Examples with ImageRegion qupath.lib.regions.ImageRegion used on opensource projects

Example 6 with ImageRegion

use of qupath.lib.regions.ImageRegion in project qupath by qupath.

the class IJTools method convertToROI.

/**
 * Create a ROI from an ImageJ Roi.
 *
 * @param roi
 * @param pathImage
 * @return
 */
public static <T extends PathImage<? extends ImagePlus>> ROI convertToROI(Roi roi, T pathImage) {
    Calibration cal = null;
    double downsampleFactor = 1;
    ImageRegion region = pathImage.getImageRegion();
    if (pathImage != null) {
        cal = pathImage.getImage().getCalibration();
        downsampleFactor = pathImage.getDownsampleFactor();
    }
    return convertToROI(roi, cal, downsampleFactor, region.getPlane());
}

Example 7 with ImageRegion

use of qupath.lib.regions.ImageRegion 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;
}

Example 8 with ImageRegion

use of qupath.lib.regions.ImageRegion in project qupath by qupath.

the class BufferedImageOverlay method paintOverlay.

// /**
// * Add another region to the overlay.
// * @param region
// * @param img
// * @return any existing region with the same key
// */
// public BufferedImage put(ImageRegion region, BufferedImage img) {
// var previous = regions.put(region, img);
// if (viewer != null)
// viewer.repaint();
// return previous;
// }
@Override
public void paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsampleFactor, ImageData<BufferedImage> imageData, boolean paintCompletely) {
    // Don't show if pixel classifications aren't being shown
    if (!isVisible() || !getOverlayOptions().getShowPixelClassification())
        return;
    super.paintOverlay(g2d, imageRegion, downsampleFactor, imageData, paintCompletely);
    // Paint the regions we have
    for (Map.Entry<ImageRegion, BufferedImage> entry : regions.entrySet()) {
        ImageRegion region = entry.getKey();
        // Check if the region intersects or not
        if (!imageRegion.intersects(region))
            continue;
        // Draw the region
        BufferedImage img = entry.getValue();
        if (colorModel != null && colorModel != img.getColorModel()) {
            // Apply the color model to get a version of the image we can draw quickly
            var imgRGB = cacheRGB.get(img);
            if (imgRGB == null) {
                var img2 = new BufferedImage(colorModel, img.getRaster(), img.getColorModel().isAlphaPremultiplied(), null);
                imgRGB = convertToDrawable(img2);
                cacheRGB.put(img, imgRGB);
            }
            img = imgRGB;
        } else {
            img = cacheRGB.computeIfAbsent(img, img2 -> convertToDrawable(img2));
        }
        g2d.drawImage(img, region.getX(), region.getY(), region.getWidth(), region.getHeight(), null);
    }
}

Example 9 with ImageRegion

use of qupath.lib.regions.ImageRegion in project qupath by qupath.

the class ViewTrackerDataMaps method updateDataMaps.

Map<ImageRegion, BufferedImage> updateDataMaps(long timeStart, long timeStop, double downsampleMin, double downsampleMax, Feature feature, ColorMap colorMap) {
    if (timeStart == -1 || timeStop == -1 || downsampleMin == -1 || downsampleMax == -1 || colorMap == null)
        return null;
    var startTime = System.currentTimeMillis();
    regionMaps.clear();
    regionMapsOriginal.clear();
    for (int z = 0; z < nZSlices; z++) {
        for (int t = 0; t < nTimepoints; t++) {
            var relevantFrames = getRelevantFrames(timeStart, timeStop, downsampleMin, downsampleMax, z, t);
            ImageRegion region = ImageRegion.createInstance(0, 0, fullWidth, fullHeight, z, t);
            var dataMap = new ViewTrackerDataMap(region, feature, relevantFrames, downsample, dataMapWidth, dataMapHeight);
            regionMapsOriginal.put(region, dataMap);
            regionMaps.put(region, dataMap.getBufferedImage(colorMap));
        }
    }
    // TODO: remove next line
    logger.info("Processing time for populateRegionMap(): " + (System.currentTimeMillis() - startTime));
    return regionMaps;
}

Example 10 with ImageRegion

use of qupath.lib.regions.ImageRegion in project qupath by qupath.

the class Commands method createFullImageAnnotation.

/**
 * Create a full image annotation for the image in the specified viewer.
 * The z and t positions of the viewer will be used.
 * @param viewer the viewer containing the image to be processed
 */
public static void createFullImageAnnotation(QuPathViewer viewer) {
    if (viewer == null)
        return;
    ImageData<?> imageData = viewer.getImageData();
    if (imageData == null)
        return;
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    // Check if we already have a comparable annotation
    int z = viewer.getZPosition();
    int t = viewer.getTPosition();
    ImageRegion bounds = viewer.getServerBounds();
    ROI roi = ROIs.createRectangleROI(bounds.getX(), bounds.getY(), bounds.getWidth(), bounds.getHeight(), ImagePlane.getPlane(z, t));
    for (PathObject pathObject : hierarchy.getAnnotationObjects()) {
        ROI r2 = pathObject.getROI();
        if (r2 instanceof RectangleROI && roi.getBoundsX() == r2.getBoundsX() && roi.getBoundsY() == r2.getBoundsY() && roi.getBoundsWidth() == r2.getBoundsWidth() && roi.getBoundsHeight() == r2.getBoundsHeight() && roi.getImagePlane().equals(r2.getImagePlane())) {
            logger.info("Full image annotation already exists! {}", pathObject);
            viewer.setSelectedObject(pathObject);
            return;
        }
    }
    PathObject pathObject = PathObjects.createAnnotationObject(roi);
    hierarchy.addPathObject(pathObject);
    viewer.setSelectedObject(pathObject);
    // Log in the history
    if (z == 0 && t == 0)
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", "createSelectAllObject(true);"));
    else
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Create full image annotation", String.format("createSelectAllObject(true, %d, %d);", z, t)));
}