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

Example 6 with PathObject

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

the class SplitAnnotationsPlugin method getTasks.

@Override
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    // Add a single task, to avoid multithreading - which may complicate setting parents
    List<Runnable> tasks = new ArrayList<>(1);
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    // Want to reset selection
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    tasks.add(() -> {
        /*
			 * Resolving the hierarchy with many objects can be very slow.
			 * Here, we take an object, split it and then add it below the original object in the hierarchy.
			 * We then just need to remove the originals, allowing the newly-added objects to have their 
			 * parents reassigned.
			 */
        List<PathObject> toAdd = new ArrayList<>();
        List<PathObject> toRemove = new ArrayList<>();
        List<PathObject> localSplit = new ArrayList<>();
        Set<PathObject> toSelect = new HashSet<>();
        for (PathObject pathObject : parentObjects) {
            localSplit.clear();
            ROI roiOrig = pathObject.getROI();
            if (roiOrig == null) {
                toSelect.add(pathObject);
                continue;
            }
            var splitROIs = RoiTools.splitROI(roiOrig);
            if (splitROIs.size() == 1)
                continue;
            toRemove.add(pathObject);
            for (var r : splitROIs) {
                var annotation = PathObjects.createAnnotationObject(r, pathObject.getPathClass());
                annotation.setLocked(pathObject.isLocked());
                localSplit.add(annotation);
            }
            if (pathObject.hasChildren()) {
                for (var temp : localSplit) hierarchy.addPathObjectBelowParent(pathObject, temp, false);
            } else
                pathObject.addPathObjects(localSplit);
            toAdd.addAll(localSplit);
        }
        if (toAdd.isEmpty() && toRemove.isEmpty())
            return;
        hierarchy.getSelectionModel().clearSelection();
        toSelect.addAll(toAdd);
        hierarchy.removeObjects(toRemove, true);
        // hierarchy.addPathObjects(toAdd, false);
        hierarchy.getSelectionModel().selectObjects(toSelect);
        if (toSelect.contains(selected))
            hierarchy.getSelectionModel().setSelectedObject(selected, true);
    });
    return tasks;
}

Example 7 with PathObject

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

the class QP method clearTMAGrid.

/**
 * Remove the TMA grid from the current {@code PathObjectHierarchy}.
 *
 * @see #getCurrentHierarchy
 */
public static void clearTMAGrid() {
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return;
    hierarchy.setTMAGrid(null);
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    if (selected instanceof TMACoreObject)
        hierarchy.getSelectionModel().setSelectedObject(null);
}

Example 8 with PathObject

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

the class FindConvexHullDetectionsPlugin method addRunnableTasks.

@Override
protected void addRunnableTasks(ImageData<T> imageData, PathObject parentObject, List<Runnable> tasks) {
    boolean deleteImmediately = Boolean.TRUE.equals(params.getBooleanParameterValue("deleteImmediately"));
    tasks.add(new PathTask() {

        private List<PathObject> toRemove;

        private int nRemoved;

        @Override
        public void run() {
            toRemove = getConvexHullDetections(imageData.getHierarchy(), parentObject, params.getIntParameterValue("nIterations"));
            nRemoved = toRemove.size();
        }

        @Override
        public void taskComplete(boolean wasCancelled) {
            if (wasCancelled)
                return;
            if (toRemove != null && !toRemove.isEmpty()) {
                if (deleteImmediately)
                    imageData.getHierarchy().removeObjects(toRemove, false);
                else {
                    imageData.getHierarchy().getSelectionModel().deselectObject(parentObject);
                    imageData.getHierarchy().getSelectionModel().selectObjects(toRemove);
                }
                toRemove = null;
                nObjectsRemoved.addAndGet(nRemoved);
            }
        }

        @Override
        public String getLastResultsDescription() {
            String process = deleteImmediately ? "Removed " : "Selected ";
            if (Boolean.TRUE.equals(params.getBooleanParameterValue("deleteImmediately")))
                if (nRemoved == 1)
                    return process + " 1 object";
            return process + nRemoved + " objects";
        }
    });
}

Example 9 with PathObject

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

the class FindConvexHullDetectionsPlugin method getConvexHullDetections.

static List<PathObject> getConvexHullDetections(final PathObjectHierarchy hierarchy, final PathObject parent, final int nIterations) {
    Map<Point2, PathObject> pointsMap = new HashMap<>();
    List<PathObject> convexDetections = new ArrayList<>();
    Collection<PathObject> pathObjects = PathObjectTools.getDescendantObjects(parent, null, PathDetectionObject.class);
    if (pathObjects.isEmpty())
        return Collections.emptyList();
    // Populate the points map
    pointsMap.clear();
    for (PathObject child : pathObjects) {
        if (!child.hasROI())
            continue;
        pointsMap.put(new Point2(child.getROI().getCentroidX(), child.getROI().getCentroidY()), child);
    }
    // Determine what to remove
    List<Point2> points = new ArrayList<>(pointsMap.keySet());
    for (int i = 0; i < nIterations; i++) {
        List<Point2> convexPoints = ConvexHull.getConvexHull(points);
        if (convexPoints != null) {
            for (Point2 p : convexPoints) convexDetections.add(pointsMap.get(p));
            points.removeAll(convexPoints);
        }
    }
    return convexDetections;
}

Example 10 with PathObject

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

the class RigidObjectEditorCommand method run.

@Override
public void run() {
    // Object is already being edited
    if (this.originalObject != null) {
        // viewer.setSelectedObject(tempObject);
        return;
    }
    // Get the selected object
    viewer = qupath.getViewer();
    PathObject pathObject = getSelectedObject(viewer);
    if (pathObject == null || !(pathObject.isAnnotation() || pathObject.isTMACore())) {
        Dialogs.showErrorNotification("Rotate annotation", "No annotation selected!");
        return;
    }
    if (pathObject.isLocked()) {
        Dialogs.showErrorNotification("Rotate annotation", "Selected annotation is locked!");
        return;
    }
    // if (pathObject.getROI().isPoint()) {
    // Dialogs.showErrorNotification("Rotate annotation", "Point annotations cannot be rotated, sorry!");
    // return;
    // }
    ImageRegion bounds = viewer.getServerBounds();
    if (pathObject.isTMACore()) {
        for (PathObject child : pathObject.getChildObjectsAsArray()) {
            if (isSuitableAnnotation(child)) {
                originalObjectROIs.put(child, child.getROI());
            }
        }
        if (originalObjectROIs.isEmpty()) {
            Dialogs.showErrorMessage("Rigid refinement problem", "TMA core must contain empty annotations objects for rigid refinement");
            return;
        }
    }
    originalObjectROIs.put(pathObject, pathObject.getROI());
    this.originalObject = pathObject;
    viewer.setActiveTool(null);
    qupath.setToolSwitchingEnabled(false);
    viewer.addViewerListener(this);
    viewer.getView().addEventHandler(MouseEvent.ANY, mouseListener);
    // // Remove selected object & create an overlay showing the currently-being-edited version
    // viewer.getHierarchy().removeObject(originalObject, true, true);
    transformer = new RoiAffineTransformer(bounds, originalObject.getROI());
    // editingROI = new RotatedROI((PathArea)originalObject.getROI());
    // editingROI.setAngle(Math.PI/3);
    overlay = new AffineEditOverlay(viewer.getOverlayOptions());
    viewer.getCustomOverlayLayers().add(overlay);
    PathPrefs.paintSelectedBoundsProperty().set(false);
    // Create & show temporary object
    for (Entry<PathObject, ROI> entry : originalObjectROIs.entrySet()) ((PathROIObject) entry.getKey()).setROI(transformer.getTransformedROI(entry.getValue(), false));
    // Reset any existing editor (and its visible handles)
    viewer.getROIEditor().setROI(null);
    viewer.repaint();
// tempObject = createTransformedObject();
// ((PathAnnotationObject)tempObject).setLocked(true);
// viewer.setSelectedObject(tempObject);
}