Examples with PathObjects qupath.lib.objects.PathObjects used on opensource projects

Example 6 with PathObjects

use of qupath.lib.objects.PathObjects 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 7 with PathObjects

use of qupath.lib.objects.PathObjects in project qupath by qupath.

the class Commands method promptToSimplifySelectedAnnotations.

/**
 * Show a prompt to selected annotations in a hierarchy.
 * @param imageData the current image data
 * @param altitudeThreshold default altitude value for simplification
 */
public static void promptToSimplifySelectedAnnotations(ImageData<?> imageData, double altitudeThreshold) {
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    List<PathObject> pathObjects = hierarchy.getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation() && p.hasROI() && p.isEditable() && !p.getROI().isPoint()).collect(Collectors.toList());
    if (pathObjects.isEmpty()) {
        Dialogs.showErrorMessage("Simplify annotations", "No unlocked shape annotations selected!");
        return;
    }
    String input = Dialogs.showInputDialog("Simplify shape", "Set altitude threshold in pixels.\nHigher values give simpler shapes.", Double.toString(altitudeThreshold));
    if (input == null || !(input instanceof String) || ((String) input).trim().length() == 0)
        return;
    try {
        altitudeThreshold = Double.parseDouble(((String) input).trim());
    } catch (NumberFormatException e) {
        logger.error("Could not parse altitude threshold from {}", input);
        return;
    }
    if (altitudeThreshold <= 0) {
        Dialogs.showErrorMessage("Simplify shape", "Amplitude threshold should be greater than zero!");
        return;
    }
    long startTime = System.currentTimeMillis();
    for (var pathObject : pathObjects) {
        ROI pathROI = pathObject.getROI();
        if (pathROI instanceof PolygonROI) {
            PolygonROI polygonROI = (PolygonROI) pathROI;
            pathROI = ShapeSimplifier.simplifyPolygon(polygonROI, altitudeThreshold);
        } else {
            pathROI = ShapeSimplifier.simplifyShape(pathROI, altitudeThreshold);
        }
        ((PathAnnotationObject) pathObject).setROI(pathROI);
    }
    long endTime = System.currentTimeMillis();
    logger.debug("Shapes simplified in " + (endTime - startTime) + " ms");
    hierarchy.fireObjectsChangedEvent(hierarchy, pathObjects);
}