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

Example 26 with MemoryPeakResults

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

the class CreateData method copyMemoryPeakResults.

/**
	 * Copy all the settings from the results into a new results set labelled with the name suffix
	 * 
	 * @param nameSuffix
	 * @return The new results set
	 */
private MemoryPeakResults copyMemoryPeakResults(String nameSuffix) {
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(this.results);
    newResults.setName(newResults.getSource().getName() + " (" + TITLE + " " + nameSuffix + ")");
    newResults.setSortAfterEnd(true);
    newResults.begin();
    MemoryPeakResults.addResults(newResults);
    return newResults;
}

Example 27 with MemoryPeakResults

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

the class CalibrateResults method run.

/*
	 * (non-)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (!showInputDialog())
        return;
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    if (!showDialog(results))
        return;
    IJ.showStatus("Calibrated " + results.getName());
}

Example 28 with MemoryPeakResults

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

the class PSFCreator method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
	 */
public void run(ImageProcessor ip) {
    loadConfiguration();
    BasePoint[] spots = getSpots();
    if (spots.length == 0) {
        IJ.error(TITLE, "No spots without neighbours within " + (boxRadius * 2) + "px");
        return;
    }
    ImageStack stack = getImageStack();
    final int width = imp.getWidth();
    final int height = imp.getHeight();
    final int currentSlice = imp.getSlice();
    // Adjust settings for a single maxima
    config.setIncludeNeighbours(false);
    fitConfig.setDuplicateDistance(0);
    ArrayList<double[]> centres = new ArrayList<double[]>(spots.length);
    int iterations = 1;
    LoessInterpolator loess = new LoessInterpolator(smoothing, iterations);
    // TODO - The fitting routine may not produce many points. In this instance the LOESS interpolator
    // fails to smooth the data very well. A higher bandwidth helps this but perhaps 
    // try a different smoothing method.
    // For each spot
    Utils.log(TITLE + ": " + imp.getTitle());
    Utils.log("Finding spot locations...");
    Utils.log("  %d spot%s without neighbours within %dpx", spots.length, ((spots.length == 1) ? "" : "s"), (boxRadius * 2));
    StoredDataStatistics averageSd = new StoredDataStatistics();
    StoredDataStatistics averageA = new StoredDataStatistics();
    Statistics averageRange = new Statistics();
    MemoryPeakResults allResults = new MemoryPeakResults();
    allResults.setName(TITLE);
    allResults.setBounds(new Rectangle(0, 0, width, height));
    MemoryPeakResults.addResults(allResults);
    for (int n = 1; n <= spots.length; n++) {
        BasePoint spot = spots[n - 1];
        final int x = (int) spot.getX();
        final int y = (int) spot.getY();
        MemoryPeakResults results = fitSpot(stack, width, height, x, y);
        allResults.addAllf(results.getResults());
        if (results.size() < 5) {
            Utils.log("  Spot %d: Not enough fit results %d", n, results.size());
            continue;
        }
        // Get the results for the spot centre and width
        double[] z = new double[results.size()];
        double[] xCoord = new double[z.length];
        double[] yCoord = new double[z.length];
        double[] sd = new double[z.length];
        double[] a = new double[z.length];
        int i = 0;
        for (PeakResult peak : results.getResults()) {
            z[i] = peak.getFrame();
            xCoord[i] = peak.getXPosition() - x;
            yCoord[i] = peak.getYPosition() - y;
            sd[i] = FastMath.max(peak.getXSD(), peak.getYSD());
            a[i] = peak.getAmplitude();
            i++;
        }
        // Smooth the amplitude plot
        double[] smoothA = loess.smooth(z, a);
        // Find the maximum amplitude
        int maximumIndex = findMaximumIndex(smoothA);
        // Find the range at a fraction of the max. This is smoothed to find the X/Y centre
        int start = 0, stop = smoothA.length - 1;
        double limit = smoothA[maximumIndex] * amplitudeFraction;
        for (int j = 0; j < smoothA.length; j++) {
            if (smoothA[j] > limit) {
                start = j;
                break;
            }
        }
        for (int j = smoothA.length; j-- > 0; ) {
            if (smoothA[j] > limit) {
                stop = j;
                break;
            }
        }
        averageRange.add(stop - start + 1);
        // Extract xy centre coords and smooth
        double[] smoothX = new double[stop - start + 1];
        double[] smoothY = new double[smoothX.length];
        double[] smoothSd = new double[smoothX.length];
        double[] newZ = new double[smoothX.length];
        for (int j = start, k = 0; j <= stop; j++, k++) {
            smoothX[k] = xCoord[j];
            smoothY[k] = yCoord[j];
            smoothSd[k] = sd[j];
            newZ[k] = z[j];
        }
        smoothX = loess.smooth(newZ, smoothX);
        smoothY = loess.smooth(newZ, smoothY);
        smoothSd = loess.smooth(newZ, smoothSd);
        // Since the amplitude is not very consistent move from this peak to the 
        // lowest width which is the in-focus spot.
        maximumIndex = findMinimumIndex(smoothSd, maximumIndex - start);
        // Find the centre at the amplitude peak
        double cx = smoothX[maximumIndex] + x;
        double cy = smoothY[maximumIndex] + y;
        int cz = (int) newZ[maximumIndex];
        double csd = smoothSd[maximumIndex];
        double ca = smoothA[maximumIndex + start];
        // The average should weight the SD using the signal for each spot
        averageSd.add(smoothSd[maximumIndex]);
        averageA.add(ca);
        if (ignoreSpot(n, z, a, smoothA, xCoord, yCoord, sd, newZ, smoothX, smoothY, smoothSd, cx, cy, cz, csd)) {
            Utils.log("  Spot %d was ignored", n);
            continue;
        }
        // Store result - it may have been moved interactively
        maximumIndex += this.slice - cz;
        cz = (int) newZ[maximumIndex];
        csd = smoothSd[maximumIndex];
        ca = smoothA[maximumIndex + start];
        Utils.log("  Spot %d => x=%.2f, y=%.2f, z=%d, sd=%.2f, A=%.2f\n", n, cx, cy, cz, csd, ca);
        centres.add(new double[] { cx, cy, cz, csd, n });
    }
    if (interactiveMode) {
        imp.setSlice(currentSlice);
        imp.setOverlay(null);
        // Hide the amplitude and spot plots
        Utils.hide(TITLE_AMPLITUDE);
        Utils.hide(TITLE_PSF_PARAMETERS);
    }
    if (centres.isEmpty()) {
        String msg = "No suitable spots could be identified centres";
        Utils.log(msg);
        IJ.error(TITLE, msg);
        return;
    }
    // Find the limits of the z-centre
    int minz = (int) centres.get(0)[2];
    int maxz = minz;
    for (double[] centre : centres) {
        if (minz > centre[2])
            minz = (int) centre[2];
        else if (maxz < centre[2])
            maxz = (int) centre[2];
    }
    IJ.showStatus("Creating PSF image");
    // Create a stack that can hold all the data.
    ImageStack psf = createStack(stack, minz, maxz, magnification);
    // For each spot
    Statistics stats = new Statistics();
    boolean ok = true;
    for (int i = 0; ok && i < centres.size(); i++) {
        double progress = (double) i / centres.size();
        final double increment = 1.0 / (stack.getSize() * centres.size());
        IJ.showProgress(progress);
        double[] centre = centres.get(i);
        // Extract the spot
        float[][] spot = new float[stack.getSize()][];
        Rectangle regionBounds = null;
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            ImageExtractor ie = new ImageExtractor((float[]) stack.getPixels(slice), width, height);
            if (regionBounds == null)
                regionBounds = ie.getBoxRegionBounds((int) centre[0], (int) centre[1], boxRadius);
            spot[slice - 1] = ie.crop(regionBounds);
        }
        int n = (int) centre[4];
        final float b = getBackground(n, spot);
        if (!subtractBackgroundAndWindow(spot, b, regionBounds.width, regionBounds.height, centre, loess)) {
            Utils.log("  Spot %d was ignored", n);
            continue;
        }
        stats.add(b);
        // Adjust the centre using the crop
        centre[0] -= regionBounds.x;
        centre[1] -= regionBounds.y;
        // This takes a long time so this should track progress
        ok = addToPSF(maxz, magnification, psf, centre, spot, regionBounds, progress, increment, centreEachSlice);
    }
    if (interactiveMode) {
        Utils.hide(TITLE_INTENSITY);
    }
    IJ.showProgress(1);
    if (threadPool != null) {
        threadPool.shutdownNow();
        threadPool = null;
    }
    if (!ok || stats.getN() == 0)
        return;
    final double avSd = getAverage(averageSd, averageA, 2);
    Utils.log("  Average background = %.2f, Av. SD = %s px", stats.getMean(), Utils.rounded(avSd, 4));
    normalise(psf, maxz, avSd * magnification, false);
    IJ.showProgress(1);
    psfImp = Utils.display("PSF", psf);
    psfImp.setSlice(maxz);
    psfImp.resetDisplayRange();
    psfImp.updateAndDraw();
    double[][] fitCom = new double[2][psf.getSize()];
    Arrays.fill(fitCom[0], Double.NaN);
    Arrays.fill(fitCom[1], Double.NaN);
    double fittedSd = fitPSF(psf, loess, maxz, averageRange.getMean(), fitCom);
    // Compute the drift in the PSF:
    // - Use fitted centre if available; otherwise find CoM for each frame
    // - express relative to the average centre
    double[][] com = calculateCentreOfMass(psf, fitCom, nmPerPixel / magnification);
    double[] slice = Utils.newArray(psf.getSize(), 1, 1.0);
    String title = TITLE + " CoM Drift";
    Plot2 plot = new Plot2(title, "Slice", "Drift (nm)");
    plot.addLabel(0, 0, "Red = X; Blue = Y");
    //double[] limitsX = Maths.limits(com[0]);
    //double[] limitsY = Maths.limits(com[1]);
    double[] limitsX = getLimits(com[0]);
    double[] limitsY = getLimits(com[1]);
    plot.setLimits(1, psf.getSize(), Math.min(limitsX[0], limitsY[0]), Math.max(limitsX[1], limitsY[1]));
    plot.setColor(Color.red);
    plot.addPoints(slice, com[0], Plot.DOT);
    plot.addPoints(slice, loess.smooth(slice, com[0]), Plot.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(slice, com[1], Plot.DOT);
    plot.addPoints(slice, loess.smooth(slice, com[1]), Plot.LINE);
    Utils.display(title, plot);
    // TODO - Redraw the PSF with drift correction applied. 
    // This means that the final image should have no drift.
    // This is relevant when combining PSF images. It doesn't matter too much for simulations 
    // unless the drift is large.
    // Add Image properties containing the PSF details
    final double fwhm = getFWHM(psf, maxz);
    psfImp.setProperty("Info", XmlUtils.toXML(new PSFSettings(maxz, nmPerPixel / magnification, nmPerSlice, stats.getN(), fwhm, createNote())));
    Utils.log("%s : z-centre = %d, nm/Pixel = %s, nm/Slice = %s, %d images, PSF SD = %s nm, FWHM = %s px\n", psfImp.getTitle(), maxz, Utils.rounded(nmPerPixel / magnification, 3), Utils.rounded(nmPerSlice, 3), stats.getN(), Utils.rounded(fittedSd * nmPerPixel, 4), Utils.rounded(fwhm));
    createInteractivePlots(psf, maxz, nmPerPixel / magnification, fittedSd * nmPerPixel);
    IJ.showStatus("");
}

Example 29 with MemoryPeakResults

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

the class FIRE method showFrcTimeEvolution.

private void showFrcTimeEvolution(String name, double fireNumber, ThresholdMethod thresholdMethod, double fourierImageScale, int imageSize) {
    IJ.showStatus("Calculating FRC time evolution curve...");
    List<PeakResult> list = results.getResults();
    int nSteps = 10;
    int maxT = list.get(list.size() - 1).getFrame();
    if (maxT == 0)
        maxT = list.size();
    int step = maxT / nSteps;
    TDoubleArrayList x = new TDoubleArrayList();
    TDoubleArrayList y = new TDoubleArrayList();
    double yMin = fireNumber;
    double yMax = fireNumber;
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    int i = 0;
    for (int t = step; t <= maxT - step; t += step) {
        while (i < list.size()) {
            if (list.get(i).getFrame() <= t) {
                newResults.add(list.get(i));
                i++;
            } else
                break;
        }
        x.add((double) t);
        FIRE f = this.copy();
        FireResult result = f.calculateFireNumber(fourierMethod, samplingMethod, thresholdMethod, fourierImageScale, imageSize);
        double fire = (result == null) ? 0 : result.fireNumber;
        y.add(fire);
        yMin = FastMath.min(yMin, fire);
        yMax = FastMath.max(yMax, fire);
    }
    // Add the final fire number
    x.add((double) maxT);
    y.add(fireNumber);
    double[] xValues = x.toArray();
    double[] yValues = y.toArray();
    String units = "px";
    if (results.getCalibration() != null) {
        nmPerPixel = results.getNmPerPixel();
        units = "nm";
    }
    String title = name + " FRC Time Evolution";
    Plot2 plot = new Plot2(title, "Frames", "Resolution (" + units + ")", (float[]) null, (float[]) null);
    double range = Math.max(1, yMax - yMin) * 0.05;
    plot.setLimits(xValues[0], xValues[xValues.length - 1], yMin - range, yMax + range);
    plot.setColor(Color.red);
    plot.addPoints(xValues, yValues, Plot.CONNECTED_CIRCLES);
    Utils.display(title, plot);
}

Example 30 with MemoryPeakResults

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

the class FilterResults method filterResults.

/**
	 * Apply the filters to the data
	 */
private void filterResults() {
    checkLimits();
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    newResults.setName(results.getName() + " Filtered");
    // Initialise the mask
    ByteProcessor mask = getMask(filterSettings.maskTitle);
    MaskDistribution maskFilter = null;
    final float centreX = results.getBounds().width / 2.0f;
    final float centreY = results.getBounds().height / 2.0f;
    if (mask != null) {
        double scaleX = (double) results.getBounds().width / mask.getWidth();
        double scaleY = (double) results.getBounds().height / mask.getHeight();
        maskFilter = new MaskDistribution((byte[]) mask.getPixels(), mask.getWidth(), mask.getHeight(), 0, scaleX, scaleY);
    }
    int i = 0;
    final int size = results.size();
    final double maxVariance = filterSettings.maxPrecision * filterSettings.maxPrecision;
    for (PeakResult result : results.getResults()) {
        if (i % 64 == 0)
            IJ.showProgress(i, size);
        if (getDrift(result) > filterSettings.maxDrift)
            continue;
        if (result.getSignal() < filterSettings.minSignal)
            continue;
        if (getSNR(result) < filterSettings.minSNR)
            continue;
        if (getVariance(result) > maxVariance)
            continue;
        final float width = getWidth(result);
        if (width < filterSettings.minWidth || width > filterSettings.maxWidth)
            continue;
        if (maskFilter != null) {
            // Check the coordinates are inside the mask
            double[] xy = new double[] { result.getXPosition() - centreX, result.getYPosition() - centreY };
            if (!maskFilter.isWithinXY(xy))
                continue;
        }
        // Passed all filters. Add to the results
        newResults.add(result);
    }
    IJ.showProgress(1);
    IJ.showStatus(newResults.size() + " Filtered localisations");
    MemoryPeakResults.addResults(newResults);
}