance to increase speed
        // by only comparing to neighbours within range.
        // An all-vs-all analysis does not account for a border. 
        // A simple solution is to only process molecules within the border but compare them 
        // to all molecules within the region. Thus every molecule has a complete circle of the max 
        // radius around them to use:
        // ----------------------
        // |                    |
        // |   --------------   |
        // |   |  Within    |   |
        // |   |  Border    |   |
        // |   |            |   |
        // |   --------------   |
        // |      Region        |
        // ----------------------
        // If the fraction of points within the correlation distance of the edge is low then this 
        // will not make much difference. 
        final double boundaryMinx = (useBorder) ? minx + correlationDistance : minx;
        final double boundaryMaxx = (useBorder) ? maxx - correlationDistance : maxx;
        final double boundaryMiny = (useBorder) ? miny + correlationDistance : miny;
        final double boundaryMaxy = (useBorder) ? maxy - correlationDistance : maxy;
        int N = 0;
        if (boundaryMaxx <= boundaryMinx || boundaryMaxy <= boundaryMiny) {
            log("ERROR: 'Use border' option of %s nm is not possible: Width = %s nm, Height = %s nm", Utils.rounded(correlationDistance, 4), Utils.rounded(maxx - minx, 3), Utils.rounded(maxy - miny, 3));
            return;
        } else {
            for (int i = molecules.size(); i-- > 0; ) {
                final Molecule m = molecules.get(i);
                // Optionally ignore molecules that are near the edge of the boundary
                if (useBorder && (m.x < boundaryMinx || m.x > boundaryMaxx || m.y < boundaryMiny || m.y > boundaryMaxy))
                    continue;
                N++;
                for (int j = molecules.size(); j-- > 0; ) {
                    if (i == j)
                        continue;
                    double d = m.distance2(molecules.get(j));
                    if (d < maxDistance2) {
                        H[(int) (Math.sqrt(d) / correlationInterval)]++;
                    }
                }
            }
        }
        double[] r = new double[nBins + 1];
        for (int i = 0; i <= nBins; i++) r[i] = i * correlationInterval;
        double[] pcf = new double[nBins];
        if (N > 0) {
            // Note: Convert nm^2 to um^2
            final double N_pi = N * Math.PI / 1000000.0;
            for (int i = 0; i < nBins; i++) {
                // Pair-correlation is the count at the given distance divided by N and the area at distance ri:
                // H(r_i) / (N x (pi x (r_i+1)^2 - pi x r_i^2))
                pcf[i] = H[i] / (N_pi * (r[i + 1] * r[i + 1] - r[i] * r[i]));
            }
        }
        // The final bin may be empty if the correlation interval was a factor of the correlation distance
        if (pcf[pcf.length - 1] == 0) {
            r = Arrays.copyOf(r, nBins - 1);
            pcf = Arrays.copyOf(pcf, nBins - 1);
        } else {
            r = Arrays.copyOf(r, nBins);
        }
        double[][] gr = new double[][] { r, pcf, null };
        CorrelationResult result = new CorrelationResult(results.size() + 1, PCPALMMolecules.results.getSource(), boundaryMinx, boundaryMiny, boundaryMaxx, boundaryMaxy, N, correlationInterval, 0, false, gr, true);
        results.add(result);
        noPlots = WindowManager.getFrame(spatialPlotTitle) == null;
        topPlotTitle = frequencyDomainTitle;
        plotCorrelation(gr, 0, spatialPlotTitle, "molecules/um^2", true, false);
    } else {
        // -----------------
        // Image correlation in the Frequency Domain
        // -----------------
        log("Frequency domain analysis");
        // Create a binary image for the molecules
        ImageProcessor im = PCPALMMolecules.drawImage(molecules, minx, miny, maxx, maxy, nmPerPixel, true, binaryImage);
        log("Image scale = %.2f nm/pixel : %d x %d pixels", nmPerPixel, im.getWidth(), im.getHeight());
        // Apply a window function to the image to reduce FFT edge artifacts.
        if (applyWindow) {
            im = applyWindow(im, imageWindow);
        }
        if (showHighResolutionImage) {
            PCPALMMolecules.displayImage(PCPALMMolecules.results.getName() + " " + ((binaryImage) ? "Binary" : "Count") + " Image (high res)", im, nmPerPixel);
        }
        // Create weight image (including windowing)
        ImageProcessor w = createWeightImage(im, applyWindow);
        // Store the area of the image in um^2
        weightedAreaInPx = areaInPx = im.getWidth() * im.getHeight();
        if (applyWindow) {
            weightedAreaInPx *= w.getStatistics().mean;
        }
        area = areaInPx * nmPerPixel * nmPerPixel / 1e6;
        weightedArea = weightedAreaInPx * nmPerPixel * nmPerPixel / 1e6;
        noOfMolecules = molecules.size();
        // Pad the images to the largest scale being investigated by the correlation function.
        // Original Sengupta paper uses 800nm for the padding size.
        // Limit to within 80% of the minimum dimension of the image.
        double maxRadius = correlationDistance / nmPerPixel;
        int imageSize = FastMath.min(im.getWidth(), im.getHeight());
        if (imageSize < 1.25 * maxRadius)
            maxRadius = imageSize / 1.25;
        int pad = (int) Math.round(maxRadius);
        log("Analysing up to %.0f nm = %d pixels", maxRadius * nmPerPixel, pad);
        im = padImage(im, pad);
        w = padImage(w, pad);
        //		// Used for debugging
        //		{
        //			ImageProcessor w2 = w.duplicate();
        //			w2.setMinAndMax(0, 1);
        //			PCPALMMolecules.displayImage(PCPALMMolecules.results.getName() + " Binary Image Mask", w2, nmPerPixel);
        //		}
        final double peakDensity = getDensity(im);
        // Create 2D auto-correlation
        double[][] gr;
        try {
            // Use the FFT library as it is multi-threaded. This may not be in the user's path.
            gr = computeAutoCorrelationCurveFFT(im, w, pad, nmPerPixel, peakDensity);
        } catch (Exception e) {
            // Default to the ImageJ built-in FHT
            gr = computeAutoCorrelationCurveFHT(im, w, pad, nmPerPixel, peakDensity);
        }
        if (gr == null)
            return;
        // Add the g(r) curve to the results
        addResult(peakDensity, gr);
        noPlots = WindowManager.getFrame(frequencyDomainTitle) == null;
        topPlotTitle = spatialPlotTitle;
        // Do not plot r=0 value on the curve
        plotCorrelation(gr, 1, frequencyDomainTitle, "g(r)", false, showErrorBars);
    }
    if (noPlots) {
        // Position the plot underneath the other one
        Frame f1 = WindowManager.getFrame(topPlotTitle);
        if (f1 != null) {
            String bottomPlotTitle = (topPlotTitle.equals(spatialPlotTitle) ? frequencyDomainTitle : spatialPlotTitle);
            Frame f2 = WindowManager.getFrame(bottomPlotTitle);
            if (f2 != null)
                f2.setLocation(f2.getLocation().x, f2.getLocation().y + f1.getHeight());
        }
    }
    log("%s domain analysis computed in %s ms", (spatialDomain) ? "Spatial" : "Frequency", Utils.rounded((System.nanoTime() - start) * 1e-6, 4));
    log("---");
}

Example 15 with ImageProcessor

use of ij.process.ImageProcessor 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;
}