Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 31 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class CMOSAnalysis method run.

private void run() {
    long start = System.currentTimeMillis();
    // Avoid all the file saves from updating the progress bar and status line
    Utils.setShowProgress(false);
    Utils.setShowStatus(false);
    JLabel statusLine = Utils.getStatusLine();
    progressBar = Utils.getProgressBar();
    // Create thread pool and workers
    ExecutorService executor = Executors.newFixedThreadPool(getThreads());
    TurboList<Future<?>> futures = new TurboList<Future<?>>(nThreads);
    TurboList<ImageWorker> workers = new TurboList<ImageWorker>(nThreads);
    double[][][] data = new double[subDirs.size()][2][];
    double[] pixelOffset = null, pixelVariance = null;
    Statistics statsOffset = null, statsVariance = null;
    // For each sub-directory compute the mean and variance
    final int nSubDirs = subDirs.size();
    boolean error = false;
    for (int n = 0; n < nSubDirs; n++) {
        SubDir sd = subDirs.getf(n);
        statusLine.setText("Analysing " + sd.name);
        // Open the series
        SeriesImageSource source = new SeriesImageSource(sd.name, sd.path.getPath());
        //source.setLogProgress(true);
        if (!source.open()) {
            error = true;
            IJ.error(TITLE, "Failed to open image series: " + sd.path.getPath());
            break;
        }
        // So the bar remains at 99% when workers have finished
        totalProgress = source.getFrames() + 1;
        stepProgress = Utils.getProgressInterval(totalProgress);
        progress = 0;
        progressBar.show(0);
        ArrayMoment moment = (rollingAlgorithm) ? new RollingArrayMoment() : new SimpleArrayMoment();
        final BlockingQueue<ImageJob> jobs = new ArrayBlockingQueue<ImageJob>(nThreads * 2);
        for (int i = 0; i < nThreads; i++) {
            final ImageWorker worker = new ImageWorker(jobs, moment);
            workers.add(worker);
            futures.add(executor.submit(worker));
        }
        // Process the data
        for (float[] pixels = source.next(); pixels != null; pixels = source.next()) {
            put(jobs, new ImageJob(pixels));
        }
        // Finish all the worker threads by passing in a null job
        for (int i = 0; i < nThreads; i++) {
            put(jobs, new ImageJob(null));
        }
        // Wait for all to finish
        for (int t = futures.size(); t-- > 0; ) {
            try {
                // The future .get() method will block until completed
                futures.get(t).get();
            } catch (Exception e) {
                // This should not happen. 
                e.printStackTrace();
            }
        }
        // Create the final aggregate statistics
        for (ImageWorker w : workers) moment.add(w.moment);
        data[n][0] = moment.getFirstMoment();
        data[n][1] = moment.getVariance();
        // Reset
        futures.clear();
        workers.clear();
        Statistics s = new Statistics(data[n][0]);
        if (n != 0) {
            // Compute mean ADU
            Statistics signal = new Statistics();
            double[] mean = data[n][0];
            for (int i = 0; i < pixelOffset.length; i++) signal.add(mean[i] - pixelOffset[i]);
            Utils.log("%s Mean = %s +/- %s. Signal = %s +/- %s ADU", sd.name, Utils.rounded(s.getMean()), Utils.rounded(s.getStandardDeviation()), Utils.rounded(signal.getMean()), Utils.rounded(signal.getStandardDeviation()));
            // TODO - optionally save
            ImageStack stack = new ImageStack(source.getWidth(), source.getHeight());
            stack.addSlice("Mean", Utils.toFloat(data[n][0]));
            stack.addSlice("Variance", Utils.toFloat(data[n][1]));
            IJ.save(new ImagePlus("PerPixel", stack), new File(directory, "perPixel" + sd.name + ".tif").getPath());
        } else {
            pixelOffset = data[0][0];
            pixelVariance = data[0][1];
            statsOffset = s;
            statsVariance = new Statistics(pixelVariance);
            Utils.log("%s Offset = %s +/- %s. Variance = %s +/- %s", sd.name, Utils.rounded(s.getMean()), Utils.rounded(s.getStandardDeviation()), Utils.rounded(statsVariance.getMean()), Utils.rounded(statsVariance.getStandardDeviation()));
        }
    }
    Utils.setShowStatus(true);
    Utils.setShowProgress(true);
    IJ.showProgress(1);
    executor.shutdown();
    if (error)
        return;
    // Compute the gain
    statusLine.setText("Computing gain");
    double[] pixelGain = new double[pixelOffset.length];
    // Ignore first as this is the 0 exposure image
    for (int i = 0; i < pixelGain.length; i++) {
        // Use equation 2.5 from the Huang et al paper.
        double bibiT = 0;
        double biaiT = 0;
        for (int n = 1; n < nSubDirs; n++) {
            double bi = data[n][0][i] - pixelOffset[i];
            double ai = data[n][1][i] - pixelVariance[i];
            bibiT += bi * bi;
            biaiT += bi * ai;
        }
        pixelGain[i] = biaiT / bibiT;
    }
    Statistics statsGain = new Statistics(pixelGain);
    Utils.log("Gain Mean = %s +/- %s", Utils.rounded(statsGain.getMean()), Utils.rounded(statsGain.getStandardDeviation()));
    // Histogram of offset, variance and gain
    int bins = Utils.getBinsSturges(pixelGain.length);
    WindowOrganiser wo = new WindowOrganiser();
    showHistogram("Offset", pixelOffset, bins, statsOffset, wo);
    showHistogram("Variance", pixelVariance, bins, statsVariance, wo);
    showHistogram("Gain", pixelGain, bins, statsGain, wo);
    wo.tile();
    // Save
    measuredStack = new ImageStack(size, size);
    measuredStack.addSlice("Offset", Utils.toFloat(pixelOffset));
    measuredStack.addSlice("Variance", Utils.toFloat(pixelVariance));
    measuredStack.addSlice("Gain", Utils.toFloat(pixelGain));
    IJ.save(new ImagePlus("PerPixel", measuredStack), new File(directory, "perPixel.tif").getPath());
    // Remove the status from the ij.io.ImageWriter class
    IJ.showStatus("");
    Utils.log("Analysis time = " + Utils.timeToString(System.currentTimeMillis() - start));
}

Example 32 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class CMOSAnalysis method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    extraOptions = Utils.isExtraOptions();
    // Avoid the status bar talking to the current image
    WindowManager.setTempCurrentImage(null);
    //@formatter:off
    IJ.log(TextUtils.wrap(TITLE + ": Analyse the per-pixel offset, variance and gain of sCMOS images. " + "See Huang et al (2013) Video-rate nanoscopy using sCMOS camera–specific " + "single-molecule localization algorithms. Nature Methods 10, 653-658 " + "(Supplementary Information).", 80));
    //@formatter:on
    String dir = Utils.getDirectory(TITLE, directory);
    if (Utils.isNullOrEmpty(dir))
        return;
    directory = dir;
    boolean simulate = "simulate".equals(arg);
    if (simulate || extraOptions) {
        if (!showSimulateDialog())
            return;
        simulate();
    }
    if (!showDialog())
        return;
    run();
    if (simulationImp == null) {
        // Just in case an old simulation is in the directory
        ImagePlus imp = IJ.openImage(new File(directory, "perPixelSimulation.tif").getPath());
        if (imp != null && imp.getStackSize() == 3 && imp.getWidth() == measuredStack.getWidth() && imp.getHeight() == measuredStack.getHeight())
            simulationImp = imp;
    }
    if (simulationImp != null)
        computeError();
}

Example 33 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class CreateData method createBackgroundPixels.

private synchronized void createBackgroundPixels() {
    // Cache illumination background
    if (backgroundPixels == null) {
        backgroundPixels = new float[settings.size * settings.size];
        ImagePlus imp = WindowManager.getImage(settings.backgroundImage);
        if (imp != null) {
            // Use an image for the background
            ImageProcessor ip = imp.getProcessor().duplicate().toFloat(0, null);
            ip.setInterpolationMethod(ImageProcessor.BILINEAR);
            ip = ip.resize(settings.size, settings.size);
            float[] data = (float[]) ip.getPixels();
            final double max = FastMath.max(0, Maths.max(data));
            if (max != 0) {
                final double scale = settings.background / max;
                for (int i = 0; i < backgroundPixels.length; i++) {
                    // Ignore pixels below zero
                    backgroundPixels[i] = (float) (FastMath.max(0, data[i]) * scale);
                }
                return;
            }
        }
        // Use the illumination (this is the fall-back method if the background image has no
        // maximum)
        SpatialIllumination illumination = createIllumination(settings.background, 0);
        double[] xyz = new double[3];
        for (int y = 0, i = 0; y < settings.size; y++) {
            xyz[1] = y - settings.size / 2;
            for (int x = 0, x2 = -settings.size / 2; x < settings.size; x++, x2++, i++) {
                xyz[0] = x2;
                backgroundPixels[i] = (float) illumination.getPhotons(xyz);
            }
        }
    }
}

Example 34 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method updateResults.

/**
	 * Update the results window using the current selected slice from the template image.
	 *
	 * @param slice
	 *            the slice
	 * @return the text window
	 */
public TextWindow updateResults(int slice) {
    if (slice == currentSlice || text == null)
        return resultsWindow;
    currentSlice = slice;
    if (resultsWindow == null || !resultsWindow.isVisible()) {
        resultsWindow = new TextWindow(TITLE + " Results", headings, "", 450, 250);
        // Put next to the image
        ImagePlus imp = WindowManager.getImage(templateId);
        if (imp != null && imp.getWindow() != null) {
            ImageWindow iw = imp.getWindow();
            Point p = iw.getLocation();
            p.x += iw.getWidth();
            resultsWindow.setLocation(p);
        }
    }
    resultsWindow.getTextPanel().clear();
    String data = text.get(slice);
    if (!Utils.isNullOrEmpty(data))
        resultsWindow.append(data);
    return resultsWindow;
}

Example 35 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method showTemplateImage.

private void showTemplateImage(String name) {
    ImagePlus imp = getTemplateImage(name);
    if (imp == null) {
        IJ.error(TITLE, "Failed to load example image for template: " + name);
    } else {
        this.imp = displayTemplate(TITLE, imp);
        if (Utils.isNewWindow()) {
            // Zoom a bit
            ImageWindow iw = this.imp.getWindow();
            for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                iw.getCanvas().zoomIn(0, 0);
            }
        }
        createResults(this.imp);
        showTemplateInfo(name);
    }
}