Examples with MemoryPeakResults uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults used on opensource projects

Example 21 with MemoryPeakResults

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

the class TcPalmAnalysis method runSelection.

/**
 * Run selection of the current clusters.
 *
 * @param work the current work
 */
private void runSelection(Work work) {
    // Support square ROI
    // - Map image ROI bounds to the data
    // - Check if the cluster is inside the rectangle bounds
    final Roi roi = work.roi;
    final TcPalmAnalysisSettings settings = work.settings;
    final Rectangle2D scaledBounds = createScaledBounds(roi);
    final BiPredicate<ClusterData, Rectangle2D> filter = createSelectionFilter(roi, settings);
    clusters = new LocalList<>();
    clusterData.forEach(c -> {
        if (filter.test(c, scaledBounds)) {
            clusters.add(c);
        }
    });
    // Build total activations data
    countData = createCumulativeCountData(clusters, true);
    // Add a table of the clusters.
    final ClusterDataTableModelFrame clustersTable = createGroupsTable();
    clustersTable.getModel().setData(clusters, dataCalibration);
    // Allow a configurable action that accepts the array of ClusterData that is selected.
    clustersTable.selectedAction = clusterSelectedListener;
    // Extract the localisations into a loop view
    final MemoryPeakResults subset = new MemoryPeakResults();
    subset.copySettings(results);
    clusters.forEach(c -> {
        c.results.forEach(peak -> {
            if (scaledBounds.contains(peak.getXPosition(), peak.getYPosition())) {
                subset.add(peak);
            }
        });
    });
    // Clear bounds to force a recompute
    subset.setBounds(null);
    loopImage.setSettings(settings).setResults(subset).update();
}

Example 22 with MemoryPeakResults

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

the class PulseActivationAnalysis method runSimulation.

private void runSimulation() {
    title += " Simulation";
    if (!showSimulationDialog()) {
        return;
    }
    final long start = System.currentTimeMillis();
    final UniformRandomProvider rng = getUniformRandomProvider();
    // Draw the molecule positions
    ImageJUtils.showStatus("Simulating molecules ...");
    final float[][][] molecules = new float[3][][];
    final MemoryPeakResults[] channelResults = new MemoryPeakResults[3];
    final Calibration calibration = CalibrationHelper.create(settings.nmPerPixel, 1, 100);
    final Rectangle bounds = new Rectangle(settings.size, settings.size);
    for (int c = 0; c < 3; c++) {
        molecules[c] = simulateMolecules(rng, c);
        // Create a dataset to store the activations
        final MemoryPeakResults r = new MemoryPeakResults();
        r.setCalibration(calibration);
        r.setBounds(bounds);
        r.setName(title + " C" + (c + 1));
        channelResults[c] = r;
    }
    // Simulate activation
    ImageJUtils.showStatus("Simulating activations ...");
    for (int c = 0; c < 3; c++) {
        simulateActivations(rng, molecules, c, channelResults);
    }
    // Combine
    ImageJUtils.showStatus("Producing simulation output ...");
    final MemoryPeakResults r = new MemoryPeakResults();
    r.setCalibration(calibration);
    r.setBounds((Rectangle) bounds.clone());
    r.setName(title);
    final ImageProcessor[] images = new ImageProcessor[3];
    for (int c = 0; c < 3; c++) {
        final PeakResult[] list = channelResults[c].toArray();
        r.addAll(list);
        // Draw the unmixed activations
        final ResultsImageSettings.Builder builder = ResultsImageSettings.newBuilder().setImageType(ResultsImageType.DRAW_LOCALISATIONS).setImageMode(ResultsImageMode.IMAGE_ADD).setWeighted(true).setEqualised(true).setImageSizeMode(ResultsImageSizeMode.IMAGE_SIZE).setImageSize(1024);
        final ImageJImagePeakResults image = ImagePeakResultsFactory.createPeakResultsImage(builder, title, bounds, settings.nmPerPixel);
        image.setCalibration(calibration);
        image.setLiveImage(false);
        image.setDisplayImage(false);
        image.begin();
        image.addAll(list);
        image.end();
        images[c] = image.getImagePlus().getProcessor();
    }
    displayComposite(images, title);
    // Add to memory. Set the composite dataset first.
    MemoryPeakResults.addResults(r);
    for (int c = 0; c < 3; c++) {
        MemoryPeakResults.addResults(channelResults[c]);
    }
    // TODO:
    // Show an image of what it looks like with no unmixing, i.e. colours allocated
    // from the frame
    ImageJUtils.showStatus("Simulation complete: " + TextUtils.millisToString(System.currentTimeMillis() - start));
}

Example 23 with MemoryPeakResults

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

the class PsfCreator method runUsingFitting.

private void runUsingFitting() {
    if (!showFittingDialog()) {
        return;
    }
    if (!loadConfiguration()) {
        return;
    }
    final BasePoint[] spots = getSpots(0, true);
    if (spots.length == 0) {
        IJ.error(TITLE, "No spots without neighbours within " + (boxRadius * 2) + "px");
        return;
    }
    final 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);
    final ArrayList<double[]> centres = new ArrayList<>(spots.length);
    final int iterations = 1;
    final LoessInterpolator loess = new LoessInterpolator(settings.getSmoothing(), 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
    ImageJUtils.log(TITLE + ": " + imp.getTitle());
    ImageJUtils.log("Finding spot locations...");
    ImageJUtils.log("  %d spot%s without neighbours within %dpx", spots.length, ((spots.length == 1) ? "" : "s"), (boxRadius * 2));
    final StoredDataStatistics averageSd = new StoredDataStatistics();
    final StoredDataStatistics averageA = new StoredDataStatistics();
    final Statistics averageRange = new Statistics();
    final MemoryPeakResults allResults = new MemoryPeakResults();
    allResults.setCalibration(fitConfig.getCalibration());
    allResults.setPsf(fitConfig.getPsf());
    allResults.setName(TITLE);
    allResults.setBounds(new Rectangle(0, 0, width, height));
    MemoryPeakResults.addResults(allResults);
    for (int n = 1; n <= spots.length; n++) {
        final BasePoint spot = spots[n - 1];
        final int x = (int) spot.getX();
        final int y = (int) spot.getY();
        final MemoryPeakResults results = fitSpot(stack, width, height, x, y);
        allResults.add(results);
        if (results.size() < 5) {
            ImageJUtils.log("  Spot %d: Not enough fit results %d", n, results.size());
            continue;
        }
        // Get the results for the spot centre and width
        final double[] z = new double[results.size()];
        final double[] xCoord = new double[z.length];
        final double[] yCoord = new double[z.length];
        final double[] sd;
        final double[] a;
        final Counter counter = new Counter();
        // We have fit the results so they will be in the preferred units
        results.forEach(new PeakResultProcedure() {

            @Override
            public void execute(PeakResult peak) {
                final int i = counter.getAndIncrement();
                z[i] = peak.getFrame();
                xCoord[i] = peak.getXPosition() - x;
                yCoord[i] = peak.getYPosition() - y;
            }
        });
        final WidthResultProcedure wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
        wp.getW();
        sd = SimpleArrayUtils.toDouble(wp.wx);
        final HeightResultProcedure hp = new HeightResultProcedure(results, IntensityUnit.COUNT);
        hp.getH();
        a = SimpleArrayUtils.toDouble(hp.heights);
        // Smooth the amplitude plot
        final 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;
        int stop = smoothA.length - 1;
        final double limit = smoothA[maximumIndex] * settings.getAmplitudeFraction();
        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];
        final 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
        final double cx = smoothX[maximumIndex] + x;
        final 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)) {
            ImageJUtils.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];
        ImageJUtils.log("  Spot %d => x=%.2f, y=%.2f, z=%d, sd=%.2f, A=%.2f", n, cx, cy, cz, csd, ca);
        centres.add(new double[] { cx, cy, cz, csd, n });
    }
    if (settings.getInteractiveMode()) {
        imp.setSlice(currentSlice);
        imp.setOverlay(null);
        // Hide the amplitude and spot plots
        ImageJUtils.hide(TITLE_AMPLITUDE);
        ImageJUtils.hide(TITLE_PSF_PARAMETERS);
    }
    if (centres.isEmpty()) {
        final String msg = "No suitable spots could be identified";
        ImageJUtils.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 (final 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.
    final ImageStack psf = createStack(stack, minz, maxz, settings.getMagnification());
    // For each spot
    final Statistics stats = new Statistics();
    boolean ok = true;
    for (int i = 0; ok && i < centres.size(); i++) {
        final double increment = 1.0 / (stack.getSize() * centres.size());
        setProgress((double) i / centres.size());
        final double[] centre = centres.get(i);
        // Extract the spot
        final float[][] spot = new float[stack.getSize()][];
        Rectangle regionBounds = null;
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            final ImageExtractor ie = ImageExtractor.wrap((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);
        }
        if (regionBounds == null) {
            // Empty stack
            continue;
        }
        final int n = (int) centre[4];
        final float b = getBackground(n, spot);
        if (!subtractBackgroundAndWindow(spot, b, regionBounds.width, regionBounds.height, centre, loess)) {
            ImageJUtils.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, settings.getMagnification(), psf, centre, spot, regionBounds, increment, settings.getCentreEachSlice());
    }
    if (settings.getInteractiveMode()) {
        ImageJUtils.hide(TITLE_INTENSITY);
    }
    IJ.showProgress(1);
    if (!ok || stats.getN() == 0) {
        return;
    }
    final double avSd = getAverage(averageSd, averageA, 2);
    ImageJUtils.log("  Average background = %.2f, Av. SD = %s px", stats.getMean(), MathUtils.rounded(avSd, 4));
    normalise(psf, maxz, avSd * settings.getMagnification(), false);
    IJ.showProgress(1);
    psfImp = ImageJUtils.display(TITLE_PSF, psf);
    psfImp.setSlice(maxz);
    psfImp.resetDisplayRange();
    psfImp.updateAndDraw();
    final double[][] fitCom = new double[2][psf.getSize()];
    Arrays.fill(fitCom[0], Double.NaN);
    Arrays.fill(fitCom[1], Double.NaN);
    final 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
    final double[][] com = calculateCentreOfMass(psf, fitCom, nmPerPixel / settings.getMagnification());
    final double[] slice = SimpleArrayUtils.newArray(psf.getSize(), 1, 1.0);
    final String title = TITLE + " CoM Drift";
    final Plot plot = new Plot(title, "Slice", "Drift (nm)");
    plot.addLabel(0, 0, "Red = X; Blue = Y");
    // double[] limitsX = Maths.limits(com[0]);
    // double[] limitsY = Maths.limits(com[1]);
    final double[] limitsX = getLimits(com[0]);
    final 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);
    ImageJUtils.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", ImagePsfHelper.toString(ImagePsfHelper.create(maxz, nmPerPixel / settings.getMagnification(), settings.getNmPerSlice(), stats.getN(), fwhm, createNote())));
    ImageJUtils.log("%s : z-centre = %d, nm/Pixel = %s, nm/Slice = %s, %d images, " + "PSF SD = %s nm, FWHM = %s px\n", psfImp.getTitle(), maxz, MathUtils.rounded(nmPerPixel / settings.getMagnification(), 3), MathUtils.rounded(settings.getNmPerSlice(), 3), stats.getN(), MathUtils.rounded(fittedSd * nmPerPixel, 4), MathUtils.rounded(fwhm));
    createInteractivePlots(psf, maxz, nmPerPixel / settings.getMagnification(), fittedSd * nmPerPixel);
    IJ.showStatus("");
}

Example 24 with MemoryPeakResults

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

the class RenameResults method renameResults.

private int renameResults() {
    // Start with the original names for the mapping from old to new
    final HashMap<String, String> mappedNames = new HashMap<>();
    for (final String name : MemoryPeakResults.getResultNames()) {
        mappedNames.put(name, name);
    }
    // Get the new names
    final String[] lines = renameText.split("[;\n]");
    for (final String line : lines) {
        final String[] fields = line.split("[=]");
        if (fields.length == 2) {
            final String oldName = fields[0].trim();
            final String newName = fields[1].trim();
            if (!mappedNames.containsKey(oldName)) {
                IJ.error(TITLE, "An unknown original name has been specified: " + oldName);
                return 0;
            }
            if (oldName.equals(newName)) {
                // No update required
                continue;
            }
            mappedNames.put(oldName, newName);
        }
    }
    // Check the new names are unique
    final Set<String> newNames = new HashSet<>();
    for (final String newName : mappedNames.values()) {
        if (newNames.contains(newName)) {
            IJ.error(TITLE, "A duplicate new name has been specified: " + newName);
            return 0;
        }
        newNames.add(newName);
    }
    // Rename
    final List<MemoryPeakResults> renamedResults = new LinkedList<>();
    for (final Entry<String, String> entry : mappedNames.entrySet()) {
        if (entry.getKey().equals(entry.getValue())) {
            continue;
        }
        // Remove from memory and store in a list
        final MemoryPeakResults results = MemoryPeakResults.removeResults(entry.getKey());
        if (results != null) {
            results.setName(entry.getValue());
            renamedResults.add(results);
        }
    }
    // Add back to memory
    for (final MemoryPeakResults results : renamedResults) {
        MemoryPeakResults.addResults(results);
    }
    return renamedResults.size();
}

Example 25 with MemoryPeakResults

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

the class ResequenceResults method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    if (!showDialog()) {
        return;
    }
    final MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, true, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    if (resequenceResults(results, settings.start, settings.block, settings.skip, (settings.logMapping) ? SimpleImageJTrackProgress.getInstance() : null)) {
        IJ.showStatus("Resequenced " + results.getName());
    }
}