Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 6 with ImagePlus

use of ij.ImagePlus 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 7 with ImagePlus

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

the class DriftCalculator method showStackDialog.

private ImageStack showStackDialog(String[] stackTitles) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Compute the drift using a reference stack alignment");
    gd.addChoice("Stack_image", stackTitles, stackTitle);
    gd.addMessage("Frame = previous + spacing");
    gd.addNumericField("Start_frame", startFrame, 0);
    gd.addSlider("Frame_spacing", 1, 20, frameSpacing);
    String[] methods = ImageProcessor.getInterpolationMethods();
    gd.addChoice("Interpolation_method", methods, methods[interpolationMethod]);
    methods = new String[] { AlignImagesFFT.SubPixelMethod.CUBIC.toString(), AlignImagesFFT.SubPixelMethod.GAUSSIAN.toString() };
    gd.addChoice("Sub-pixel_method", methods, subPixelMethod.toString());
    gd.showDialog();
    if (gd.wasCanceled())
        return null;
    stackTitle = gd.getNextChoice();
    startFrame = (int) gd.getNextNumber();
    frameSpacing = (int) gd.getNextNumber();
    interpolationMethod = gd.getNextChoiceIndex();
    subPixelMethod = (gd.getNextChoiceIndex() == 0) ? AlignImagesFFT.SubPixelMethod.CUBIC : AlignImagesFFT.SubPixelMethod.GAUSSIAN;
    try {
        Parameters.isAboveZero("Start frame", startFrame);
        Parameters.isAboveZero("Frame spacing", frameSpacing);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return null;
    }
    ImagePlus imp = WindowManager.getImage(stackTitle);
    if (imp != null && imp.getStackSize() > 1)
        return imp.getImageStack();
    return null;
}

Example 8 with ImagePlus

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

the class SplitResults 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, "There are no fitting results in memory");
        return;
    }
    String[] items = Utils.getImageList(Utils.GREY_8_16);
    if (items.length == 0) {
        IJ.error(TITLE, "There are no suitable mask images");
        return;
    }
    // Show a dialog allowing the results set to be filtered
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Select a dataset to split");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    gd.addChoice("Object_mask", items, objectMask);
    gd.addCheckbox("Show_object_mask", showObjectMask);
    gd.addCheckbox("Non_mask_dataset", nonMaskDataset);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    inputOption = ResultsManager.getInputSource(gd);
    objectMask = gd.getNextChoice();
    showObjectMask = gd.getNextBoolean();
    nonMaskDataset = gd.getNextBoolean();
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    ImagePlus imp = WindowManager.getImage(objectMask);
    if (imp == null) {
        IJ.error(TITLE, "No object mask could be found");
        return;
    }
    splitResults(results, imp.getProcessor());
}

Example 9 with ImagePlus

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

the class SpotAnalysis method createProfile.

private void createProfile() {
    if (!parametersReady()) {
        return;
    }
    double psfWidth, blur;
    // Read settings
    try {
        psfWidth = Double.parseDouble(widthTextField.getText());
        blur = Double.parseDouble(blurTextField.getText());
        gain = Double.parseDouble(gainTextField.getText());
        msPerFrame = Double.parseDouble(exposureTextField.getText());
    } catch (NumberFormatException e) {
        IJ.error(TITLE, "Invalid numbers in the input parameters");
        return;
    }
    ImagePlus imp = WindowManager.getImage(inputChoice.getSelectedItem());
    // This should not be a problem but leave it in for now
    if (imp == null || (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 && imp.getType() != ImagePlus.GRAY32)) {
        IJ.showMessage(TITLE, "Images must be grayscale.");
        return;
    }
    Roi roi = imp.getRoi();
    if (roi == null || !roi.isArea()) {
        IJ.showMessage(TITLE, "Image must have an area ROI");
        return;
    }
    int recommendedSize = (int) Math.ceil(8 * psfWidth);
    Rectangle bounds = roi.getBounds();
    if (bounds.width < recommendedSize || bounds.height < recommendedSize) {
        IJ.showMessage(TITLE, String.format("Recommend using an ROI of at least %d x %d for the PSF width", recommendedSize, recommendedSize));
        return;
    }
    // Check no existing spots are within the ROI
    if (resultsWithinBounds(bounds)) {
        GenericDialog gd = new GenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("The results list contains a spot within the selected bounds\n \nDo you want to continue?");
        gd.showDialog();
        if (!gd.wasOKed())
            return;
    }
    createProfile(imp, bounds, psfWidth, blur);
}

Example 10 with ImagePlus

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

the class SpotAnalysis method setup.

private void setup() {
    ImagePlus imp = WindowManager.getCurrentImage();
    if (imp == null)
        return;
    fillImagesList();
}