Examples with ImageStack ij.ImageStack used on opensource projects

Example 6 with ImageStack

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

the class ResultsImageSampler method getSample.

/**
	 * Gets the sample image. The image is a stack of the samples with an overlay of the localisation positions. The
	 * info property is set with details of the localisations and the image is calibrated.
	 *
	 * @param nNo
	 *            the number of samples with no localisations
	 * @param nLow
	 *            the number of samples with low localisations
	 * @param nHigh
	 *            the number of samples with high localisations
	 * @return the sample image (could be null if no samples were made)
	 */
public ImagePlus getSample(int nNo, int nLow, int nHigh) {
    ImageStack out = new ImageStack(size, size);
    if (!isValid())
        return null;
    list.clearf();
    // empty
    for (int i : Random.sample(nNo, no.length, r)) list.add(ResultsSample.createEmpty(no[i]));
    // low
    for (int i : Random.sample(nLow, lower, r)) list.add(data[i]);
    // high
    for (int i : Random.sample(nHigh, upper, r)) list.add(data[i + lower]);
    if (list.isEmpty())
        return null;
    double nmPerPixel = 1;
    if (results.getCalibration() != null) {
        Calibration calibration = results.getCalibration();
        if (calibration.hasNmPerPixel()) {
            nmPerPixel = calibration.getNmPerPixel();
        }
    }
    // Sort descending by number in the frame
    ResultsSample[] sample = list.toArray(new ResultsSample[list.size()]);
    Arrays.sort(sample, rcc);
    int[] xyz = new int[3];
    Rectangle stackBounds = new Rectangle(stack.getWidth(), stack.getHeight());
    Overlay overlay = new Overlay();
    float[] ox = new float[10], oy = new float[10];
    StringBuilder sb = new StringBuilder();
    if (nmPerPixel == 1)
        sb.append("Sample X Y Z Signal\n");
    else
        sb.append("Sample X(nm) Y(nm) Z(nm) Signal\n");
    for (ResultsSample s : sample) {
        getXYZ(s.index, xyz);
        // Construct the region to extract
        Rectangle target = new Rectangle(xyz[0], xyz[1], size, size);
        target = target.intersection(stackBounds);
        if (target.width == 0 || target.height == 0)
            continue;
        // Extract the frame
        int slice = xyz[2];
        ImageProcessor ip = stack.getProcessor(slice);
        // Cut out the desired pixels (some may be blank if the block overruns the source image)
        ImageProcessor ip2 = ip.createProcessor(size, size);
        for (int y = 0; y < target.height; y++) for (int x = 0, i = y * size, index = (y + target.y) * ip.getWidth() + target.x; x < target.width; x++, i++, index++) {
            ip2.setf(i, ip.getf(index));
        }
        int size = s.size();
        if (size > 0) {
            int position = out.getSize() + 1;
            // Create an ROI with the localisations
            for (int i = 0; i < size; i++) {
                PeakResult p = s.list.get(i);
                ox[i] = p.getXPosition() - xyz[0];
                oy[i] = p.getYPosition() - xyz[1];
                sb.append(position).append(' ');
                sb.append(Utils.rounded(ox[i] * nmPerPixel)).append(' ');
                sb.append(Utils.rounded(oy[i] * nmPerPixel)).append(' ');
                // Z can be stored in the error field
                sb.append(Utils.rounded(p.error * nmPerPixel)).append(' ');
                sb.append(Utils.rounded(p.getSignal())).append('\n');
            }
            PointRoi roi = new PointRoi(ox, oy, size);
            roi.setPosition(position);
            overlay.add(roi);
        }
        out.addSlice(String.format("Frame=%d @ %d,%d px (n=%d)", slice, xyz[0], xyz[1], size), ip2.getPixels());
    }
    if (out.getSize() == 0)
        return null;
    ImagePlus imp = new ImagePlus("Sample", out);
    imp.setOverlay(overlay);
    // Note: Only the info property can be saved to a TIFF file
    imp.setProperty("Info", sb.toString());
    if (nmPerPixel != 1) {
        ij.measure.Calibration cal = new ij.measure.Calibration();
        cal.setUnit("nm");
        cal.pixelHeight = cal.pixelWidth = nmPerPixel;
        imp.setCalibration(cal);
    }
    return imp;
}

Example 7 with ImageStack

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

the class IJImagePeakResults method createNewImageStack.

private ImageStack createNewImageStack(int w, int h) {
    if ((displayFlags & DISPLAY_MAPPED) != 0) {
        MappedImageStack stack = new MappedImageStack(w, h);
        stack.setMapZero((displayFlags & DISPLAY_MAP_ZERO) != 0);
        return stack;
    }
    return new ImageStack(w, h);
}

Example 8 with ImageStack

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

the class EMGainAnalysis method buildHistogram.

/**
	 * Build a histogram using pixels within the image ROI
	 * 
	 * @param image
	 *            The image
	 * @return The image histogram
	 */
private static int[] buildHistogram(ImagePlus imp) {
    ImageStack stack = imp.getImageStack();
    Roi roi = imp.getRoi();
    int[] data = getHistogram(stack.getProcessor(1), roi);
    for (int n = 2; n <= stack.getSize(); n++) {
        int[] tmp = getHistogram(stack.getProcessor(n), roi);
        for (int i = 0; i < tmp.length; i++) data[i] += tmp[i];
    }
    // Avoid super-saturated pixels by using 98% of histogram
    long sum = 0;
    for (int i = 0; i < data.length; i++) {
        sum += data[i];
    }
    final long sum2 = (long) (sum * 0.99);
    sum = 0;
    for (int i = 0; i < data.length; i++) {
        sum += data[i];
        if (sum > sum2) {
            for (; i < data.length; i++) data[i] = 0;
            break;
        }
    }
    return data;
}

Example 9 with ImageStack

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

the class DrawClusters method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
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(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    // Get the traces
    Trace[] traces = TraceManager.convert(results);
    if (traces == null || traces.length == 0) {
        IJ.error(TITLE, "No traces could be loaded");
        return;
    }
    // Filter traces to a min size
    int maxFrame = 0;
    int count = 0;
    final int myMaxSize = (maxSize < minSize) ? Integer.MAX_VALUE : maxSize;
    final boolean myDrawLines = (myMaxSize < 2) ? false : drawLines;
    for (int i = 0; i < traces.length; i++) {
        if (expandToSingles)
            traces[i].expandToSingles();
        if (traces[i].size() >= minSize && traces[i].size() <= myMaxSize) {
            traces[count++] = traces[i];
            traces[i].sort();
            if (maxFrame < traces[i].getTail().getFrame())
                maxFrame = traces[i].getTail().getFrame();
        }
    }
    if (count == 0) {
        IJ.error(TITLE, "No traces achieved the size limits");
        return;
    }
    String msg = String.format(TITLE + ": %d / %s (%s)", count, Utils.pleural(traces.length, "trace"), Utils.pleural(results.size(), "localisation"));
    IJ.showStatus(msg);
    //Utils.log(msg);
    Rectangle bounds = results.getBounds(true);
    ImagePlus imp = WindowManager.getImage(title);
    boolean isUseStackPosition = useStackPosition;
    if (imp == null) {
        // Create a default image using 100 pixels as the longest edge
        double maxD = (bounds.width > bounds.height) ? bounds.width : bounds.height;
        int w, h;
        if (maxD == 0) {
            // Note that imageSize can be zero (for auto sizing)
            w = h = (imageSize == 0) ? 20 : imageSize;
        } else {
            // Note that imageSize can be zero (for auto sizing)
            if (imageSize == 0) {
                w = bounds.width;
                h = bounds.height;
            } else {
                w = (int) (imageSize * bounds.width / maxD);
                h = (int) (imageSize * bounds.height / maxD);
            }
        }
        ByteProcessor bp = new ByteProcessor(w, h);
        if (isUseStackPosition) {
            ImageStack stack = new ImageStack(w, h, maxFrame);
            for (int i = 1; i <= maxFrame; i++) // Do not clone as the image is empty
            stack.setPixels(bp.getPixels(), i);
            imp = Utils.display(TITLE, stack);
        } else
            imp = Utils.display(TITLE, bp);
        // Enlarge
        ImageWindow iw = imp.getWindow();
        for (int i = 9; i-- > 0 && iw.getWidth() < 500 && iw.getHeight() < 500; ) {
            iw.getCanvas().zoomIn(imp.getWidth() / 2, imp.getHeight() / 2);
        }
    } else {
        // Check if the image has enough frames for all the traces
        if (maxFrame > imp.getNFrames())
            isUseStackPosition = false;
    }
    final float xScale = (float) (imp.getWidth() / bounds.getWidth());
    final float yScale = (float) (imp.getHeight() / bounds.getHeight());
    // Create ROIs and store data to sort them
    Roi[] rois = new Roi[count];
    int[][] frames = (isUseStackPosition) ? new int[count][] : null;
    int[] indices = Utils.newArray(count, 0, 1);
    double[] values = new double[count];
    for (int i = 0; i < count; i++) {
        Trace trace = traces[i];
        int nPoints = trace.size();
        float[] xPoints = new float[nPoints];
        float[] yPoints = new float[nPoints];
        int j = 0;
        if (isUseStackPosition)
            frames[i] = new int[nPoints];
        for (PeakResult result : trace.getPoints()) {
            xPoints[j] = (result.getXPosition() - bounds.x) * xScale;
            yPoints[j] = (result.getYPosition() - bounds.y) * yScale;
            if (isUseStackPosition)
                frames[i][j] = result.getFrame();
            j++;
        }
        Roi roi;
        if (myDrawLines) {
            roi = new PolygonRoi(xPoints, yPoints, nPoints, Roi.POLYLINE);
            if (splineFit)
                ((PolygonRoi) roi).fitSpline();
        } else {
            roi = new PointRoi(xPoints, yPoints, nPoints);
            ((PointRoi) roi).setShowLabels(false);
        }
        rois[i] = roi;
        switch(sort) {
            case 0:
            default:
                break;
            case // Sort by ID
            1:
                values[i] = traces[i].getId();
                break;
            case // Sort by time
            2:
                values[i] = traces[i].getHead().getFrame();
                break;
            case // Sort by size descending
            3:
                values[i] = -traces[i].size();
                break;
            case // Sort by length descending
            4:
                values[i] = -roi.getLength();
                break;
            case // Mean Square Displacement
            5:
                values[i] = -traces[i].getMSD();
                break;
            case // Mean / Frame
            6:
                values[i] = -traces[i].getMeanPerFrame();
                break;
        }
    }
    if (sort > 0)
        Sort.sort(indices, values);
    // Draw the traces as ROIs on an overlay
    Overlay o = new Overlay();
    LUT lut = LUTHelper.createLUT(DrawClusters.lut);
    final double scale = 256.0 / count;
    if (isUseStackPosition) {
        // Add the tracks on the frames containing the results
        final boolean isHyperStack = imp.isDisplayedHyperStack();
        for (int i = 0; i < count; i++) {
            final int index = indices[i];
            final Color c = LUTHelper.getColour(lut, (int) (i * scale));
            final PolygonRoi roi = (PolygonRoi) rois[index];
            roi.setFillColor(c);
            roi.setStrokeColor(c);
            final FloatPolygon fp = roi.getNonSplineFloatPolygon();
            // For each frame in the track, add the ROI track and a point ROI for the current position
            for (int j = 0; j < frames[index].length; j++) {
                addToOverlay(o, (Roi) roi.clone(), isHyperStack, frames[index][j]);
                //PointRoi pointRoi = new PointRoi(pos.x + fp.xpoints[j], pos.y + fp.ypoints[j]);
                PointRoi pointRoi = new PointRoi(fp.xpoints[j], fp.ypoints[j]);
                pointRoi.setPointType(3);
                pointRoi.setFillColor(c);
                pointRoi.setStrokeColor(Color.black);
                addToOverlay(o, pointRoi, isHyperStack, frames[index][j]);
            }
        }
    } else {
        // Add the tracks as a single overlay
        for (int i = 0; i < count; i++) {
            final Roi roi = rois[indices[i]];
            roi.setStrokeColor(new Color(lut.getRGB((int) (i * scale))));
            o.add(roi);
        }
    }
    imp.setOverlay(o);
    IJ.showStatus(msg);
}

Example 10 with ImageStack

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

the class SpotAnalysis method createProfile.

private void createProfile(ImagePlus imp, Rectangle bounds, double psfWidth, double blur) {
    areaBounds = bounds;
    this.imp = imp;
    area = bounds.width * bounds.height;
    clearSelectedFrames();
    // Get a profile through the images
    IJ.showStatus("Calculating raw profile");
    final int nSlices = imp.getStackSize();
    ImageStack rawSpot = new ImageStack(bounds.width, bounds.height, nSlices);
    double[][] profile = extractSpotProfile(imp, bounds, rawSpot);
    // Retain the existing display range
    double min = 0, max = Double.POSITIVE_INFINITY;
    if (rawImp != null) {
        min = rawImp.getDisplayRangeMin();
        max = rawImp.getDisplayRangeMax();
    }
    rawImp = showSpot(rawSpotTitle, rawSpot);
    if (max != Double.POSITIVE_INFINITY) {
        rawImp.setDisplayRange(min, max);
    }
    rawMean = profile[0];
    rawSd = profile[1];
    // Check if there are fitted results in memory
    addCandidateFrames(imp.getTitle());
    updateProfilePlots();
    if (blur > 0) {
        IJ.showStatus("Calculating blur ...");
        ImageStack stack = imp.getImageStack();
        ImageStack newStack = new ImageStack(stack.getWidth(), stack.getHeight(), stack.getSize());
        // Multi-thread the blur stage
        ExecutorService threadPool = Executors.newFixedThreadPool(Prefs.getThreads());
        List<Future<?>> futures = new LinkedList<Future<?>>();
        Utils.setShowProgress(false);
        blurCount = 0;
        // TODO - See if this is faster if processing multiple slices in each worker
        int slices = 5;
        for (int n = 1; n <= nSlices; n += slices) {
            futures.add(threadPool.submit(new BlurWorker(stack, n, slices, bounds, blur * psfWidth, newStack)));
        }
        IJ.showStatus("Calculating blur ... Finishing");
        Utils.waitForCompletion(futures);
        threadPool.shutdown();
        Utils.setShowProgress(false);
        IJ.showStatus("Calculating blur ... Drawing");
        ImageStack blurSpot = new ImageStack(bounds.width, bounds.height, nSlices);
        extractSpotProfile(new ImagePlus("Blur", newStack), bounds, blurSpot);
        // Retain the existing display range
        max = Double.POSITIVE_INFINITY;
        if (blurImp != null) {
            min = blurImp.getDisplayRangeMin();
            max = blurImp.getDisplayRangeMax();
        }
        blurImp = showSpot(blurSpotTitle, blurSpot);
        if (max != Double.POSITIVE_INFINITY) {
            blurImp.setDisplayRange(min, max);
        }
        IJ.showStatus("");
    } else {
        blurImp = null;
    }
    // Add a z-projection of the blur/original image
    ZProjector project = new ZProjector((blurImp == null) ? rawImp : blurImp);
    project.setMethod(ZProjector.AVG_METHOD);
    project.doProjection();
    showSpot(avgSpotTitle, project.getProjection().getImageStack());
    if (!candidateFrames.isEmpty())
        // Set the first candidate frame
        rawImp.setSlice(candidateFrames.get(0));
    else
        updateCurrentSlice(rawImp.getCurrentSlice());
    IJ.showStatus("");
}