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

Example 81 with MemoryPeakResults

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

the class OverlayResults method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    names = new String[MemoryPeakResults.getResultNames().size() + 1];
    ids = new int[names.length];
    int c = 0;
    names[c++] = "(None)";
    for (MemoryPeakResults results : MemoryPeakResults.getAllResults()) {
        if (results.getSource().getOriginal() instanceof IJImageSource) {
            IJImageSource source = (IJImageSource) (results.getSource().getOriginal());
            ImagePlus imp = WindowManager.getImage(source.getName());
            if (imp != null) {
                ids[c] = imp.getID();
                names[c++] = results.getName();
            }
        }
    }
    if (c == 1) {
        IJ.error(TITLE, "There are no result images available");
        return;
    }
    names = Arrays.copyOf(names, c);
    Thread t = null;
    Worker w = null;
    NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
    gd.addMessage("Overlay results on current image frame");
    gd.addChoice("Results", names, (name == null) ? "" : name);
    gd.addCheckbox("Show_table", showTable);
    gd.addMessage("");
    gd.addHelp(About.HELP_URL);
    gd.hideCancelButton();
    gd.setOKLabel("Close");
    if (!(IJ.isMacro() || java.awt.GraphicsEnvironment.isHeadless())) {
        choice = (Choice) gd.getChoices().get(0);
        choice.addItemListener(this);
        checkbox = (Checkbox) gd.getCheckboxes().get(0);
        checkbox.addItemListener(this);
        label = (Label) gd.getMessage();
        // Listen for changes to an image
        ImagePlus.addImageListener(this);
        show();
        t = new Thread(w = new Worker());
        t.setDaemon(true);
        t.start();
    }
    gd.showDialog();
    if (!(IJ.isMacro() || java.awt.GraphicsEnvironment.isHeadless()))
        ImagePlus.removeImageListener(this);
    if (!gd.wasCanceled()) {
        name = gd.getNextChoice();
        showTable = gd.getNextBoolean();
    }
    if (t != null) {
        w.running = false;
        inbox.close();
        try {
            t.join(0);
        } catch (InterruptedException e) {
        }
        t = null;
    }
}

Example 82 with MemoryPeakResults

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

the class LoadLocalisations method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    GlobalSettings globalSettings = SettingsManager.loadSettings();
    CreateDataSettings settings = globalSettings.getCreateDataSettings();
    String[] path = Utils.decodePath(settings.localisationsFilename);
    OpenDialog chooser = new OpenDialog("Localisations_File", path[0], path[1]);
    if (chooser.getFileName() == null)
        return;
    settings.localisationsFilename = chooser.getDirectory() + chooser.getFileName();
    SettingsManager.saveSettings(globalSettings);
    LocalisationList localisations = loadLocalisations(settings.localisationsFilename);
    if (localisations == null)
        // Cancelled
        return;
    if (localisations.isEmpty()) {
        IJ.error(TITLE, "No localisations could be loaded");
        return;
    }
    MemoryPeakResults results = localisations.toPeakResults();
    // Ask the user what depth to use to create the in-memory results
    if (!getZDepth(results))
        return;
    if (myLimitZ) {
        MemoryPeakResults results2 = new MemoryPeakResults(results.size());
        results.setName(name);
        results.copySettings(results);
        for (PeakResult peak : results.getResults()) {
            if (peak.error < minz || peak.error > maxz)
                continue;
            results2.add(peak);
        }
        results = results2;
    }
    // Create the in-memory results
    if (results.size() > 0) {
        MemoryPeakResults.addResults(results);
    }
    IJ.showStatus(String.format("Loaded %d localisations", results.size()));
    if (myLimitZ)
        Utils.log("Loaded %d localisations, z between %.2f - %.2f", results.size(), minz, maxz);
    else
        Utils.log("Loaded %d localisations", results.size());
}

Example 83 with MemoryPeakResults

use of gdsc.smlm.results.MemoryPeakResults 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 84 with MemoryPeakResults

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

the class TraceMolecules method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    altKeyDown = Utils.isExtraOptions();
    Trace[] traces = null;
    int totalFiltered = 0;
    if ("cluster".equals(arg)) {
        // --=-=-=-=-=-
        // Clustering
        // --=-=-=-=-=-
        outputName = "Cluster";
        if (!showClusterDialog())
            return;
        ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), settings.getClusteringAlgorithm(), new IJTrackProgress());
        if (settings.splitPulses) {
            engine.setPulseInterval(settings.pulseInterval);
            if (settings.getTimeUnit() == TimeUnit.FRAME) {
                if (settings.getTimeThreshold() > settings.pulseInterval) {
                    settings.setTimeThreshold(settings.pulseInterval);
                }
            } else {
                if (timeInFrames(settings) > settings.pulseInterval) {
                    settings.setTimeThreshold(settings.pulseInterval * exposureTime);
                }
            }
        }
        ArrayList<Cluster> clusters = engine.findClusters(convertToClusterPoints(), settings.distanceThreshold / results.getCalibration().getNmPerPixel(), timeInFrames(settings));
        if (clusters == null) {
            Utils.log("Aborted");
            return;
        }
        traces = convertToTraces(clusters);
    } else {
        // --=-=-=-=-=-
        // Tracing
        // --=-=-=-=-=-
        outputName = "Trace";
        if (!showDialog())
            return;
        TraceManager manager = new TraceManager(results);
        manager.setTraceMode(settings.getTraceMode());
        manager.setActivationFrameInterval(settings.pulseInterval);
        manager.setActivationFrameWindow(settings.pulseWindow);
        manager.setDistanceExclusion(settings.distanceExclusion / results.getCalibration().getNmPerPixel());
        if (settings.optimise) {
            // Optimise before configuring for a pulse interval
            runOptimiser(manager);
        }
        if (settings.splitPulses) {
            manager.setPulseInterval(settings.pulseInterval);
            if (settings.getTimeUnit() == TimeUnit.FRAME) {
                if (settings.getTimeThreshold() > settings.pulseInterval) {
                    settings.setTimeThreshold(settings.pulseInterval);
                }
            } else {
                if (timeInFrames(settings) > settings.pulseInterval) {
                    settings.setTimeThreshold(settings.pulseInterval * exposureTime);
                }
            }
        }
        manager.setTracker(new IJTrackProgress());
        manager.traceMolecules(settings.distanceThreshold / results.getCalibration().getNmPerPixel(), timeInFrames(settings));
        traces = manager.getTraces();
        totalFiltered = manager.getTotalFiltered();
    }
    // --=-=-=-=-=-
    // Results processing
    // --=-=-=-=-=-
    outputName += (outputName.endsWith("e") ? "" : "e") + "d";
    saveResults(results, traces, outputName);
    // Save singles + single localisations in a trace
    saveCentroidResults(results, getSingles(traces), outputName + " Singles");
    Trace[] multiTraces = getTraces(traces);
    saveResults(results, multiTraces, outputName + " Multi");
    // Save centroids
    outputName += " Centroids";
    MemoryPeakResults tracedResults = saveCentroidResults(results, traces, outputName);
    // Save traces separately
    saveCentroidResults(results, multiTraces, outputName + " Multi");
    // Sort traces by time to assist the results source in extracting frames sequentially.
    // Do this before saving to assist in debugging using the saved traces file.
    sortByTime(traces);
    if (settings.saveTraces)
        saveTraces(traces);
    summarise(traces, totalFiltered, settings.distanceThreshold, timeInSeconds(settings));
    IJ.showStatus(String.format("%d localisations => %d traces (%d filtered)", results.size(), tracedResults.size(), totalFiltered));
    // Provide option to refit the traces as single peaks and save to memory
    if (settings.refitOption)
        fitTraces(results, traces);
}

Example 85 with MemoryPeakResults

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

the class SphericalDistributionTest method drawImage.

private void drawImage(boolean useRejctionMethod) {
    MemoryPeakResults results = new MemoryPeakResults();
    results.setSortAfterEnd(true);
    int radius = 10;
    Rectangle bounds = new Rectangle(0, 0, radius * 2, radius * 2);
    SphericalDistribution dist = new SphericalDistribution(radius, rand);
    dist.setUseRejectionMethod(useRejctionMethod);
    float scale = 10;
    results.begin();
    for (int i = 100000; i-- > 0; ) {
        double[] xyz = dist.next();
        int peak = (int) (1 + scale * radius + Math.round(scale * xyz[2]));
        float[] params = new float[7];
        params[Gaussian2DFunction.X_POSITION] = radius + (float) xyz[0];
        params[Gaussian2DFunction.Y_POSITION] = radius + (float) xyz[1];
        results.addf(peak, 0, 0, 0, 0, 0, params, null);
    }
    results.end();
    IJImagePeakResults image = new IJImagePeakResults((useRejctionMethod) ? "Rejection Method" : "Transformation Method", bounds, scale);
    image.setRollingWindowSize(1);
    image.begin();
    image.addAll(results.getResults());
    // Place breakpoint here in debug mode to view the image. 
    // It should have an even colour through the stack.
    image.end();
}