Examples with ImageStack ij.ImageStack used on opensource projects

Example 21 with ImageStack

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

the class YeastMask method createNucleusSphere.

/**
	 * Create a sphere using the given pixel width and stack depth using a fraction of the original cell radius
	 * 
	 * @param width
	 * @param depth
	 * @return A sphere
	 */
private ImageStack createNucleusSphere(int width, int depth) {
    // Create a sphere. This could be done exploiting symmetry to be more efficient
    // but is left as a simple implementation
    final double centreX = width * 0.5;
    final double centreZ = depth * 0.5;
    // Precompute squares for the width
    double[] s = new double[width];
    for (int iy = 0; iy < width; iy++) {
        final double y = (centreX - (iy + 0.5)) * nmPerPixel;
        s[iy] = y * y;
    }
    ImageStack stack = new ImageStack(width, width, depth);
    final byte on = (byte) 255;
    final double r = radius * 1000 * nucleus;
    final double r2 = r * r;
    for (int iz = 0; iz < depth; iz++) {
        final double z = (centreZ - (iz + 0.5)) * nmPerSlice;
        final double z2 = z * z;
        byte[] mask = new byte[width * width];
        for (int iy = 0, i = 0; iy < width; iy++) {
            final double y2z2 = s[iy] + z2;
            for (int ix = 0; ix < width; ix++, i++) {
                final double d2 = s[ix] + y2z2;
                if (d2 < r2)
                    mask[i] = on;
            }
        }
        stack.setPixels(mask, iz + 1);
    }
    return stack;
}

Example 22 with ImageStack

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

the class BenchmarkSpotFit method run.

private void run() {
    // Extract all the results in memory into a list per frame. This can be cached
    boolean refresh = false;
    if (lastId != simulationParameters.id) {
        // Do not get integer coordinates
        // The Coordinate objects will be PeakResultPoint objects that store the original PeakResult
        // from the MemoryPeakResults
        actualCoordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
        lastId = simulationParameters.id;
        refresh = true;
    }
    // Extract all the candidates into a list per frame. This can be cached if the settings have not changed
    final int width = (config.isIncludeNeighbours()) ? config.getRelativeFitting() : 0;
    final Settings settings = new Settings(BenchmarkSpotFilter.filterResult.id, fractionPositives, fractionNegativesAfterAllPositives, negativesAfterAllPositives, width);
    if (refresh || !settings.equals(lastSettings)) {
        filterCandidates = subsetFilterResults(BenchmarkSpotFilter.filterResult.filterResults, width);
        lastSettings = settings;
        lastFilterId = BenchmarkSpotFilter.filterResult.id;
    }
    stopWatch = StopWatch.createStarted();
    final ImageStack stack = imp.getImageStack();
    clearFitResults();
    // Save results to memory
    MemoryPeakResults peakResults = new MemoryPeakResults();
    peakResults.copySettings(this.results);
    peakResults.setName(TITLE);
    MemoryPeakResults.addResults(peakResults);
    // Create a pool of workers
    final int nThreads = Prefs.getThreads();
    BlockingQueue<Integer> jobs = new ArrayBlockingQueue<Integer>(nThreads * 2);
    List<Worker> workers = new LinkedList<Worker>();
    List<Thread> threads = new LinkedList<Thread>();
    for (int i = 0; i < nThreads; i++) {
        Worker worker = new Worker(jobs, stack, actualCoordinates, filterCandidates, peakResults);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Fit the frames
    long runTime = System.nanoTime();
    totalProgress = stack.getSize();
    stepProgress = Utils.getProgressInterval(totalProgress);
    progress = 0;
    for (int i = 1; i <= totalProgress; i++) {
        put(jobs, i);
    }
    // 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();
    IJ.showProgress(1);
    runTime = System.nanoTime() - runTime;
    if (Utils.isInterrupted()) {
        return;
    }
    stopWatch.stop();
    final String timeString = stopWatch.toString();
    IJ.log("Spot fit time : " + timeString);
    IJ.showStatus("Collecting results ...");
    fitResultsId++;
    fitResults = new TIntObjectHashMap<FilterCandidates>();
    for (Worker w : workers) {
        fitResults.putAll(w.results);
    }
    // Assign a unique ID to each result
    int count = 0;
    // Materialise into an array since we use it twice
    FilterCandidates[] candidates = fitResults.values(new FilterCandidates[fitResults.size()]);
    for (FilterCandidates result : candidates) {
        for (int i = 0; i < result.fitResult.length; i++) {
            final MultiPathFitResult fitResult = result.fitResult[i];
            count += count(fitResult.getSingleFitResult());
            count += count(fitResult.getMultiFitResult());
            count += count(fitResult.getDoubletFitResult());
            count += count(fitResult.getMultiDoubletFitResult());
        }
    }
    PreprocessedPeakResult[] preprocessedPeakResults = new PreprocessedPeakResult[count];
    count = 0;
    for (FilterCandidates result : candidates) {
        for (int i = 0; i < result.fitResult.length; i++) {
            final MultiPathFitResult fitResult = result.fitResult[i];
            count = store(fitResult.getSingleFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getMultiFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getDoubletFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getMultiDoubletFitResult(), count, preprocessedPeakResults);
        }
    }
    summariseResults(fitResults, runTime, preprocessedPeakResults, count);
    IJ.showStatus("");
}

Example 23 with ImageStack

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

the class BenchmarkFilterAnalysis method saveTemplate.

/**
	 * Save PeakFit configuration template using the current benchmark settings.
	 * 
	 * @param topFilterSummary
	 */
private void saveTemplate(String topFilterSummary) {
    FitEngineConfiguration config = new FitEngineConfiguration(new FitConfiguration());
    if (!updateAllConfiguration(config, true)) {
        IJ.log("Unable to create the template configuration");
        return;
    }
    // Remove the PSF width to make the template generic
    config.getFitConfiguration().setInitialPeakStdDev(0);
    String filename = getFilename("Template_File", templateFilename);
    if (filename != null) {
        templateFilename = filename;
        Prefs.set(KEY_TEMPLATE_FILENAME, filename);
        GlobalSettings settings = new GlobalSettings();
        settings.setNotes(getNotes(topFilterSummary));
        settings.setFitEngineConfiguration(config);
        if (!SettingsManager.saveSettings(settings, filename, true)) {
            IJ.log("Unable to save the template configuration");
            return;
        }
        // Save some random frames from the test image data
        ImagePlus imp = CreateData.getImage();
        if (imp == null)
            return;
        // Get the number of frames
        final ImageStack stack = imp.getImageStack();
        if (sampler == null || sampler.getResults() != results) {
            sampler = new ResultsImageSampler(results, stack, 32);
            sampler.analyse();
        }
        if (!sampler.isValid())
            return;
        // Iteratively show the example until the user is happy.
        // Yes = OK, No = Repeat, Cancel = Do not save
        String keyNo = "nNo";
        String keyLow = "nLower";
        String keyHigh = "nHigher";
        if (Utils.isMacro()) {
            // Collect the options if running in a macro
            String options = Macro.getOptions();
            nNo = Integer.parseInt(Macro.getValue(options, keyNo, Integer.toString(nNo)));
            nLow = Integer.parseInt(Macro.getValue(options, keyLow, Integer.toString(nLow)));
            nHigh = Integer.parseInt(Macro.getValue(options, keyHigh, Integer.toString(nHigh)));
        } else {
            if (nLow + nHigh == 0)
                nLow = nHigh = 1;
        }
        final ImagePlus[] out = new ImagePlus[1];
        out[0] = sampler.getSample(nNo, nLow, nHigh);
        if (!Utils.isMacro()) {
            // Show the template results
            final ConfigurationTemplate configTemplate = new ConfigurationTemplate();
            // Interactively show the sample image data
            final boolean[] close = new boolean[1];
            final ImagePlus[] outImp = new ImagePlus[1];
            if (out[0] != null) {
                outImp[0] = display(out[0]);
                if (Utils.isNewWindow()) {
                    close[0] = true;
                    // Zoom a bit
                    ImageWindow iw = outImp[0].getWindow();
                    for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                        iw.getCanvas().zoomIn(0, 0);
                    }
                }
                configTemplate.createResults(outImp[0]);
            }
            // TODO - fix this when a second sample is made as the results are not updated.
            ImageListener listener = new ImageListener() {

                public void imageOpened(ImagePlus imp) {
                }

                public void imageClosed(ImagePlus imp) {
                }

                public void imageUpdated(ImagePlus imp) {
                    if (imp != null && imp == outImp[0]) {
                        configTemplate.updateResults(imp.getCurrentSlice());
                    }
                }
            };
            ImagePlus.addImageListener(listener);
            // For the dialog
            String msg = String.format("Showing image data for the template example.\n \nSample Frames:\nEmpty = %d\nLower density = %d\nHigher density = %d\n", sampler.getNumberOfEmptySamples(), sampler.getNumberOfLowDensitySamples(), sampler.getNumberOfHighDensitySamples());
            // Turn off the recorder when the dialog is showing
            boolean record = Recorder.record;
            Recorder.record = false;
            NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
            gd.addMessage(msg);
            //gd.enableYesNoCancel(" Save ", " Resample ");
            gd.addSlider(keyNo, 0, 10, nNo);
            gd.addSlider(keyLow, 0, 10, nLow);
            gd.addSlider(keyHigh, 0, 10, nHigh);
            gd.addDialogListener(new DialogListener() {

                public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
                    // image the user has not seen.
                    if (e == null)
                        return true;
                    nNo = (int) gd.getNextNumber();
                    nLow = (int) gd.getNextNumber();
                    nHigh = (int) gd.getNextNumber();
                    out[0] = sampler.getSample(nNo, nLow, nHigh);
                    if (out[0] != null) {
                        outImp[0] = display(out[0]);
                        if (Utils.isNewWindow()) {
                            close[0] = true;
                            // Zoom a bit
                            ImageWindow iw = outImp[0].getWindow();
                            for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                                iw.getCanvas().zoomIn(0, 0);
                            }
                        }
                        configTemplate.createResults(outImp[0]);
                    }
                    return true;
                }
            });
            gd.showDialog();
            if (gd.wasCanceled()) {
                out[0] = null;
                // For the recorder
                nNo = nLow = nHigh = 0;
            }
            if (close[0]) {
                // Because closing the image sets the stack pixels array to null
                if (out[0] != null)
                    out[0] = out[0].duplicate();
                outImp[0].close();
            }
            configTemplate.closeResults();
            ImagePlus.removeImageListener(listener);
            if (record) {
                Recorder.record = true;
                Recorder.recordOption(keyNo, Integer.toString(nNo));
                Recorder.recordOption(keyLow, Integer.toString(nLow));
                Recorder.recordOption(keyHigh, Integer.toString(nHigh));
            }
        }
        if (out[0] == null)
            return;
        ImagePlus example = out[0];
        filename = Utils.replaceExtension(filename, ".tif");
        IJ.save(example, filename);
    }
}

Example 24 with ImageStack

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

the class PSFCombiner method combineImages.

private void combineImages() {
    double nmPerPixel = getNmPerPixel();
    if (nmPerPixel <= 0)
        return;
    double nmPerSlice = getNmPerSlice();
    if (nmPerPixel <= 0)
        return;
    // Find the lowest start point
    int min = 0;
    for (PSF psf : input) {
        if (min > psf.start)
            min = psf.start;
    }
    // Shift all stacks and find the dimensions
    final int shift = -min;
    int max = 0, size = 0;
    int totalImages = 0;
    for (PSF psf : input) {
        psf.start += shift;
        totalImages += psf.psfSettings.nImages;
        if (max < psf.getEnd())
            max = psf.getEnd();
        if (size < psf.getSize())
            size = psf.getSize();
    }
    // Create a stack to hold all the images
    ImageStack stack = new ImageStack(size, size, max);
    for (int n = 1; n <= max; n++) stack.setPixels(new float[size * size], n);
    // Insert all the PSFs
    IJ.showStatus("Creating combined image ...");
    int imageNo = 0;
    double fraction = 1.0 / input.size();
    for (PSF psf : input) {
        double progress = imageNo * fraction;
        ImageStack psfStack = psf.psfStack;
        final int offsetXY = (psf.getSize() - size) / 2;
        final int offsetZ = psf.start;
        final int w = psf.getSize();
        final double weight = (1.0 * psf.psfSettings.nImages) / totalImages;
        final double increment = fraction / psfStack.getSize();
        for (int n = 1; n <= psfStack.getSize(); n++) {
            IJ.showProgress(progress += increment);
            // Get the data and adjust using the weight
            float[] psfData = ImageConverter.getData(psfStack.getProcessor(n));
            for (int i = 0; i < psfData.length; i++) psfData[i] *= weight;
            // Insert into the combined PSF
            ImageProcessor ip = stack.getProcessor(n + offsetZ);
            ip.copyBits(new FloatProcessor(w, w, psfData, null), offsetXY, offsetXY, Blitter.ADD);
        }
        imageNo++;
    }
    // IJ.showStatus("Normalising ...");
    // PSFCreator.normalise(stack, 1 + shift);
    IJ.showProgress(1);
    IJ.showStatus("");
    ImagePlus imp = Utils.display("Combined PSF", stack);
    imp.setSlice(1 + shift);
    imp.resetDisplayRange();
    imp.updateAndDraw();
    final double fwhm = getFWHM();
    imp.setProperty("Info", XmlUtils.toXML(new PSFSettings(imp.getSlice(), nmPerPixel, nmPerSlice, totalImages, fwhm)));
    Utils.log("%s : z-centre = %d, nm/Pixel = %s, nm/Slice = %s, %d images, FWHM = %s\n", imp.getTitle(), imp.getSlice(), Utils.rounded(nmPerPixel), Utils.rounded(nmPerSlice), totalImages, Utils.rounded(fwhm));
}

Example 25 with ImageStack

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

the class MedianFilter method run.

public void run(ImageProcessor ip) {
    long start = System.currentTimeMillis();
    ImageStack stack = imp.getImageStack();
    final int width = stack.getWidth();
    final int height = stack.getHeight();
    size = width * height;
    float[][] imageStack = new float[stack.getSize()][];
    float[] mean = new float[imageStack.length];
    // Get the mean for each frame and normalise the data using the mean
    ExecutorService threadPool = Executors.newFixedThreadPool(Prefs.getThreads());
    List<Future<?>> futures = new LinkedList<Future<?>>();
    counter = 0;
    IJ.showStatus("Calculating means...");
    for (int n = 1; n <= stack.getSize(); n++) {
        futures.add(threadPool.submit(new ImageNormaliser(stack, imageStack, mean, n)));
    }
    // Finish processing data
    Utils.waitForCompletion(futures);
    futures = new LinkedList<Future<?>>();
    counter = 0;
    IJ.showStatus("Calculating medians...");
    for (int i = 0; i < size; i += blockSize) {
        futures.add(threadPool.submit(new ImageGenerator(imageStack, mean, i, FastMath.min(i + blockSize, size))));
    }
    // Finish processing data
    Utils.waitForCompletion(futures);
    if (Utils.isInterrupted())
        return;
    if (subtract) {
        counter = 0;
        IJ.showStatus("Subtracting medians...");
        for (int n = 1; n <= stack.getSize(); n++) {
            futures.add(threadPool.submit(new ImageFilter(stack, imageStack, n)));
        }
        // Finish processing data
        Utils.waitForCompletion(futures);
    }
    // Update the image
    ImageStack outputStack = new ImageStack(stack.getWidth(), stack.getHeight(), stack.getSize());
    for (int n = 1; n <= stack.getSize(); n++) {
        outputStack.setPixels(imageStack[n - 1], n);
    }
    imp.setStack(outputStack);
    imp.updateAndDraw();
    IJ.showTime(imp, start, "Completed");
    long milliseconds = System.currentTimeMillis() - start;
    Utils.log(TITLE + " : Radius %d, Interval %d, Block size %d = %s, %s / frame", radius, interval, blockSize, Utils.timeToString(milliseconds), Utils.timeToString((double) milliseconds / imp.getStackSize()));
}