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

Example 31 with Point2

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

the class PointIOTest method test2ReadPoints.

@Test
public void test2ReadPoints() {
    List<PathObject> pathObjects = null;
    List<Double[]> pointsList = new ArrayList<>();
    try {
        pathObjects = PointIO.readPoints(file);
        for (var pathObject : pathObjects) {
            Point2 point = pathObject.getROI().getAllPoints().get(0);
            pointsList.add(new Double[] { point.getX(), point.getY() });
        }
    } catch (IOException e) {
        fail();
    }
    // Check that we have the same number of sets as originally
    assertTrue(pathObjects.size() == 5);
    // Check that all coordinates are the same
    assertTrue(map.values().stream().allMatch(p -> {
        return Arrays.stream(p).anyMatch(o -> pointsList.stream().anyMatch(m -> Arrays.equals(m, o)));
    }));
    // Check that classes were correctly assigned (Sets 3 & 5)
    assertTrue(pathObjects.stream().filter(p -> isInside(map.get(3), p.getROI().getAllPoints().get(0))).allMatch(q -> q.getPathClass().getName().equals("Other")));
    assertTrue(pathObjects.stream().filter(p -> isInside(map.get(5), p.getROI().getAllPoints().get(0))).allMatch(q -> q.getPathClass().getName().equals("Tumor")));
    // Check that name were correctly assigned (Sets 4 & 5)
    assertTrue(pathObjects.stream().filter(p -> isInside(map.get(4), p.getROI().getAllPoints().get(0))).allMatch(q -> q.getName().equals("foo")));
    assertTrue(pathObjects.stream().filter(p -> isInside(map.get(5), p.getROI().getAllPoints().get(0))).allMatch(q -> q.getName().equals("bar")));
    // Check C, Z and T
    assertTrue(pathObjects.stream().allMatch(q -> {
        if (isInside(map.get(2), q.getROI().getAllPoints().get(0)))
            return (q.getROI().getC() == 2 && q.getROI().getZ() == 1 && q.getROI().getT() == 7);
        else
            return (q.getROI().getC() == -1 && q.getROI().getZ() == 0 && q.getROI().getT() == 0);
    }));
    file.delete();
}

Example 32 with Point2

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

the class PointIOTest method test1WritePoints.

/**
 * Uses the map generated in init() method and writes all its points down to a TSV file.
 */
@Test
public void test1WritePoints() {
    List<PathObject> pathObjects = new ArrayList<>();
    Integer[] colors = new Integer[] { -14336, -13487566, null, -3342337, -1305168 };
    for (var entry : map.entrySet()) {
        ArrayList<Point2> pointsList = new ArrayList<>();
        int c = entry.getKey() == 2 ? 2 : -1;
        int z = entry.getKey() == 2 ? 1 : 0;
        int t = entry.getKey() == 2 ? 7 : 0;
        for (var coord : entry.getValue()) {
            pointsList.add(new Point2(coord[0], coord[1]));
        }
        ROI points = ROIs.createPointsROI(pointsList, ImagePlane.getPlaneWithChannel(c, z, t));
        PathObject pathObject = PathObjects.createAnnotationObject(points);
        if (entry.getKey() == 3)
            pathObject.setPathClass(PathClassFactory.getPathClass("Other"));
        if (entry.getKey() == 4)
            pathObject.setName("foo");
        else if (entry.getKey() == 5) {
            pathObject.setPathClass(PathClassFactory.getPathClass("Tumor"));
            pathObject.setName("bar");
        }
        pathObject.setColorRGB(colors[entry.getKey() - 1]);
        pathObjects.add(pathObject);
    }
    try {
        file = File.createTempFile("tmp", ".tsv");
        PointIO.writePoints(file, pathObjects);
    } catch (IOException e) {
        fail();
    }
}

Example 33 with Point2

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

the class ShapeSimplifier method simplifyPolygonPoints.

/**
 * Create a simplified polygon (fewer coordinates) using method based on Visvalingam’s Algorithm.
 * The input is a list of points (the vertices) belonging to a closed polygon.
 * This list is modified in place.
 * <p>
 * See references:
 * https://hydra.hull.ac.uk/resources/hull:8338
 * https://www.jasondavies.com/simplify/
 * http://bost.ocks.org/mike/simplify/
 *
 * @param points
 * @param altitudeThreshold
 */
public static void simplifyPolygonPoints(final List<Point2> points, final double altitudeThreshold) {
    if (points.size() <= 1)
        return;
    // Remove duplicates first
    var iter = points.iterator();
    Point2 lastPoint = iter.next();
    while (iter.hasNext()) {
        var nextPoint = iter.next();
        if (nextPoint.equals(lastPoint))
            iter.remove();
        else
            lastPoint = nextPoint;
    }
    if (lastPoint.equals(points.get(0)))
        iter.remove();
    if (points.size() <= 3)
        return;
    int n = points.size();
    // Populate the priority queue
    PriorityQueue<PointWithArea> queue = new PriorityQueue<>();
    Point2 pPrevious = points.get(points.size() - 1);
    Point2 pCurrent = points.get(0);
    PointWithArea pwaPrevious = null;
    PointWithArea pwaFirst = null;
    for (int i = 0; i < n; i++) {
        Point2 pNext = points.get((i + 1) % n);
        PointWithArea pwa = new PointWithArea(pCurrent, calculateArea(pPrevious, pCurrent, pNext));
        pwa.setPrevious(pwaPrevious);
        if (pwaPrevious != null)
            pwaPrevious.setNext(pwa);
        queue.add(pwa);
        pwaPrevious = pwa;
        pPrevious = pCurrent;
        pCurrent = pNext;
        // Handle first and last cases for closed polygon
        if (i == n - 1) {
            pwa.setNext(pwaFirst);
            pwaFirst.setPrevious(pwa);
        } else if (i == 0)
            pwaFirst = pwa;
    }
    double maxArea = 0;
    int minSize = Math.max(n / 100, 3);
    Set<Point2> toRemove = new HashSet<>();
    while (queue.size() > minSize) {
        PointWithArea pwa = queue.poll();
        // logger.info("BEFORE: " + pwa + " (counter " + counter + ")");
        // Altitude check (?)
        double altitude = pwa.getArea() * 2 / pwa.getNext().getPoint().distance(pwa.getPrevious().getPoint());
        if (altitude > altitudeThreshold)
            break;
        if (pwa.getArea() < maxArea)
            pwa.setArea(maxArea);
        else
            maxArea = pwa.getArea();
        // Remove the point & update accordingly
        // points.remove(pwa.getPoint());
        toRemove.add(pwa.getPoint());
        pwaPrevious = pwa.getPrevious();
        PointWithArea pwaNext = pwa.getNext();
        pwaPrevious.setNext(pwaNext);
        pwaPrevious.updateArea();
        pwaNext.setPrevious(pwaPrevious);
        pwaNext.updateArea();
        // Reinsert into priority queue
        queue.remove(pwaPrevious);
        queue.remove(pwaNext);
        queue.add(pwaPrevious);
        queue.add(pwaNext);
    // logger.info(pwa);
    }
    points.removeAll(toRemove);
}