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

Example 1 with PathOverlay

use of qupath.lib.gui.viewer.overlays.PathOverlay 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 2 with PathOverlay

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

the class QuPathViewer method paintViewer.

protected void paintViewer(Graphics g, int w, int h) {
    ImageServer<BufferedImage> server = getServer();
    if (server == null) {
        g.setColor(background);
        g.fillRect(0, 0, w, h);
        updateRepaintTimestamp();
        return;
    }
    // // Get dimensions
    // int w = getWidth();
    // int h = getHeight();
    Rectangle clip = g.getClipBounds();
    boolean clipFull;
    if (clip == null) {
        clip = new Rectangle(0, 0, w, h);
        g.setClip(0, 0, w, h);
        clipFull = true;
    } else
        clipFull = clip.x == 0 && clip.y == 0 && clip.width == w && clip.height == h;
    // Ensure we have a sufficiently-large buffer
    if (imgBuffer == null || imgBuffer.getWidth() != w || imgBuffer.getHeight() != h) {
        // Create buffered images & buffers for RGB pixel values
        imgBuffer = createBufferedImage(w, h);
        imgBuffer.setAccelerationPriority(1f);
        logger.trace("New buffered image created: {}", imgBuffer);
        // imgVolatile = createVolatileImage(w, h);
        imageUpdated = true;
        // If the size changed, ensure the AffineTransform is up-to-date
        updateAffineTransform();
    }
    // Get the displayed region
    Shape shapeRegion = getDisplayedRegionShape();
    // The visible shape must have changed if there wasn't one previously...
    // Otherwise check if it has changed & update accordingly
    // This will be used to notify listeners soon
    boolean shapeChanged = lastVisibleShape == null || !lastVisibleShape.equals(shapeRegion);
    long t1 = System.currentTimeMillis();
    // Only repaint the image if this is requested, otherwise only overlays need to be repainted
    if (imageUpdated || locationUpdated) {
        // || imgVolatile.contentsLost()) {
        // Set flags that image no longer requiring an update
        // By setting them early, they might still be reset during this run... in which case we don't want to thwart the re-run
        imageUpdated = false;
        locationUpdated = false;
        // updateBufferedImage(imgVolatile, shapeRegion, w, h);
        updateBufferedImage(imgBuffer, shapeRegion, w, h);
    }
    // if (imageUpdated || locationUpdated) {
    // updateBufferedImage(imgVolatile, shapeRegion, w, h);
    // //			updateBufferedImage(imgBuffer, shapeRegion, w, h);
    // //			logger.info("INITIAL Image drawing time: " + (System.currentTimeMillis() - t1));
    // imgVolatile.createGraphics().drawImage(imgBuffer, 0, 0, this);
    // }
    // while (imgVolatile.contentsLost()) {
    // imgVolatile.createGraphics().drawImage(imgBuffer, 0, 0, this);
    // }
    // Store the last shape visible
    lastVisibleShape = shapeRegion;
    // Draw the image from the buffer
    // The call to super.paintComponent is delayed until here to try to stop occasional flickering on Apple's Java 6
    g.setColor(background);
    if (clipFull)
        paintFinalImage(g, imgBuffer, this);
    else
        // g2d.drawImage(imgBuffer, 0, 0, getWidth(), getHeight(), this);
        g.drawImage(imgBuffer, clip.x, clip.y, clip.x + clip.width, clip.y + clip.height, clip.x, clip.y, clip.x + clip.width, clip.y + clip.height, null);
    if (logger.isTraceEnabled()) {
        long t2 = System.currentTimeMillis();
        logger.trace("Final image drawing time: {}", (t2 - t1));
    }
    // Really useful only for debugging graphics
    if (!(g instanceof Graphics2D)) {
        imageUpdated = false;
        // Notify any listeners of shape changes
        if (shapeChanged)
            fireVisibleRegionChangedEvent(lastVisibleShape);
        return;
    }
    double downsample = getDownsampleFactor();
    float opacity = overlayOptions.getOpacity();
    Graphics2D g2d = (Graphics2D) g.create();
    // Apply required transform to the graphics object (rotation, scaling, shifting...)
    g2d.transform(transform);
    Composite previousComposite = g2d.getComposite();
    boolean paintCompletely = thumbnailIsFullImage || !doFasterRepaint;
    // var regionBounds = AwtTools.getImageRegion(clip, getZPosition(), getTPosition());
    if (opacity > 0 || PathPrefs.alwaysPaintSelectedObjectsProperty().get()) {
        if (opacity < 1) {
            AlphaComposite composite = AlphaComposite.getInstance(AlphaComposite.SRC_OVER, opacity);
            g2d.setComposite(composite);
        }
        Color color = getSuggestedOverlayColor();
        // Paint the overlay layers
        var imageData = this.imageDataProperty.get();
        for (PathOverlay overlay : allOverlayLayers.toArray(PathOverlay[]::new)) {
            logger.trace("Painting overlay: {}", overlay);
            if (overlay instanceof AbstractOverlay)
                ((AbstractOverlay) overlay).setPreferredOverlayColor(color);
            // overlay.paintOverlay(g2d, regionBounds, downsample, null, paintCompletely);
            overlay.paintOverlay(g2d, getServerBounds(), downsample, imageData, paintCompletely);
        }
    // if (hierarchyOverlay != null) {
    // hierarchyOverlay.setPreferredOverlayColor(color);
    // hierarchyOverlay.paintOverlay(g2d, getServerBounds(), downsampleFactor, null, paintCompletely);
    // }
    }
    // Paint the selected object
    PathObjectHierarchy hierarchy = getHierarchy();
    PathObject mainSelectedObject = getSelectedObject();
    Rectangle2D boundsRect = null;
    boolean useSelectedColor = PathPrefs.useSelectedColorProperty().get();
    boolean paintSelectedBounds = PathPrefs.paintSelectedBoundsProperty().get();
    for (PathObject selectedObject : hierarchy.getSelectionModel().getSelectedObjects().toArray(new PathObject[0])) {
        // TODO: Simplify this...
        if (selectedObject != null && selectedObject.hasROI() && selectedObject.getROI().getZ() == getZPosition() && selectedObject.getROI().getT() == getTPosition()) {
            if (!selectedObject.isDetection()) {
                // Ensure a selected ROI can be seen clearly
                if (previousComposite != null)
                    g2d.setComposite(previousComposite);
                g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
            }
            Rectangle boundsDisplayed = shapeRegion.getBounds();
            ROI pathROI = selectedObject.getROI();
            // if ((PathPrefs.getPaintSelectedBounds() || (selectedObject.isDetection() && !PathPrefs.getUseSelectedColor())) && !(pathROI instanceof RectangleROI)) {
            if (pathROI != null && (paintSelectedBounds || (!useSelectedColor)) && !(pathROI instanceof RectangleROI) && !pathROI.isEmpty()) {
                Shape boundsShape = null;
                if (pathROI.isPoint()) {
                    var hull = pathROI.getConvexHull();
                    if (hull != null)
                        boundsShape = hull.getShape();
                }
                if (boundsShape == null) {
                    boundsRect = AwtTools.getBounds2D(pathROI, boundsRect);
                    boundsShape = boundsRect;
                }
                // Tried to match to pixel boundaries... but resulted in too much jiggling
                // boundsShape.setFrame(
                // Math.round(boundsShape.getX()/downsampleFactor)*downsampleFactor-downsampleFactor,
                // Math.round(boundsShape.getY()/downsampleFactor)*downsampleFactor-downsampleFactor,
                // Math.round(boundsShape.getWidth()/downsampleFactor)*downsampleFactor+2*downsampleFactor,
                // Math.round(boundsShape.getHeight()/downsampleFactor)*downsampleFactor+2*downsampleFactor);
                // boundsShape.setFrame(boundsShape.getX()-downsampleFactor, boundsShape.getY()-downsampleFactor, boundsShape.getWidth()+2*downsampleFactor, boundsShape.getHeight()+2*downsampleFactor);
                PathHierarchyPaintingHelper.paintShape(boundsShape, g2d, getSuggestedOverlayColor(), PathHierarchyPaintingHelper.getCachedStroke(Math.max(downsample, 1) * 2), null);
            // boundsShape.setFrame(boundsShape.getX()+downsampleFactor, boundsShape.getY()-downsampleFactor, boundsShape.getWidth(), boundsShape.getHeight());
            // PathHierarchyPaintingHelper.paintShape(boundsShape, g2d, new Color(1f, 1f, 1f, 0.75f), PathHierarchyPaintingHelper.getCachedStroke(Math.max(downsampleFactor, 1)*2), null, downsampleFactor);
            }
            // in a cached way
            if ((selectedObject.isDetection() && PathPrefs.useSelectedColorProperty().get()) || !PathObjectTools.hierarchyContainsObject(hierarchy, selectedObject))
                PathHierarchyPaintingHelper.paintObject(selectedObject, false, g2d, boundsDisplayed, overlayOptions, getHierarchy().getSelectionModel(), downsample);
            // Paint ROI handles, if required
            if (selectedObject == mainSelectedObject && roiEditor.hasROI()) {
                Stroke strokeThick = PathHierarchyPaintingHelper.getCachedStroke(PathPrefs.annotationStrokeThicknessProperty().get() * downsample);
                Color color = useSelectedColor ? ColorToolsAwt.getCachedColor(PathPrefs.colorSelectedObjectProperty().get()) : null;
                if (color == null)
                    color = ColorToolsAwt.getCachedColor(ColorToolsFX.getDisplayedColorARGB(selectedObject));
                g2d.setStroke(strokeThick);
                // Draw ROI handles using adaptive size
                double maxHandleSize = getMaxROIHandleSize();
                double minHandleSize = downsample;
                PathHierarchyPaintingHelper.paintHandles(roiEditor, g2d, minHandleSize, maxHandleSize, color, ColorToolsAwt.getTranslucentColor(color));
            }
        }
    }
    // Notify any listeners of shape changes
    if (shapeChanged)
        fireVisibleRegionChangedEvent(lastVisibleShape);
    updateRepaintTimestamp();
}