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

Example 6 with Point2

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

the class PathHierarchyPaintingHelper method paintHandles.

/**
 * Paint the handles onto a Graphics object.
 *
 * @param g2d
 * @param handleSize The width & height of the shape used to draw the handles
 * @param colorStroke
 * @param colorFill
 */
/**
 * Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
 * <p>
 * The minimum and maximum handle size can be specified; if the same, all handles will have the same size.  If different,
 * then the distance between consecutive handles will be used to influence the actual handle size.  This is helpful
 * when handles are densely packed.
 *
 * @param handles
 * @param g2d
 * @param minHandleSize
 * @param maxHandleSize
 * @param colorStroke
 * @param colorFill
 */
public static void paintHandles(final List<Point2> handles, final Graphics2D g2d, final double minHandleSize, final double maxHandleSize, final Color colorStroke, final Color colorFill) {
    RectangularShape handleShape = new Rectangle2D.Double();
    // handleShape = new Ellipse2D.Double();
    int n = handles.size();
    if (minHandleSize == maxHandleSize) {
        for (Point2 p : handles) {
            double handleSize = minHandleSize;
            handleShape.setFrame(p.getX() - handleSize / 2, p.getY() - handleSize / 2, handleSize, handleSize);
            if (colorFill != null) {
                g2d.setColor(colorFill);
                g2d.fill(handleShape);
            }
            if (colorStroke != null) {
                g2d.setColor(colorStroke);
                g2d.draw(handleShape);
            }
        }
        return;
    } else {
        for (int i = 0; i < handles.size(); i++) {
            var current = handles.get(i);
            var before = handles.get((i + n - 1) % n);
            var after = handles.get((i + 1) % n);
            double distance = Math.sqrt(Math.min(current.distanceSq(before), current.distanceSq(after))) * 0.5;
            double size = Math.max(minHandleSize, Math.min(distance, maxHandleSize));
            var p = current;
            handleShape.setFrame(p.getX() - size / 2, p.getY() - size / 2, size, size);
            if (colorFill != null) {
                g2d.setColor(colorFill);
                g2d.fill(handleShape);
            }
            if (colorStroke != null) {
                g2d.setColor(colorStroke);
                g2d.draw(handleShape);
            }
        }
    }
}

Example 7 with Point2

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

the class ROIConverterIJ method convertToPointsList.

private static List<Point2> convertToPointsList(FloatPolygon polygon, double xOrigin, double yOrigin, double downsampleFactor) {
    List<Point2> points = new ArrayList<>();
    for (int i = 0; i < polygon.npoints; i++) {
        float x = (float) convertLocationfromIJ(polygon.xpoints[i], xOrigin, downsampleFactor);
        float y = (float) convertLocationfromIJ(polygon.ypoints[i], yOrigin, downsampleFactor);
        points.add(new Point2(x, y));
    }
    return points;
}

Example 8 with Point2

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

the class TestDistanceTools method test_detectionCentroidDistance2D.

@Test
public void test_detectionCentroidDistance2D() {
    double radius = 5;
    List<Point2> tumorCoordinates = Arrays.asList(new Point2(100, 100), new Point2(100, 200), new Point2(150, 150));
    List<Point2> stromaCoordinates = Arrays.asList(new Point2(120, 100), new Point2(100, 210));
    var planes = Arrays.asList(ImagePlane.getDefaultPlane(), ImagePlane.getPlane(2, 0), ImagePlane.getPlane(1, 1));
    for (var sourcePlane : planes) {
        for (var targetPlane : planes) {
            var tumorDetections = tumorCoordinates.stream().map(p -> PathObjects.createDetectionObject(ROIs.createEllipseROI(p.getX() - radius, p.getY() - radius, radius * 2, radius * 2, sourcePlane), PathClassFactory.getPathClass(StandardPathClasses.TUMOR))).collect(Collectors.toList());
            var stromaDetections = stromaCoordinates.stream().map(p -> PathObjects.createDetectionObject(ROIs.createEllipseROI(p.getX() - radius, p.getY() - radius, radius * 2, radius * 2, targetPlane), PathClassFactory.getPathClass(StandardPathClasses.STROMA))).collect(Collectors.toList());
            if (sourcePlane.equals(targetPlane)) {
                // Distance to stroma, default pixels
                DistanceTools.centroidToCentroidDistance2D(tumorDetections, stromaDetections, 1.0, 1.0, "Distance to stroma");
                assertEquals(tumorDetections.get(0).getMeasurementList().getMeasurementValue("Distance to stroma"), 20, 0.0001);
                assertEquals(tumorDetections.get(1).getMeasurementList().getMeasurementValue("Distance to stroma"), 10, 0.0001);
                assertEquals(tumorDetections.get(2).getMeasurementList().getMeasurementValue("Distance to stroma"), Math.sqrt(30 * 30 + 50 * 50), 0.0001);
                // Distance to stroma, scaled pixels
                DistanceTools.centroidToCentroidDistance2D(tumorDetections, stromaDetections, 2.0, 2.0, "Distance to stroma");
                assertEquals(tumorDetections.get(0).getMeasurementList().getMeasurementValue("Distance to stroma"), 20 * 2, 0.0001);
                assertEquals(tumorDetections.get(1).getMeasurementList().getMeasurementValue("Distance to stroma"), 10 * 2, 0.0001);
                assertEquals(tumorDetections.get(2).getMeasurementList().getMeasurementValue("Distance to stroma"), Math.sqrt(30 * 30 * 4 + 50 * 50 * 4), 0.0001);
                // Distance to stroma, scaled non-square pixels
                DistanceTools.centroidToCentroidDistance2D(tumorDetections, stromaDetections, 1.4, 1.6, "Distance to stroma");
                assertEquals(tumorDetections.get(0).getMeasurementList().getMeasurementValue("Distance to stroma"), 20 * 1.4, 0.0001);
                assertEquals(tumorDetections.get(1).getMeasurementList().getMeasurementValue("Distance to stroma"), 10 * 1.6, 0.0001);
                assertEquals(tumorDetections.get(2).getMeasurementList().getMeasurementValue("Distance to stroma"), Math.sqrt(30 * 30 * 1.4 * 1.4 + 50 * 50 * 1.6 * 1.6), 0.0001);
                // Ensure no other measurements added
                for (var stroma : stromaDetections) {
                    assertFalse(stroma.getMeasurementList().containsNamedMeasurement("Distance to stroma"));
                    assertTrue(Double.isNaN(stroma.getMeasurementList().getMeasurementValue("Distance to stroma")));
                }
                for (var tumor : tumorDetections) {
                    assertTrue(tumor.getMeasurementList().containsNamedMeasurement("Distance to stroma"));
                }
            } else {
                // Ensure no measurements added
                DistanceTools.centroidToCentroidDistance2D(tumorDetections, stromaDetections, 1.0, 1.0, "Distance to stroma");
                for (var tumor : tumorDetections) {
                    // Currently, we don't add a measurement if not on the same plane
                    // assertTrue(tumor.getMeasurementList().containsNamedMeasurement("Distance to stroma"));
                    assertTrue(Double.isNaN(tumor.getMeasurementList().getMeasurementValue("Distance to stroma")));
                }
                for (var stroma : stromaDetections) {
                    assertFalse(stroma.getMeasurementList().containsNamedMeasurement("Distance to stroma"));
                    assertTrue(Double.isNaN(stroma.getMeasurementList().getMeasurementValue("Distance to stroma")));
                }
            }
        }
    }
}

Example 9 with Point2

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

the class PointsTool method addPoint.

/**
 * Add a point only if it has a separation of at least minimumSeparation from all other points
 * currently stored, otherwise do nothing.
 *
 * @param x
 * @param y
 * @param minimumSeparation
 */
private ROI addPoint(final ROI points, final double x, final double y, final double minimumSeparation, final ImagePlane plane) {
    // Can't add NaN points
    if (Double.isNaN(x + y))
        return points;
    List<Point2> pointsList = points.getAllPoints();
    if (minimumSeparation > 0) {
        // Test for separation
        double threshold = minimumSeparation * minimumSeparation;
        for (Point2 p : pointsList) if (p.distanceSq(x, y) < threshold)
            return points;
    }
    List<Point2> pointsList2 = new ArrayList<>(pointsList);
    pointsList2.add(new Point2(x, y));
    return ROIs.createPointsROI(pointsList2, plane);
}

Example 10 with Point2

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

the class PointsROI method getNearest.

/**
 * Identify the closest point within a specified distance to coordinates x,y - or null if no points are found.
 * @param x
 * @param y
 * @param maxDist
 * @return
 */
public Point2 getNearest(double x, double y, double maxDist) {
    double maxDistSq = maxDist * maxDist;
    Point2 pClosest = null;
    double distClosestSq = Double.POSITIVE_INFINITY;
    for (Point2 p : points) {
        double distSq = p.distanceSq(x, y);
        if (distSq <= maxDistSq && distSq < distClosestSq) {
            pClosest = p;
            distClosestSq = distSq;
        }
    }
    return pClosest;
}