Examples with HierarchyOverlay qupath.lib.gui.viewer.overlays.HierarchyOverlay used on opensource projects

Example 1 with HierarchyOverlay

use of qupath.lib.gui.viewer.overlays.HierarchyOverlay in project qupath by qupath.

the class TMADataIO method writeTMAData.

/**
 * Write TMA data in a human-readable (and viewable) way, with JPEGs and TXT/CSV files.
 *
 * @param file
 * @param imageData
 * @param overlayOptions
 * @param downsampleFactor The downsample factor used for the TMA cores. If NaN, an automatic downsample value will be selected (>= 1).  If <= 0, no cores are exported.
 */
public static void writeTMAData(File file, final ImageData<BufferedImage> imageData, OverlayOptions overlayOptions, final double downsampleFactor) {
    if (imageData == null || imageData.getHierarchy() == null || imageData.getHierarchy().getTMAGrid() == null) {
        logger.error("No TMA data available to save!");
        return;
    }
    final ImageServer<BufferedImage> server = imageData.getServer();
    String coreExt = imageData.getServer().isRGB() ? ".jpg" : ".tif";
    if (file == null) {
        file = Dialogs.promptToSaveFile("Save TMA data", null, ServerTools.getDisplayableImageName(server), "TMA data", "qptma");
        if (file == null)
            return;
    } else if (file.isDirectory() || (!file.exists() && file.getAbsolutePath().endsWith(File.pathSeparator))) {
        // Put inside the specified directory
        file = new File(file, ServerTools.getDisplayableImageName(server) + TMA_DEARRAYING_DATA_EXTENSION);
        if (!file.getParentFile().exists())
            file.getParentFile().mkdirs();
    }
    final File dirData = new File(file + ".data");
    if (!dirData.exists())
        dirData.mkdir();
    // Write basic file info
    String delimiter = "\t";
    TMAGrid tmaGrid = imageData.getHierarchy().getTMAGrid();
    try {
        PrintWriter writer = new PrintWriter(file);
        writer.println(server.getPath());
        writer.println(ServerTools.getDisplayableImageName(server));
        writer.println();
        writer.println("TMA grid width: " + tmaGrid.getGridWidth());
        writer.println("TMA grid height: " + tmaGrid.getGridHeight());
        writer.println("Core name" + delimiter + "X" + delimiter + "Y" + delimiter + "Width" + delimiter + "Height" + delimiter + "Present" + delimiter + TMACoreObject.KEY_UNIQUE_ID);
        for (int row = 0; row < tmaGrid.getGridHeight(); row++) {
            for (int col = 0; col < tmaGrid.getGridWidth(); col++) {
                TMACoreObject core = tmaGrid.getTMACore(row, col);
                if (!core.hasROI()) {
                    writer.println(core.getName() + delimiter + delimiter + delimiter + delimiter);
                    continue;
                }
                ROI pathROI = core.getROI();
                int x = (int) pathROI.getBoundsX();
                int y = (int) pathROI.getBoundsY();
                int w = (int) Math.ceil(pathROI.getBoundsWidth());
                int h = (int) Math.ceil(pathROI.getBoundsHeight());
                String id = core.getUniqueID() == null ? "" : core.getUniqueID();
                writer.println(core.getName() + delimiter + x + delimiter + y + delimiter + w + delimiter + h + delimiter + !core.isMissing() + delimiter + id);
            }
        }
        writer.close();
    } catch (Exception e) {
        logger.error("Error writing TMA data: " + e.getLocalizedMessage(), e);
        return;
    }
    // Save the summary results
    ObservableMeasurementTableData tableData = new ObservableMeasurementTableData();
    tableData.setImageData(imageData, tmaGrid.getTMACoreList());
    SummaryMeasurementTableCommand.saveTableModel(tableData, new File(dirData, "TMA results - " + ServerTools.getDisplayableImageName(server) + ".txt"), Collections.emptyList());
    boolean outputCoreImages = Double.isNaN(downsampleFactor) || downsampleFactor > 0;
    if (outputCoreImages) {
        // Create new overlay options, if we don't have some already
        if (overlayOptions == null) {
            overlayOptions = new OverlayOptions();
            overlayOptions.setFillDetections(true);
        }
        final OverlayOptions options = overlayOptions;
        // Write an overall TMA map (for quickly checking if the dearraying is ok)
        File fileTMAMap = new File(dirData, "TMA map - " + ServerTools.getDisplayableImageName(server) + ".jpg");
        double downsampleThumbnail = Math.max(1, (double) Math.max(server.getWidth(), server.getHeight()) / 1024);
        RegionRequest request = RegionRequest.createInstance(server.getPath(), downsampleThumbnail, 0, 0, server.getWidth(), server.getHeight());
        OverlayOptions optionsThumbnail = new OverlayOptions();
        optionsThumbnail.setShowTMAGrid(true);
        optionsThumbnail.setShowGrid(false);
        optionsThumbnail.setShowAnnotations(false);
        optionsThumbnail.setShowDetections(false);
        try {
            var renderedServer = new RenderedImageServer.Builder(imageData).layers(new TMAGridOverlay(overlayOptions)).downsamples(downsampleThumbnail).build();
            ImageWriterTools.writeImageRegion(renderedServer, request, fileTMAMap.getAbsolutePath());
        // ImageWriters.writeImageRegionWithOverlay(imageData.getServer(), Collections.singletonList(new TMAGridOverlay(overlayOptions, imageData)), request, fileTMAMap.getAbsolutePath());
        } catch (IOException e) {
            logger.warn("Unable to write image overview: " + e.getLocalizedMessage(), e);
        }
        final double downsample = Double.isNaN(downsampleFactor) ? (server.getPixelCalibration().hasPixelSizeMicrons() ? ServerTools.getDownsampleFactor(server, preferredExportPixelSizeMicrons) : 1) : downsampleFactor;
        // Creating a plugin makes it possible to parallelize & show progress easily
        var renderedImageServer = new RenderedImageServer.Builder(imageData).layers(new HierarchyOverlay(null, options, imageData)).downsamples(downsample).build();
        ExportCoresPlugin plugin = new ExportCoresPlugin(dirData, renderedImageServer, downsample, coreExt);
        PluginRunner<BufferedImage> runner;
        var qupath = QuPathGUI.getInstance();
        if (qupath == null || qupath.getImageData() != imageData) {
            runner = new CommandLinePluginRunner<>(imageData);
            plugin.runPlugin(runner, null);
        } else {
            try {
                qupath.runPlugin(plugin, null, false);
            } catch (Exception e) {
                logger.error("Error writing TMA data: " + e.getLocalizedMessage(), e);
            }
        // new Thread(() -> qupath.runPlugin(plugin, null, false)).start();
        // runner = new PluginRunnerFX(QuPathGUI.getInstance());
        // new Thread(() -> plugin.runPlugin(runner, null)).start();
        }
    }
}

Example 2 with HierarchyOverlay

use of qupath.lib.gui.viewer.overlays.HierarchyOverlay in project qupath by qupath.

the class WandToolCV method createShape.

@Override
protected Geometry createShape(MouseEvent e, double x, double y, boolean useTiles, Geometry addToShape) {
    GeometryFactory factory = getGeometryFactory();
    if (addToShape != null && pLast != null && pLast.distanceSq(x, y) < 2)
        return null;
    long startTime = System.currentTimeMillis();
    QuPathViewer viewer = getViewer();
    if (viewer == null)
        return null;
    double downsample = Math.max(1, Math.round(viewer.getDownsampleFactor() * 4)) / 4.0;
    var regionStore = viewer.getImageRegionStore();
    // Paint the image as it is currently being viewed
    var type = wandType.get();
    boolean doGray = type == WandType.GRAY;
    BufferedImage imgTemp = doGray ? imgGray : imgBGR;
    int nChannels = doGray ? 1 : 3;
    Graphics2D g2d = imgTemp.createGraphics();
    g2d.setColor(Color.BLACK);
    g2d.setClip(0, 0, w, w);
    g2d.fillRect(0, 0, w, w);
    double xStart = Math.round(x - w * downsample * 0.5);
    double yStart = Math.round(y - w * downsample * 0.5);
    bounds.setFrame(xStart, yStart, w * downsample, w * downsample);
    g2d.scale(1.0 / downsample, 1.0 / downsample);
    g2d.translate(-xStart, -yStart);
    regionStore.paintRegion(viewer.getServer(), g2d, bounds, viewer.getZPosition(), viewer.getTPosition(), downsample, null, null, viewer.getImageDisplay());
    // regionStore.paintRegionCompletely(viewer.getServer(), g2d, bounds, viewer.getZPosition(), viewer.getTPosition(), viewer.getDownsampleFactor(), null, viewer.getImageDisplay(), 250);
    // Optionally include the overlay information when using the wand
    float opacity = viewer.getOverlayOptions().getOpacity();
    if (opacity > 0 && getWandUseOverlays()) {
        ImageRegion region = ImageRegion.createInstance((int) bounds.getX() - 1, (int) bounds.getY() - 1, (int) bounds.getWidth() + 2, (int) bounds.getHeight() + 2, viewer.getZPosition(), viewer.getTPosition());
        if (opacity < 1)
            g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, opacity));
        for (PathOverlay overlay : viewer.getOverlayLayers().toArray(PathOverlay[]::new)) {
            if (!(overlay instanceof HierarchyOverlay))
                overlay.paintOverlay(g2d, region, downsample, viewer.getImageData(), true);
        }
    }
    // Ensure we have Mats & the correct channel number
    if (mat != null && (mat.channels() != nChannels || mat.depth() != opencv_core.CV_8U)) {
        mat.close();
        mat = null;
    }
    if (mat == null || mat.isNull() || mat.empty())
        mat = new Mat(w, w, CV_8UC(nChannels));
    // if (matMask == null)
    // matMask = new Mat(w+2, w+2, CV_8U);
    // if (matSelected == null)
    // matSelected = new Mat(w+2, w+2, CV_8U);
    // Put pixels into an OpenCV image
    byte[] buffer = ((DataBufferByte) imgTemp.getRaster().getDataBuffer()).getData();
    ByteBuffer matBuffer = mat.createBuffer();
    matBuffer.put(buffer);
    // mat.put(0, 0, buffer);
    // opencv_imgproc.cvtColor(mat, mat, opencv_imgproc.COLOR_BGR2Lab);
    // blurSigma = 4;
    boolean doSimpleSelection = e.isShortcutDown() && !e.isShiftDown();
    if (doSimpleSelection) {
        matMask.put(Scalar.ZERO);
        // opencv_imgproc.circle(matMask, seed, radius, Scalar.ONE);
        opencv_imgproc.floodFill(mat, matMask, seed, Scalar.ONE, null, Scalar.ZERO, Scalar.ZERO, 4 | (2 << 8) | opencv_imgproc.FLOODFILL_MASK_ONLY | opencv_imgproc.FLOODFILL_FIXED_RANGE);
        subtractPut(matMask, Scalar.ONE);
    } else {
        double blurSigma = Math.max(0.5, getWandSigmaPixels());
        int size = (int) Math.ceil(blurSigma * 2) * 2 + 1;
        blurSize.width(size);
        blurSize.height(size);
        // Smooth a little
        opencv_imgproc.GaussianBlur(mat, mat, blurSize, blurSigma);
        // Choose mat to threshold (may be adjusted)
        Mat matThreshold = mat;
        // Apply color transform if required
        if (type == WandType.LAB_DISTANCE) {
            mat.convertTo(matFloat, opencv_core.CV_32F, 1.0 / 255.0, 0.0);
            opencv_imgproc.cvtColor(matFloat, matFloat, opencv_imgproc.COLOR_BGR2Lab);
            double max = 0;
            double mean = 0;
            try (FloatIndexer idx = matFloat.createIndexer()) {
                int k = w / 2;
                double v1 = idx.get(k, k, 0);
                double v2 = idx.get(k, k, 1);
                double v3 = idx.get(k, k, 2);
                double meanScale = 1.0 / (w * w);
                for (int row = 0; row < w; row++) {
                    for (int col = 0; col < w; col++) {
                        double L = idx.get(row, col, 0) - v1;
                        double A = idx.get(row, col, 1) - v2;
                        double B = idx.get(row, col, 2) - v3;
                        double dist = Math.sqrt(L * L + A * A + B * B);
                        if (dist > max)
                            max = dist;
                        mean += dist * meanScale;
                        idx.put(row, col, 0, (float) dist);
                    }
                }
            }
            if (matThreshold == null)
                matThreshold = new Mat();
            opencv_core.extractChannel(matFloat, matThreshold, 0);
            // There are various ways we might choose a threshold now...
            // Here, we use a multiple of the mean. Since values are 'distances'
            // they are all >= 0
            matThreshold.convertTo(matThreshold, opencv_core.CV_8U, 255.0 / max, 0);
            threshold.put(mean * getWandSensitivity());
            // //			OpenCVTools.matToImagePlus(matThreshold, "Before").show();
            // // Apply local Otsu threshold
            // opencv_imgproc.threshold(matThreshold, matThreshold,
            // 0,
            // 255, opencv_imgproc.THRESH_BINARY + opencv_imgproc.THRESH_OTSU);
            // threshold.put(Scalar.ZERO);
            nChannels = 1;
        } else {
            // Base threshold on local standard deviation
            meanStdDev(matThreshold, mean, stddev);
            DoubleBuffer stddevBuffer = stddev.createBuffer();
            double[] stddev2 = new double[nChannels];
            stddevBuffer.get(stddev2);
            double scale = 1.0 / getWandSensitivity();
            if (scale < 0)
                scale = 0.01;
            for (int i = 0; i < stddev2.length; i++) stddev2[i] = stddev2[i] * scale;
            threshold.put(stddev2);
        }
        // Limit maximum radius by pen
        int radius = (int) Math.round(w / 2 * QuPathPenManager.getPenManager().getPressure());
        if (radius == 0)
            return null;
        matMask.put(Scalar.ZERO);
        opencv_imgproc.circle(matMask, seed, radius, Scalar.ONE);
        opencv_imgproc.floodFill(matThreshold, matMask, seed, Scalar.ONE, null, threshold, threshold, 4 | (2 << 8) | opencv_imgproc.FLOODFILL_MASK_ONLY | opencv_imgproc.FLOODFILL_FIXED_RANGE);
        subtractPut(matMask, Scalar.ONE);
        if (strel == null)
            strel = opencv_imgproc.getStructuringElement(opencv_imgproc.MORPH_ELLIPSE, new Size(5, 5));
        opencv_imgproc.morphologyEx(matMask, matMask, opencv_imgproc.MORPH_CLOSE, strel);
    }
    MatVector contours = new MatVector();
    if (contourHierarchy == null)
        contourHierarchy = new Mat();
    opencv_imgproc.findContours(matMask, contours, contourHierarchy, opencv_imgproc.RETR_EXTERNAL, opencv_imgproc.CHAIN_APPROX_SIMPLE);
    // logger.trace("Contours: " + contours.size());
    List<Coordinate> coords = new ArrayList<>();
    List<Geometry> geometries = new ArrayList<>();
    for (Mat contour : contours.get()) {
        // Discard single pixels / lines
        if (contour.size().height() <= 2)
            continue;
        // Create a polygon geometry
        try (IntIndexer idxrContours = contour.createIndexer()) {
            for (long r = 0; r < idxrContours.size(0); r++) {
                int px = idxrContours.get(r, 0L, 0L);
                int py = idxrContours.get(r, 0L, 1L);
                // * downsample + x;
                double xx = (px - w / 2 - 1);
                // * downsample + y;
                double yy = (py - w / 2 - 1);
                coords.add(new Coordinate(xx, yy));
            }
        }
        if (coords.size() > 1) {
            // Ensure closed
            if (!coords.get(coords.size() - 1).equals(coords.get(0)))
                coords.add(coords.get(0));
            // Exclude single pixels
            var polygon = factory.createPolygon(coords.toArray(Coordinate[]::new));
            if (coords.size() > 5 || polygon.getArea() > 1)
                geometries.add(polygon);
        }
    }
    contours.close();
    if (geometries.isEmpty())
        return null;
    // Handle the fact that OpenCV contours are defined using the 'pixel center' by dilating the boundary
    var geometry = geometries.size() == 1 ? geometries.get(0) : GeometryCombiner.combine(geometries);
    geometry = geometry.buffer(0.5);
    // Transform to map to integer pixel locations in the full-resolution image
    var transform = new AffineTransformation().scale(downsample, downsample).translate(x, y);
    geometry = transform.transform(geometry);
    geometry = GeometryTools.roundCoordinates(geometry);
    geometry = GeometryTools.constrainToBounds(geometry, 0, 0, viewer.getServerWidth(), viewer.getServerHeight());
    if (geometry.getArea() <= 1)
        return null;
    long endTime = System.currentTimeMillis();
    logger.trace(getClass().getSimpleName() + " time: " + (endTime - startTime));
    if (pLast == null)
        pLast = new Point2D.Double(x, y);
    else
        pLast.setLocation(x, y);
    return geometry;
}