Examples with ImageStack ij.ImageStack used on opensource projects

Example 26 with ImageStack

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

the class FRC method getComplexFFT.

/**
	 * Convert an image into a Fourier image with real and imaginary parts
	 * 
	 * @param ip
	 *            The image
	 * @return the real and imaginary parts
	 */
public FloatProcessor[] getComplexFFT(ImageProcessor ip) {
    FloatProcessor taperedDataImage = getSquareTaperedImage(ip);
    FHT2 fht = new FHT2(taperedDataImage);
    fht.setShowProgress(false);
    fht.transform();
    ImageStack stack1 = fht.getComplexTransform();
    return getProcessors(stack1);
}

Example 27 with ImageStack

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

the class IJImageSource method initialise.

private boolean initialise(ImagePlus imp) {
    imageArray = null;
    imageStack = null;
    if (imp == null)
        return false;
    ImageStack s = imp.getImageStack();
    if (s.isVirtual()) {
        // We must use the image stack to get the image data for virtual images
        imageStack = s;
    } else {
        // We can access the image array directly
        imageArray = s.getImageArray();
    }
    width = imp.getWidth();
    height = imp.getHeight();
    // Store the number of valid frames
    if (singleFrame > 0)
        frames = 1 + this.extraFrames;
    else
        frames = imp.getStackSize();
    slice = 0;
    FileInfo info = imp.getOriginalFileInfo();
    if (info != null)
        path = info.directory + info.fileName;
    return true;
}

Example 28 with ImageStack

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

the class DoubletAnalysis method run.

/**
	 * Run.
	 */
private void run() {
    doubletResults = null;
    final ImageStack stack = imp.getImageStack();
    // Get the coordinates per frame
    TIntObjectHashMap<ArrayList<Coordinate>> actualCoordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
    final long[] sumCount = new long[1];
    actualCoordinates.forEachValue(new TObjectProcedure<ArrayList<Coordinate>>() {

        public boolean execute(ArrayList<Coordinate> list) {
            sumCount[0] += list.size();
            return true;
        }
    });
    final double density = 1e6 * sumCount[0] / (simulationParameters.a * simulationParameters.a * results.getBounds().getWidth() * results.getBounds().getHeight() * actualCoordinates.size());
    // Create a pool of workers
    final int nThreads = Prefs.getThreads();
    final BlockingQueue<Integer> jobs = new ArrayBlockingQueue<Integer>(nThreads * 2);
    List<Worker> workers = new LinkedList<Worker>();
    List<Thread> threads = new LinkedList<Thread>();
    Overlay overlay = (showOverlay) ? new Overlay() : null;
    for (int i = 0; i < nThreads; i++) {
        Worker worker = new Worker(jobs, stack, actualCoordinates, fitConfig, overlay);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Fit the frames
    long runTime = System.nanoTime();
    totalProgress = actualCoordinates.size();
    stepProgress = Utils.getProgressInterval(totalProgress);
    progress = 0;
    actualCoordinates.forEachKey(new TIntProcedure() {

        public boolean execute(int frame) {
            put(jobs, frame);
            return true;
        }
    });
    // Finish all the worker threads by passing in a null job
    for (int i = 0; i < threads.size(); i++) {
        put(jobs, -1);
    }
    // Wait for all to finish
    for (int i = 0; i < threads.size(); i++) {
        try {
            threads.get(i).join();
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
    threads.clear();
    threads = null;
    IJ.showProgress(1);
    IJ.showStatus("Collecting results ...");
    runTime = System.nanoTime() - runTime;
    // Collect the results
    int cic = 0, daic = 0, dbic = 0;
    ArrayList<DoubletResult> results = null;
    int maxH = 0, maxH2 = 0, maxH3 = 0;
    for (Worker worker : workers) {
        if (results == null)
            results = worker.results;
        else
            results.addAll(worker.results);
        cic += worker.cic;
        daic += worker.daic;
        dbic += worker.dbic;
        maxH = Maths.max(maxH, worker.spotHistogram.length);
        for (int k = 0; k < 3; k++) {
            maxH2 = Maths.max(maxH2, worker.neighbourHistogram[k].length);
            maxH3 = Maths.max(maxH3, worker.almostNeighbourHistogram[k].length);
        }
    }
    if (cic > 0)
        System.out.printf("Difference AIC %d, BIC %d, Total %d\n", daic, dbic, cic);
    if (showHistograms) {
        double[] spotHistogram = new double[maxH];
        double[] resultHistogram = new double[maxH];
        double[][] neighbourHistogram = new double[3][maxH2];
        double[][] almostNeighbourHistogram = new double[3][maxH3];
        for (Worker worker : workers) {
            final int[] h1a = worker.spotHistogram;
            final int[] h1b = worker.resultHistogram;
            for (int j = 0; j < h1a.length; j++) {
                spotHistogram[j] += h1a[j];
                resultHistogram[j] += h1b[j];
            }
            final int[][] h2 = worker.neighbourHistogram;
            final int[][] h3 = worker.almostNeighbourHistogram;
            for (int k = 0; k < 3; k++) {
                for (int j = 0; j < h2[k].length; j++) neighbourHistogram[k][j] += h2[k][j];
                for (int j = 0; j < h3[k].length; j++) almostNeighbourHistogram[k][j] += h3[k][j];
            }
        }
        showHistogram(0, spotHistogram);
        showHistogram(1, resultHistogram);
        showHistogram(2, neighbourHistogram[0]);
        showHistogram(3, neighbourHistogram[1]);
        showHistogram(4, neighbourHistogram[2]);
        showHistogram(5, almostNeighbourHistogram[0]);
        showHistogram(6, almostNeighbourHistogram[1]);
        showHistogram(7, almostNeighbourHistogram[2]);
    }
    workers.clear();
    workers = null;
    if (overlay != null)
        imp.setOverlay(overlay);
    MemoryPeakResults.freeMemory();
    Collections.sort(results);
    summariseResults(results, density, runTime);
    windowOrganiser.tile();
    IJ.showStatus("");
}

Example 29 with ImageStack

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

the class DriftCalculator method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    // Require some fit results and selected regions
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    Roi[] rois = getRois();
    String[] stackTitles = createStackImageList();
    if (!showDialog(rois, stackTitles))
        return;
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() < 2) {
        IJ.error(TITLE, "There are not enough fitting results for drift correction");
        return;
    }
    double[][] drift = null;
    int[] limits = findTimeLimits(results);
    if (method.equals(MARKED_ROIS)) {
        drift = calculateUsingMarkers(results, limits, rois);
    } else if (method.equals(STACK_ALIGNMENT)) {
        ImageStack stack = showStackDialog(stackTitles);
        if (stack == null)
            return;
        drift = calculateUsingImageStack(stack, limits);
    } else if (method.equals(DRIFT_FILE)) {
        drift = calculateUsingDriftFile(limits);
    } else {
        if (!showSubImageDialog())
            return;
        drift = calculateUsingFrames(results, limits, Integer.parseInt(reconstructionSize));
    }
    if (drift == null)
        return;
    Utils.log("Drift correction interpolated for frames [%d - %d] of [%d - %d] (%s%%)", interpolationStart, interpolationEnd, limits[0], limits[1], Utils.rounded((100.0 * (interpolationEnd - interpolationStart + 1)) / (limits[1] - limits[0] + 1)));
    applyDriftCorrection(results, drift);
}

Example 30 with ImageStack

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

the class DepthMask method createMask.

private void createMask() {
    ImagePlus impXY = WindowManager.getImage(titleXY);
    ImagePlus impXZ = WindowManager.getImage(titleXZ);
    if (impXY == null) {
        IJ.error(TITLE, "No XY mask");
        return;
    }
    if (impXZ == null) {
        IJ.error(TITLE, "No XZ mask");
        return;
    }
    if (impXY.getWidth() != impXZ.getWidth()) {
        IJ.error(TITLE, "XY mask width does not match XZ mask width");
        return;
    }
    final int maxx = impXY.getWidth();
    final int maxy = impXY.getHeight();
    final int maxz = impXZ.getHeight();
    ImageStack stack = new ImageStack(maxx, maxy, maxz);
    byte[] maskXY = getMask(impXY);
    byte[] maskXZ = getMask(impXZ);
    byte[] strip = new byte[maxx];
    for (int z = 0, p = 0; z < maxz; z++, p += maxx) {
        byte[] mask = maskXY.clone();
        System.arraycopy(maskXZ, p, strip, 0, maxx);
        for (int y = 0, i = 0; y < maxy; y++) {
            for (int x = 0; x < maxx; x++, i++) {
                if (strip[x] == 0)
                    mask[i] = 0;
            }
        }
        stack.setPixels(mask, z + 1);
    }
    Utils.display(TITLE, stack);
}