Examples with Point2 qupath.lib.geom.Point2 used on opensource projects

Example 11 with Point2

use of qupath.lib.geom.Point2 in project qupath by qupath.

the class WindingTest method getWindingNumber.

public static int getWindingNumber(final List<Point2> points, final double x, final double y) {
    if (points.size() <= 2)
        return 0;
    int nPoints = points.size();
    int wn = 0;
    for (int i = 0; i < nPoints; i++) {
        Point2 p = points.get(i);
        Point2 p2 = points.get((i + 1) % nPoints);
        if (p.getY() <= y) {
            // start y <= P.y
            if (// an upward crossing
            p2.getY() > y)
                if (// P left of  edge
                isLeft(p.getX(), p.getY(), p2.getX(), p2.getY(), x, y) > 0)
                    // have  a valid up intersect
                    wn++;
        } else {
            // start y > P.y (no test needed)
            if (// a downward crossing
            p2.getY() <= y)
                if (// P right of  edge
                isLeft(p.getX(), p.getY(), p2.getX(), p2.getY(), x, y) < 0)
                    // have  a valid down intersect
                    wn--;
        }
    }
    return wn;
}

Example 12 with Point2

use of qupath.lib.geom.Point2 in project qupath by qupath.

the class WindingTest method getWindingNumber.

public static int getWindingNumber(final Vertices vertices, final double x, final double y) {
    if (vertices.size() <= 2)
        return 0;
    int nPoints = vertices.size();
    int wn = 0;
    for (int i = 0; i < nPoints; i++) {
        Point2 p = vertices.get(i);
        Point2 p2 = vertices.get((i + 1) % nPoints);
        if (p.getY() <= y) {
            // start y <= P.y
            if (// an upward crossing
            p2.getY() > y)
                if (// P left of  edge
                isLeft(p.getX(), p.getY(), p2.getX(), p2.getY(), x, y) > 0)
                    // have  a valid up intersect
                    wn++;
        } else {
            // start y > P.y (no test needed)
            if (// a downward crossing
            p2.getY() <= y)
                if (// P right of  edge
                isLeft(p.getX(), p.getY(), p2.getX(), p2.getY(), x, y) < 0)
                    // have  a valid down intersect
                    wn--;
        }
    }
    return wn;
}

Example 13 with Point2

use of qupath.lib.geom.Point2 in project qupath by qupath.

the class ShapeSimplifier method smoothPoints.

/**
 * Apply a simple 3-point moving average to a list of points.
 *
 * @param points
 * @return
 */
public static List<Point2> smoothPoints(List<Point2> points) {
    List<Point2> points2 = new ArrayList<>(points.size());
    for (int i = 0; i < points.size(); i++) {
        Point2 p1 = points.get((i + points.size() - 1) % points.size());
        Point2 p2 = points.get(i);
        Point2 p3 = points.get((i + 1) % points.size());
        points2.add(new Point2((p1.getX() + p2.getX() + p3.getX()) / 3, (p1.getY() + p2.getY() + p3.getY()) / 3));
    }
    return points2;
}

Example 14 with Point2

use of qupath.lib.geom.Point2 in project qupath by qupath.

the class PathClassificationLabellingHelper method getClassificationMap.

/**
 * Get a map of training data, based on the child objects of some classified annotations.
 *
 * @param hierarchy the hierarchy containing all the objects and annotations.
 * @param pointsOnly if true, only Point annotations will be used for training.
 *
 * @return
 */
public static Map<PathClass, List<PathObject>> getClassificationMap(final PathObjectHierarchy hierarchy, final boolean pointsOnly) {
    Map<PathClass, List<PathObject>> classifications = new TreeMap<>();
    // Get the annotations & filter out those that are useful
    List<PathObject> annotations = new ArrayList<>(getAnnotations(hierarchy));
    Iterator<PathObject> iter = annotations.iterator();
    while (iter.hasNext()) {
        PathObject pathObject = iter.next();
        // We need a PathClass, and may need to only include points
        if (pathObject.getPathClass() == null || pathObject.getPathClass() == PathClassFactory.getPathClass(StandardPathClasses.REGION) || (pointsOnly && !PathObjectTools.hasPointROI(pathObject)))
            iter.remove();
        else
            classifications.put(pathObject.getPathClass(), new ArrayList<>());
    }
    // from the hierarchy
    if (annotations.size() > 1) {
        annotations.sort(new Comparator<PathObject>() {

            @Override
            public int compare(PathObject o1, PathObject o2) {
                PathAnnotationObject p1 = (PathAnnotationObject) o1;
                PathAnnotationObject p2 = (PathAnnotationObject) o2;
                int comp = 0;
                if (p1.hasROI()) {
                    if (p2.hasROI()) {
                        comp = Double.compare(p1.getROI().getCentroidY(), p2.getROI().getCentroidY());
                        if (comp == 0)
                            comp = Double.compare(p1.getROI().getCentroidX(), p2.getROI().getCentroidX());
                        if (comp == 0)
                            comp = p1.getROI().toString().compareTo(p2.getROI().toString());
                    }
                }
                if (comp == 0)
                    return Integer.compare(o1.hashCode(), o2.hashCode());
                else
                    return comp;
            }
        });
    }
    // StringBuilder sb = new StringBuilder("DETECTIONS:\t");
    for (PathObject pathObject : annotations) {
        PathClass pathClass = pathObject.getPathClass();
        List<PathObject> list = classifications.get(pathClass);
        // sb.append(list.size() + ", ");
        if (PathObjectTools.hasPointROI(pathObject)) {
            for (Point2 p : ((PointsROI) pathObject.getROI()).getAllPoints()) {
                // TODO: Pay attention to z & t position!
                Collection<PathObject> pathObjectsTemp = PathObjectTools.getObjectsForLocation(hierarchy, p.getX(), p.getY(), 0, 0, -1);
                pathObjectsTemp = PathObjectTools.getObjectsOfClass(pathObjectsTemp, PathDetectionObject.class);
                // Clumsy way to avoid duplicates...
                list.removeAll(pathObjectsTemp);
                list.addAll(pathObjectsTemp);
            }
        } else
            list.addAll(hierarchy.getObjectsForROI(PathDetectionObject.class, pathObject.getROI()));
    }
    for (Entry<PathClass, List<PathObject>> entry : classifications.entrySet()) {
        logger.info(entry.getKey() + ": " + entry.getValue().size());
    }
    return classifications;
}

Example 15 with Point2

use of qupath.lib.geom.Point2 in project qupath by qupath.

the class PixelClassificationOverlay method paintOverlay.

@Override
public void paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsampleFactor, ImageData<BufferedImage> imageData, boolean paintCompletely) {
    // For now, bind the display to the display of detections
    if (!showOverlay.get())
        return;
    if (imageData == null)
        return;
    // ImageServer<BufferedImage> server = imageData.getServer();
    var server = getPixelClassificationServer(imageData);
    if (server == null)
        return;
    // Show classified tiles. Without this, opacity can make it hard to see which regions have been processed.
    // Note that if the alpha value is too large, tile boundaries can appear at some viewing magnifications (previous default was 32)
    var colorComplete = imageData.getImageType() == ImageData.ImageType.FLUORESCENCE ? ColorToolsAwt.getCachedColor(255, 255, 255, 1) : ColorToolsAwt.getCachedColor(0, 0, 0, 1);
    // Get the displayed clip bounds for fast checking if ROIs need to be drawn
    RegionRequest fullRequest;
    Shape shapeRegion = g2d.getClip();
    if (shapeRegion == null)
        fullRequest = RegionRequest.createInstance(server.getPath(), downsampleFactor, imageRegion);
    else
        fullRequest = RegionRequest.createInstance(server.getPath(), downsampleFactor, AwtTools.getImageRegion(shapeRegion, imageRegion.getZ(), imageRegion.getT()));
    // If we have a filter, we might not need to do anything
    var filter = getOverlayOptions().getPixelClassificationRegionFilter();
    // Avoid this check; it causes confusion when zoomed in
    // if (!filter.test(imageData, fullRequest))
    // return;
    var renderer = this.renderer.get();
    if (renderer != null && rendererLastTimestamp != renderer.getLastChangeTimestamp()) {
        clearCache();
        rendererLastTimestamp = renderer.getLastChangeTimestamp();
    }
    // double requestedDownsample = classifier.getMetadata().getInputPixelSizeMicrons() / server.getAveragedPixelSizeMicrons();
    double requestedDownsample = ServerTools.getPreferredDownsampleFactor(server, downsampleFactor);
    var gCopy = (Graphics2D) g2d.create();
    if (requestedDownsample > server.getDownsampleForResolution(0))
        gCopy.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
    else
        // Only use specified interpolation when upsampling
        setInterpolation(gCopy);
    // gCopy.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR);
    var comp = getAlphaComposite();
    var previousComposite = gCopy.getComposite();
    if (comp != null) {
        if (previousComposite instanceof AlphaComposite)
            gCopy.setComposite(comp.derive(((AlphaComposite) previousComposite).getAlpha() * comp.getAlpha()));
        else
            gCopy.setComposite(comp);
    }
    Collection<TileRequest> tiles = server.getTileRequestManager().getTileRequests(fullRequest);
    if (fullRequest != null) {
        double x = (Math.max(0, fullRequest.getMinX()) + Math.min(server.getWidth(), fullRequest.getMaxX())) / 2.0;
        double y = (Math.max(0, fullRequest.getMinY()) + Math.min(server.getHeight(), fullRequest.getMaxY())) / 2.0;
        var p = new Point2(x, y);
        tiles = new ArrayList<>(tiles);
        ((List<TileRequest>) tiles).sort(Comparator.comparingDouble((TileRequest t) -> p.distanceSq(t.getImageX() + t.getImageWidth() / 2.0, t.getImageY() + t.getImageHeight() / 2.0)));
    }
    // Clear pending requests, since we'll insert new ones (perhaps in a different order)
    this.pendingRequests.clear();
    // Loop through & paint classified tiles if we have them, or request tiles if we don't
    for (TileRequest tile : tiles) {
        var request = tile.getRegionRequest();
        if (filter != null && !filter.test(imageData, request))
            continue;
        // Try to get an RGB image, supplying a server that can be queried for a corresponding non-RGB cached tile if needed
        BufferedImage imgRGB = getCachedTileRGB(tile, server);
        if (imgRGB != null) {
            gCopy.setColor(colorComplete);
            gCopy.fillRect(request.getX(), request.getY(), request.getWidth(), request.getHeight());
            // Get the cached RGB painted version (since painting can be a fairly expensive operation)
            gCopy.drawImage(imgRGB, request.getX(), request.getY(), request.getWidth(), request.getHeight(), null);
            // System.err.println(request.getHeight() == imgRGB.getHeight());
            continue;
        }
        // Request a tile
        if (livePrediction) {
            requestTile(tile, imageData, server);
        }
    }
    gCopy.dispose();
}