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

Example 31 with MemoryPeakResults

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

the class Fire method createImages.

/**
 * Creates the images to use for the FIRE calculation. This must be called after
 * {@link #initialise(MemoryPeakResults, MemoryPeakResults)}.
 *
 * @param fourierImageScale the fourier image scale (set to zero to auto compute)
 * @param imageSize the image size
 * @param useSignal Use the localisation signal to weight the intensity. The default uses a value
 *        of 1 per localisation.
 * @return the fire images
 */
public FireImages createImages(double fourierImageScale, int imageSize, boolean useSignal) {
    if (results == null) {
        return null;
    }
    final SignalProvider signalProvider = (useSignal && (results.hasIntensity())) ? new PeakSignalProvider() : new FixedSignalProvider();
    // Draw images using the existing IJ routines.
    final Rectangle bounds = new Rectangle((int) Math.ceil(dataBounds.getWidth()), (int) Math.ceil(dataBounds.getHeight()));
    final ResultsImageSettings.Builder builder = ResultsImageSettings.newBuilder().setImageType(ResultsImageType.DRAW_NONE).setWeighted(true).setEqualised(false).setImageMode(ResultsImageMode.IMAGE_ADD);
    if (fourierImageScale > 0) {
        builder.setImageSizeMode(ResultsImageSizeMode.SCALED);
        builder.setScale(fourierImageScale);
    } else {
        builder.setImageSizeMode(ResultsImageSizeMode.IMAGE_SIZE);
        builder.setImageSize(imageSize);
    }
    ImageJImagePeakResults image1 = createPeakResultsImage(bounds, builder, "IP1");
    ImageJImagePeakResults image2 = createPeakResultsImage(bounds, builder, "IP2");
    final float minx = (float) dataBounds.getX();
    final float miny = (float) dataBounds.getY();
    if (this.results2 != null) {
        // Two image comparison
        final ImageJImagePeakResults i1 = image1;
        results.forEach((PeakResultProcedure) result -> {
            final float x = result.getXPosition() - minx;
            final float y = result.getYPosition() - miny;
            i1.add(x, y, signalProvider.getSignal(result));
        });
        final ImageJImagePeakResults i2 = image2;
        results2.forEach((PeakResultProcedure) result -> {
            final float x = result.getXPosition() - minx;
            final float y = result.getYPosition() - miny;
            i2.add(x, y, signalProvider.getSignal(result));
        });
    } else {
        // Block sampling.
        // Ensure we have at least 2 even sized blocks.
        int blockSize = Math.min(results.size() / 2, Math.max(1, settings.blockSize));
        int nblocks = (int) Math.ceil((double) results.size() / blockSize);
        while (nblocks <= 1 && blockSize > 1) {
            blockSize /= 2;
            nblocks = (int) Math.ceil((double) results.size() / blockSize);
        }
        if (nblocks <= 1) {
            // This should not happen since the results should contain at least 2 localisations
            return null;
        }
        if (blockSize != settings.blockSize) {
            IJ.log(pluginTitle + " Warning: Changed block size to " + blockSize);
        }
        final Counter i = new Counter();
        final Counter block = new Counter();
        final int finalBlockSize = blockSize;
        final PeakResult[][] blocks = new PeakResult[nblocks][blockSize];
        results.forEach((PeakResultProcedure) result -> {
            if (i.getCount() == finalBlockSize) {
                block.increment();
                i.reset();
            }
            blocks[block.getCount()][i.getAndIncrement()] = result;
        });
        // Truncate last block
        blocks[block.getCount()] = Arrays.copyOf(blocks[block.getCount()], i.getCount());
        final int[] indices = SimpleArrayUtils.natural(block.getCount() + 1);
        if (settings.randomSplit) {
            MathArrays.shuffle(indices);
        }
        for (final int index : indices) {
            // Split alternating so just rotate
            final ImageJImagePeakResults image = image1;
            image1 = image2;
            image2 = image;
            for (final PeakResult p : blocks[index]) {
                final float x = p.getXPosition() - minx;
                final float y = p.getYPosition() - miny;
                image.add(x, y, signalProvider.getSignal(p));
            }
        }
    }
    image1.end();
    final ImageProcessor ip1 = image1.getImagePlus().getProcessor();
    image2.end();
    final ImageProcessor ip2 = image2.getImagePlus().getProcessor();
    if (settings.maxPerBin > 0 && signalProvider instanceof FixedSignalProvider) {
        // We can eliminate over-sampled pixels
        for (int i = ip1.getPixelCount(); i-- > 0; ) {
            if (ip1.getf(i) > settings.maxPerBin) {
                ip1.setf(i, settings.maxPerBin);
            }
            if (ip2.getf(i) > settings.maxPerBin) {
                ip2.setf(i, settings.maxPerBin);
            }
        }
    }
    return new FireImages(ip1, ip2, nmPerUnit / image1.getScale());
}

Example 32 with MemoryPeakResults

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

the class FilterMolecules method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    if (!showDialog()) {
        return;
    }
    // Load the results
    MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    // Allow reordering when filtering
    results = results.copy();
    if (settings.removeSingles) {
        results.removeIf(p -> p.getId() <= 0);
        final TIntIntHashMap count = new TIntIntHashMap(results.size());
        results.forEach((PeakResultProcedure) r -> count.adjustOrPutValue(r.getId(), 1, 1));
        results.removeIf(p -> count.get(p.getId()) == 1);
        if (results.isEmpty()) {
            IJ.error(TITLE, "No results after filtering singles");
            return;
        }
    }
    switch(settings.filterMode) {
        case D:
            new FilterDiffusionCoefficient().run(results);
            break;
        default:
            IJ.error(TITLE, "Unknown filter mode: " + settings.filterMode);
    }
}

Example 33 with MemoryPeakResults

use of uk.ac.sussex.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...");
    // Sort by time
    results.sort();
    final int nSteps = 10;
    int maxT = results.getLastFrame();
    if (maxT == 0) {
        maxT = results.size();
    }
    final int step = maxT / nSteps;
    final TDoubleArrayList x = new TDoubleArrayList();
    final TDoubleArrayList y = new TDoubleArrayList();
    double yMin = fireNumber;
    double yMax = fireNumber;
    final MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    int index = 0;
    final PeakResult[] list = results.toArray();
    for (int t = step; t <= maxT - step; t += step) {
        while (index < list.length) {
            final PeakResult r = list[index];
            if (r.getFrame() <= t) {
                newResults.add(r);
                index++;
            } else {
                break;
            }
        }
        x.add(t);
        final Fire f = this.copy();
        final FireResult result = f.calculateFireNumber(fourierMethod, samplingMethod, thresholdMethod, fourierImageScale, imageSize);
        final double fire = (result == null) ? 0 : result.fireNumber;
        y.add(fire);
        yMin = Math.min(yMin, fire);
        yMax = Math.max(yMax, fire);
    }
    // Add the final fire number
    x.add(maxT);
    y.add(fireNumber);
    final double[] xValues = x.toArray();
    final double[] yValues = y.toArray();
    String units = "px";
    if (results.getCalibration() != null) {
        nmPerUnit = results.getNmPerPixel();
        units = "nm";
    }
    final String title = name + " FRC Time Evolution";
    final Plot plot = new Plot(title, "Frames", "Resolution (" + units + ")");
    final 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);
    ImageJUtils.display(title, plot);
}

Example 34 with MemoryPeakResults

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

the class ImageJ3DResultsViewer method createRankById.

private static float[] createRankById(MemoryPeakResults results) {
    if (results.hasId()) {
        final TFloatArrayList list = new TFloatArrayList(results.size());
        results.forEach((PeakResultProcedure) r -> list.add(r.getId()));
        return list.toArray();
    }
    return null;
}

Example 35 with MemoryPeakResults

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

the class OverlayResults 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;
    }
    names = new String[MemoryPeakResults.getResultNames().size() + 1];
    ids = new int[names.length];
    int count = 0;
    names[count++] = "(None)";
    for (final MemoryPeakResults results : MemoryPeakResults.getAllResults()) {
        if (results.getSource() != null && results.getSource().getOriginal() instanceof IJImageSource) {
            final IJImageSource source = (IJImageSource) (results.getSource().getOriginal());
            final ImagePlus imp = WindowManager.getImage(source.getName());
            if (imp != null) {
                ids[count] = imp.getID();
                names[count++] = results.getName();
            }
        }
    }
    if (count == 1) {
        IJ.error(TITLE, "There are no result images available");
        return;
    }
    names = Arrays.copyOf(names, count);
    Thread thread = null;
    Worker worker = null;
    final NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
    settings = Settings.load();
    settings.save();
    gd.addMessage("Overlay results on current image frame");
    gd.addChoice("Results", names, (settings.name == null) ? "" : settings.name);
    gd.addCheckbox("Show_table", settings.showTable);
    gd.addMessage("");
    gd.addHelp(HelpUrls.getUrl("overlay-results"));
    gd.hideCancelButton();
    gd.setOKLabel("Close");
    if (!(IJ.isMacro() || java.awt.GraphicsEnvironment.isHeadless())) {
        worker = new Worker();
        choice = (Choice) gd.getChoices().get(0);
        choice.addItemListener(worker);
        checkbox = (Checkbox) gd.getCheckboxes().get(0);
        checkbox.addItemListener(worker);
        label = (Label) gd.getMessage();
        // Initialise
        worker.refresh();
        // Listen for changes to an image
        ImagePlus.addImageListener(worker);
        thread = new Thread(worker);
        thread.setDaemon(true);
        thread.start();
    }
    gd.showDialog();
    if (worker != null) {
        ImagePlus.removeImageListener(worker);
    }
    if (!gd.wasCanceled()) {
        settings.name = gd.getNextChoice();
        settings.showTable = gd.getNextBoolean();
    }
    if (thread != null && worker != null) {
        worker.running = false;
        inbox.close(true);
        try {
            thread.join(0);
        } catch (final InterruptedException ex) {
            Logger.getLogger(getClass().getName()).log(Level.WARNING, "Unexpected interruption", ex);
            Thread.currentThread().interrupt();
        }
    }
}