Examples with PeakResult gdsc.smlm.results.PeakResult used on opensource projects

Example 86 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class SplitResults method splitResults.

private void splitResults(MemoryPeakResults results, ImageProcessor ip) {
    IJ.showStatus("Splitting " + Utils.pleural(results.size(), "result"));
    // Create an object mask
    ObjectAnalyzer objectAnalyzer = new ObjectAnalyzer(ip, false);
    final int maxx = ip.getWidth();
    final int maxy = ip.getHeight();
    final float scaleX = (float) results.getBounds().width / maxx;
    final float scaleY = (float) results.getBounds().height / maxy;
    // Create a results set for each object
    final int maxObject = objectAnalyzer.getMaxObject();
    MemoryPeakResults[] resultsSet = new MemoryPeakResults[maxObject + 1];
    for (int object = 0; object <= maxObject; object++) {
        MemoryPeakResults newResults = new MemoryPeakResults();
        newResults.copySettings(results);
        newResults.setName(results.getName() + " " + object);
        resultsSet[object] = newResults;
    }
    final int[] mask = objectAnalyzer.getObjectMask();
    if (showObjectMask) {
        ImageProcessor objectIp = (maxObject <= 255) ? new ByteProcessor(maxx, maxy) : new ShortProcessor(maxx, maxy);
        for (int i = 0; i < mask.length; i++) objectIp.set(i, mask[i]);
        ImagePlus imp = Utils.display(objectMask + " Objects", objectIp);
        imp.setDisplayRange(0, maxObject);
        imp.updateAndDraw();
    }
    // Process the results mapping them to their objects
    int i = 0;
    final int size = results.size();
    final int step = Utils.getProgressInterval(size);
    for (PeakResult result : results.getResults()) {
        if (++i % step == 0)
            IJ.showProgress(i, size);
        // Map to the mask objects
        final int object;
        int x = (int) (result.getXPosition() / scaleX);
        int y = (int) (result.getYPosition() / scaleY);
        if (x < 0 || x >= maxx || y < 0 || y >= maxy) {
            object = 0;
        } else {
            final int index = y * maxx + x;
            if (index < 0 || index >= mask.length)
                object = 0;
            else
                object = mask[index];
        }
        resultsSet[object].add(result);
    }
    IJ.showProgress(1);
    // Add the new results sets to memory
    i = 0;
    for (int object = (nonMaskDataset) ? 0 : 1; object <= maxObject; object++) {
        if (!resultsSet[object].isEmpty()) {
            MemoryPeakResults.addResults(resultsSet[object]);
            i++;
        }
    }
    IJ.showStatus("Split " + Utils.pleural(results.size(), "result") + " into " + Utils.pleural(i, "set"));
}

Example 87 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class TraceMolecules method buildCombinedImage.

private float[] buildCombinedImage(ImageSource source, Trace trace, float fitWidth, Rectangle bounds, double[] combinedNoise, boolean createStack) {
    final int w = source.getWidth();
    final int h = source.getHeight();
    // Get the coordinates and the spot bounds
    float[] centre = trace.getCentroid(CentroidMethod.SIGNAL_WEIGHTED);
    int minX = (int) Math.floor(centre[0] - fitWidth);
    int maxX = (int) Math.ceil(centre[0] + fitWidth);
    int minY = (int) Math.floor(centre[1] - fitWidth);
    int maxY = (int) Math.ceil(centre[1] + fitWidth);
    // Account for crops at the edge of the image
    minX = FastMath.max(0, minX);
    maxX = FastMath.min(w, maxX);
    minY = FastMath.max(0, minY);
    maxY = FastMath.min(h, maxY);
    int width = maxX - minX;
    int height = maxY - minY;
    if (width <= 0 || height <= 0) {
        // The centre must be outside the image width and height
        return null;
    }
    bounds.x = minX;
    bounds.y = minY;
    bounds.width = width;
    bounds.height = height;
    if (createStack)
        slices = new ImageStack(width, height);
    // Combine the images. Subtract the fitted background to zero the image.
    float[] data = new float[width * height];
    float sumBackground = 0;
    double noise = 0;
    for (PeakResult result : trace.getPoints()) {
        noise += result.noise * result.noise;
        float[] sourceData = source.get(result.getFrame(), bounds);
        final float background = result.getBackground();
        sumBackground += background;
        for (int i = 0; i < data.length; i++) {
            data[i] += sourceData[i] - background;
        }
        if (createStack)
            slices.addSlice(new FloatProcessor(width, height, sourceData, null));
    }
    if (createStack) {
        // Add a final image that is the average of the individual slices. This allows
        // it to be visualised in the same intensity scale.
        float[] data2 = Arrays.copyOf(data, data.length);
        final int size = slices.getSize();
        sumBackground /= size;
        for (int i = 0; i < data2.length; i++) data2[i] = sumBackground + data2[i] / size;
        slices.addSlice(new FloatProcessor(width, height, data2, null));
    }
    // Combined noise is the sqrt of the sum-of-squares
    combinedNoise[0] = Math.sqrt(noise);
    return data;
}

Example 88 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class TraceMolecules method runOptimiser.

private void runOptimiser(TraceManager manager) {
    // Get an estimate of the number of molecules without blinking
    SummaryStatistics stats = new SummaryStatistics();
    final double nmPerPixel = this.results.getNmPerPixel();
    final double gain = this.results.getGain();
    final boolean emCCD = this.results.isEMCCD();
    for (PeakResult result : this.results.getResults()) stats.addValue(result.getPrecision(nmPerPixel, gain, emCCD));
    // Use twice the precision to get the initial distance threshold
    // Use 2.5x sigma as per the PC-PALM protocol in Sengupta, et al (2013) Nature Protocols 8, 345
    double dEstimate = stats.getMean() * 2.5 / nmPerPixel;
    int n = manager.traceMolecules(dEstimate, 1);
    if (!getParameters(n, dEstimate))
        return;
    // TODO - Convert the distance threshold to use nm instead of pixels?		
    List<double[]> results = runTracing(manager, settings.minDistanceThreshold, settings.maxDistanceThreshold, settings.minTimeThreshold, settings.maxTimeThreshold, settings.optimiserSteps);
    // Compute fractional difference from the true value:
    // Use blinking rate directly or the estimated number of molecules
    double nReference;
    int statistic;
    if (optimiseBlinkingRate) {
        nReference = settings.blinkingRate;
        statistic = 3;
        IJ.log(String.format("Estimating blinking rate: %.2f", nReference));
    } else {
        nReference = n / settings.blinkingRate;
        statistic = 2;
        IJ.log(String.format("Estimating number of molecules: %d / %.2f = %.2f", n, settings.blinkingRate, nReference));
    }
    for (double[] result : results) {
        //System.out.printf("%g %g = %g\n", result[0], result[1], result[2]);
        if (optimiseBlinkingRate)
            result[2] = (nReference - result[statistic]) / nReference;
        else
            result[2] = (result[statistic] - nReference) / nReference;
    }
    // Locate the optimal parameters with a fit of the zero contour
    boolean found = findOptimalParameters(results);
    createPlotResults(results);
    if (!found)
        return;
    // Make fractional difference absolute so that lowest is best
    for (double[] result : results) result[2] = Math.abs(result[2]);
    // Set the optimal thresholds using the lowest value
    double[] best = new double[] { 0, 0, Double.MAX_VALUE };
    for (double[] result : results) if (best[2] > result[2])
        best = result;
    settings.distanceThreshold = best[0];
    // The optimiser works using frames so convert back to the correct units
    double convert = (settings.getTimeUnit() == TimeUnit.SECOND) ? exposureTime : 1;
    settings.setTimeThreshold(settings.getTimeThreshold() * convert);
    IJ.log(String.format("Optimal fractional difference @ D-threshold=%g, T-threshold=%f (%d frames)", settings.distanceThreshold, timeInSeconds(settings), timeInFrames(settings)));
    SettingsManager.saveSettings(globalSettings);
}

Example 89 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class TraceMolecules method convertToClusterPoints.

/**
	 * Convert a list of peak results into points for the clustering engine
	 * 
	 * @param peakResults
	 * @return
	 */
public static List<ClusterPoint> convertToClusterPoints(List<PeakResult> peakResults) {
    ArrayList<ClusterPoint> points = new ArrayList<ClusterPoint>(peakResults.size());
    int id = 0;
    for (PeakResult p : peakResults) points.add(ClusterPoint.newTimeClusterPoint(id++, p.getXPosition(), p.getYPosition(), p.getSignal(), p.getFrame(), p.getEndFrame()));
    return points;
}