Examples with SeriesImageSource gdsc.smlm.ij.SeriesImageSource used on opensource projects

Example 1 with SeriesImageSource

use of gdsc.smlm.ij.SeriesImageSource in project GDSC-SMLM by aherbert.

the class PeakFit method setup.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
	 */
public int setup(String arg, ImagePlus imp) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    plugin_flags = FLAGS;
    extraOptions = Utils.isExtraOptions();
    maximaIdentification = (arg != null && arg.contains("spot"));
    fitMaxima = (arg != null && arg.contains("maxima"));
    simpleFit = (arg != null && arg.contains("simple"));
    boolean runSeries = (arg != null && arg.contains("series"));
    ImageSource imageSource = null;
    if (fitMaxima) {
        imp = null;
        // The image source will be found from the peak results.
        if (!showMaximaDialog())
            return DONE;
        MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
        if (results == null || results.size() == 0) {
            IJ.error(TITLE, "No results could be loaded");
            return DONE;
        }
        // Check for single frame
        singleFrame = results.getHead().getFrame();
        for (PeakResult result : results.getResults()) {
            if (singleFrame != result.getFrame()) {
                singleFrame = 0;
                break;
            }
        }
        imageSource = results.getSource();
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else if (runSeries) {
        imp = null;
        // Select input folder
        String inputDirectory;
        inputDirectory = IJ.getDirectory("Select image series ...");
        //inputDirectory = getInputDirectory("Select image series ...");
        if (inputDirectory == null)
            return DONE;
        // Load input series ...
        SeriesOpener series;
        if (extraOptions)
            series = new SeriesOpener(inputDirectory, true, numberOfThreads);
        else
            series = new SeriesOpener(inputDirectory);
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory);
            return DONE;
        }
        SeriesImageSource seriesImageSource = new SeriesImageSource(getName(series.getImageList()), series);
        seriesImageSource.setLogProgress(true);
        if (extraOptions) {
            numberOfThreads = Math.max(1, series.getNumberOfThreads());
            seriesImageSource.setNumberOfThreads(numberOfThreads);
        }
        imageSource = seriesImageSource;
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }
        // Check it is not a previous result
        if (imp.getTitle().endsWith(IJImagePeakResults.IMAGE_SUFFIX)) {
            IJImageSource tmpImageSource = null;
            // Check the image to see if it has an image source XML structure in the info property
            Object o = imp.getProperty("Info");
            Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL);
            Matcher match = pattern.matcher((o == null) ? "" : o.toString());
            if (match.find()) {
                ImageSource source = ImageSource.fromXML(match.group(1));
                if (source instanceof IJImageSource) {
                    tmpImageSource = (IJImageSource) source;
                    if (!tmpImageSource.open()) {
                        tmpImageSource = null;
                    } else {
                        imp = WindowManager.getImage(tmpImageSource.getName());
                    }
                }
            }
            if (tmpImageSource == null) {
                // Look for a parent using the title
                String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - IJImagePeakResults.IMAGE_SUFFIX.length() - 1);
                ImagePlus parentImp = WindowManager.getImage(parentTitle);
                if (parentImp != null) {
                    tmpImageSource = new IJImageSource(parentImp);
                    imp = parentImp;
                }
            }
            String message = "The selected image may be a previous fit result";
            if (tmpImageSource != null) {
                // are missing
                if (!Utils.isNullOrEmpty(tmpImageSource.getName()))
                    message += " of: \n \n" + tmpImageSource.getName();
                message += " \n \nFit the parent?";
            } else
                message += " \n \nDo you want to continue?";
            YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message);
            if (tmpImageSource == null) {
                if (!d.yesPressed())
                    return DONE;
            } else {
                if (d.yesPressed())
                    imageSource = tmpImageSource;
                if (d.cancelPressed())
                    return DONE;
            }
        }
        if (imageSource == null)
            imageSource = new IJImageSource(imp);
    }
    time = -1;
    if (!initialiseImage(imageSource, getBounds(imp), false)) {
        IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName());
        return DONE;
    }
    int flags = showDialog(imp);
    if ((flags & DONE) == 0) {
        // Repeat so that we pass in the selected option for ignoring the bounds.
        // This should not be necessary since it is set within the readDialog method.
        //if (ignoreBoundsForNoise)
        //	initialiseImage(imageSource, bounds, ignoreBoundsForNoise);
        initialiseFitting();
    }
    return flags;
}

Example 2 with SeriesImageSource

use of gdsc.smlm.ij.SeriesImageSource 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));
}