Examples with ImagePlane qupath.lib.regions.ImagePlane used on opensource projects

Example 11 with ImagePlane

use of qupath.lib.regions.ImagePlane in project qupath by qupath.

the class PathObjectTools method mergePointsForSelectedObjectClasses.

// private static void addPathObjectsRecursively(Collection<PathObject> pathObjectsInput, Collection<PathObject> pathObjects, Class<? extends PathObject> cls) {
// Collection<PathObject> buffer = null;
// for (PathObject childObject : pathObjectsInput) {
// if (cls == null || cls.isInstance(childObject)) {
// pathObjects.add(childObject);
// }
// if (childObject.hasChildren()) {
// if (buffer == null)
// buffer = new ArrayList<>();
// else
// buffer.clear();
// childObject.getChildObjects(buffer);
// addPathObjectsRecursively(buffer, pathObjects, cls);
// }
// }
// }
// /**
// * Split annotations containing multi-point ROIs into separate single-point ROIs.
// *
// * @param hierarchy the object hierarchy
// * @param selectedOnly if true, consider only annotations that are currently selected; if false, consider all point annotations in the hierarchy
// * @return true if changes are made to the hierarchy, false otherwise
// */
// public static boolean splitPoints(PathObjectHierarchy hierarchy, boolean selectedOnly) {
// if (hierarchy == null) {
// logger.debug("No hierarchy available, cannot split points!");
// return false;
// }
// return splitPoints(hierarchy, selectedOnly ? hierarchy.getSelectionModel().getSelectedObjects() : hierarchy.getAnnotationObjects());
// }
// 
// /**
// * Split annotations containing multi-point ROIs into separate single-point ROIs.
// *
// * @param hierarchy the object hierarchy
// * @param pathObjects a collection of point annotations to split; non-points and non-annotations will be ignored
// * @return pathObjects if changes are made to the hierarchy, false otherwise
// */
// public static boolean splitPoints(PathObjectHierarchy hierarchy, Collection<PathObject> pathObjects) {
// var points = pathObjects.stream().filter(p -> p.isAnnotation() && p.getROI().isPoint() && p.getROI().getNumPoints() > 1).collect(Collectors.toList());
// if (points.isEmpty()) {
// logger.debug("No (multi)point ROIs available to split!");
// return false;
// }
// List<PathObject> newObjects = new ArrayList<>();
// for (PathObject pathObject : points) {
// ROI p = pathObject.getROI();
// ImagePlane plane = p.getImagePlane();
// PathClass pathClass = pathObject.getPathClass();
// for (Point2 p2 : p.getAllPoints()) {
// PathObject temp = PathObjects.createAnnotationObject(ROIs.createPointsROI(p2.getX(), p2.getY(), plane), pathClass);
// newObjects.add(temp);
// }
// }
// hierarchy.removeObjects(points, true);
// hierarchy.addPathObjects(newObjects);
// // Reset the selection
// hierarchy.getSelectionModel().clearSelection();
// return true;
// }
/**
 * Merge point annotations sharing the same {@link PathClass} and {@link ImagePlane} as the selected annotations,
 * creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
 *
 * @param hierarchy object hierarchy to modify
 * @return true if changes are made to the hierarchy, false otherwise
 */
public static boolean mergePointsForSelectedObjectClasses(PathObjectHierarchy hierarchy) {
    var pathClasses = hierarchy.getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation() && p.getROI().isPoint()).map(p -> p.getPathClass()).collect(Collectors.toSet());
    boolean changes = false;
    for (PathClass pathClass : pathClasses) changes = changes || mergePointsForClass(hierarchy, pathClass);
    return changes;
}

Example 12 with ImagePlane

use of qupath.lib.regions.ImagePlane in project qupath by qupath.

the class PointsTool method mousePressed.

@Override
public void mousePressed(MouseEvent e) {
    super.mousePressed(e);
    if (!e.isPrimaryButtonDown() || e.isConsumed()) {
        return;
    }
    // Get a server, if we can
    var viewer = getViewer();
    ImageServer<?> server = viewer.getServer();
    if (server == null)
        return;
    var viewerPlane = viewer.getImagePlane();
    // Find out the coordinates in the image domain
    Point2D p = mouseLocationToImage(e, false, requestPixelSnapping());
    double xx = p.getX();
    double yy = p.getY();
    // If we are outside the image, ignore click
    if (xx < 0 || yy < 0 || xx >= server.getWidth() || yy >= server.getHeight())
        return;
    // See if we have a selected ROI
    PathObject currentObjectTemp = viewer.getSelectedObject();
    if (!(currentObjectTemp == null || currentObjectTemp instanceof PathROIObject))
        return;
    PathROIObject currentObject = (PathROIObject) currentObjectTemp;
    ROI currentROI = currentObject == null ? null : currentObject.getROI();
    RoiEditor editor = viewer.getROIEditor();
    double radius = PathPrefs.pointRadiusProperty().get();
    ROI points = null;
    if (currentROI != null && currentROI.isPoint() && (currentROI.isEmpty() || currentROI.getImagePlane().equals(viewerPlane)))
        points = currentROI;
    // If Alt is pressed, try to delete a point
    if (e.isAltDown()) {
        handleAltClick(xx, yy, currentObject);
    } else // Create a new ROI if we've got Alt & Shift pressed - or we just don't have a point ROI
    if (points == null || (!PathPrefs.multipointToolProperty().get() && !editor.grabHandle(xx, yy, radius, e.isShiftDown())) || (e.isShiftDown() && e.getClickCount() > 1)) {
        // PathPoints is effectively ready from the start - don't need to finalize
        points = ROIs.createPointsROI(xx, yy, viewerPlane);
        currentObject = (PathROIObject) PathObjects.createAnnotationObject(points, PathPrefs.autoSetAnnotationClassProperty().get());
        viewer.getHierarchy().addPathObject(currentObject);
        viewer.setSelectedObject(currentObject);
        // viewer.createAnnotationObject(points);
        editor.setROI(points);
        editor.grabHandle(xx, yy, radius, e.isShiftDown());
    } else if (points != null) {
        // Add point to current ROI, or adjust the position of a nearby point
        ImagePlane plane = points == null || points.isEmpty() ? viewerPlane : points.getImagePlane();
        ROI points2 = addPoint(points, xx, yy, radius, plane);
        if (points2 == points) {
            // If we didn't add a point, try to grab a handle
            if (!editor.grabHandle(xx, yy, radius, e.isShiftDown()))
                return;
            points2 = (PointsROI) editor.setActiveHandlePosition(xx, yy, 0.25, e.isShiftDown());
        } else {
            editor.setROI(points2);
            editor.grabHandle(xx, yy, radius, e.isShiftDown());
        }
        if (points2 != points) {
            currentObject.setROI(points2);
            viewer.getHierarchy().updateObject(currentObject, true);
        // viewer.getHierarchy().fireHierarchyChangedEvent(this, currentObject);
        }
    }
    viewer.repaint();
}

Example 13 with ImagePlane

use of qupath.lib.regions.ImagePlane in project qupath by qupath.

the class RoiTools method union.

/**
 * Create union of multiple ROIs. This assumes that ROIs fall on the same plane, if not an {@link IllegalArgumentException}
 * will be thrown. Similarly, ROIs must be of a similar type (e.g. area, point) or an exception will be thrown by Java Topology Suite.
 * @param rois
 * @return
 */
public static ROI union(Collection<ROI> rois) {
    logger.trace("Calculating union of {} ROIs", rois.size());
    if (rois.isEmpty())
        return ROIs.createEmptyROI();
    if (rois.size() == 1)
        return rois.iterator().next();
    ImagePlane plane = rois.iterator().next().getImagePlane();
    List<Geometry> geometries = new ArrayList<>();
    for (var r : rois) {
        if (!r.getImagePlane().equals(plane)) {
            throw new IllegalArgumentException("Cannot merge ROIs - found plane " + r.getImagePlane() + " but expected " + plane);
        }
        geometries.add(r.getGeometry());
    }
    return GeometryTools.geometryToROI(GeometryTools.union(geometries), plane);
}

Example 14 with ImagePlane

use of qupath.lib.regions.ImagePlane in project qupath by qupath.

the class RoiTools method intersection.

/**
 * Create intersection of multiple ROIs. This assumes that ROIs fall on the same plane, if not an {@link IllegalArgumentException}
 * will be thrown. Similarly, ROIs must be of a similar type (e.g. area, point) or an exception will be thrown by Java Topology Suite.
 * @param rois
 * @return
 */
public static ROI intersection(Collection<ROI> rois) {
    if (rois.isEmpty())
        return ROIs.createEmptyROI();
    if (rois.size() == 1)
        return rois.iterator().next();
    ImagePlane plane = rois.iterator().next().getImagePlane();
    List<Geometry> geometries = new ArrayList<>();
    for (var r : rois) {
        if (!r.getImagePlane().equals(plane)) {
            throw new IllegalArgumentException("Cannot merge ROIs - found plane " + r.getImagePlane() + " but expected " + plane);
        }
        geometries.add(r.getGeometry());
    }
    Geometry first = geometries.remove(0);
    for (var geom : geometries) first = first.intersection(geom);
    return GeometryTools.geometryToROI(first, plane);
}