Examples with PathObjectHierarchy qupath.lib.objects.hierarchy.PathObjectHierarchy used on opensource projects

Example 21 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class AbstractPathROITool method createNewAnnotation.

/**
 * Create a new annotation & set it in the current viewer.
 * @param e
 * @param x
 * @param y
 * @return
 */
PathObject createNewAnnotation(MouseEvent e, double x, double y) {
    var viewer = getViewer();
    var currentObject = viewer.getSelectedObject();
    var editor = viewer.getROIEditor();
    if (currentObject != null && currentObject.getParent() == null && currentObject.getROI() == editor.getROI() && (editor.isTranslating() || editor.hasActiveHandle())) {
        logger.warn("Creating a new annotation before a previous one was complete - {} will be discarded!", currentObject);
    }
    logger.trace("Creating new annotation at ({}, {}", x, y);
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    if (hierarchy == null) {
        logger.warn("Cannot create new annotation - no hierarchy available!");
        return null;
    }
    ROI roi = createNewROI(e, x, y, viewer.getImagePlane());
    if (roi == null)
        return null;
    PathObject pathObject = PathObjects.createAnnotationObject(roi, PathPrefs.autoSetAnnotationClassProperty().get());
    var selectionModel = hierarchy.getSelectionModel();
    if (PathPrefs.selectionModeProperty().get() && !selectionModel.noSelection())
        viewer.setSelectedObject(pathObject, true);
    else
        viewer.setSelectedObject(pathObject);
    return pathObject;
}

Example 22 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class AbstractPathROITool method commitObjectToHierarchy.

/**
 * When drawing an object is complete, add it to the hierarchy - or whatever else is required.
 *
 * @param e
 * @param pathObject
 */
void commitObjectToHierarchy(MouseEvent e, PathObject pathObject) {
    if (pathObject == null)
        return;
    var viewer = getViewer();
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    var currentROI = pathObject.getROI();
    // If we are in selection mode, try to get objects to select
    if (PathPrefs.selectionModeProperty().get()) {
        var pathClass = PathPrefs.autoSetAnnotationClassProperty().get();
        var toSelect = hierarchy.getObjectsForROI(null, currentROI);
        if (!toSelect.isEmpty() && pathClass != null) {
            boolean retainIntensityClass = !(PathClassTools.isPositiveOrGradedIntensityClass(pathClass) || PathClassTools.isNegativeClass(pathClass));
            var reclassified = toSelect.stream().filter(p -> p.getPathClass() != pathClass).map(p -> new Reclassifier(p, pathClass, retainIntensityClass)).filter(r -> r.apply()).map(r -> r.getPathObject()).collect(Collectors.toList());
            if (!reclassified.isEmpty()) {
                hierarchy.fireObjectClassificationsChangedEvent(this, reclassified);
            }
        }
        if (pathObject.getParent() != null)
            hierarchy.removeObject(pathObject, true);
        // viewer.getHierarchy().fireHierarchyChangedEvent(this);
        if (toSelect.isEmpty())
            viewer.setSelectedObject(null);
        else if (e.isShiftDown()) {
            hierarchy.getSelectionModel().deselectObject(pathObject);
            hierarchy.getSelectionModel().selectObjects(toSelect);
        } else
            hierarchy.getSelectionModel().setSelectedObjects(toSelect, null);
    } else {
        if (!requestParentClipping(e)) {
            if (currentROI.isEmpty()) {
                pathObject = null;
            } else
                // Ensure object is within the hierarchy
                hierarchy.addPathObject(pathObject);
        } else {
            ROI roiNew = refineROIByParent(pathObject.getROI());
            if (roiNew.isEmpty()) {
                hierarchy.removeObject(pathObject, true);
                pathObject = null;
            } else {
                ((PathAnnotationObject) pathObject).setROI(roiNew);
                hierarchy.addPathObjectBelowParent(getCurrentParent(), pathObject, true);
            }
        }
        if (pathObject != null)
            viewer.setSelectedObject(pathObject);
        else
            viewer.getHierarchy().getSelectionModel().clearSelection();
    }
    var editor = viewer.getROIEditor();
    editor.ensureHandlesUpdated();
    editor.resetActiveHandle();
    if (preferReturnToMove()) {
        var qupath = QuPathGUI.getInstance();
        if (qupath != null)
            qupath.setSelectedTool(PathTools.MOVE);
    }
}

Example 23 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class AbstractPathTool method getSelectableObjectList.

/**
 * Get a list of all selectable objects overlapping the specified x, y coordinates, ordered by depth in the hierarchy
 * @param x
 * @param y
 * @return
 */
List<PathObject> getSelectableObjectList(double x, double y) {
    var viewer = getViewer();
    PathObjectHierarchy hierarchy = viewer.getHierarchy();
    if (hierarchy == null)
        return Collections.emptyList();
    Collection<PathObject> pathObjects = PathObjectTools.getObjectsForLocation(hierarchy, x, y, viewer.getZPosition(), viewer.getTPosition(), viewer.getMaxROIHandleSize());
    if (pathObjects.isEmpty())
        return Collections.emptyList();
    List<PathObject> pathObjectList = new ArrayList<>(pathObjects);
    if (pathObjectList.size() == 1)
        return pathObjectList;
    Collections.sort(pathObjectList, PathObjectHierarchy.HIERARCHY_COMPARATOR);
    return pathObjectList;
}

Example 24 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class ObservableMeasurementTableDataTest method test.

@SuppressWarnings("javadoc")
@Test
public void test() {
    // See https://github.com/locationtech/jts/issues/571
    for (int counter = 0; counter < 50; counter++) {
        ImageData<BufferedImage> imageData = new ImageData<>(null);
        PathClass tumorClass = PathClassFactory.getPathClass(StandardPathClasses.TUMOR);
        PathClass stromaClass = PathClassFactory.getPathClass(StandardPathClasses.STROMA);
        // PathClass otherClass = PathClassFactory.getDefaultPathClass(PathClasses.OTHER);
        PathClass artefactClass = PathClassFactory.getPathClass("Artefact");
        PathObjectHierarchy hierarchy = imageData.getHierarchy();
        // Add a parent annotation
        PathObject parent = PathObjects.createAnnotationObject(ROIs.createRectangleROI(500, 500, 1000, 1000, ImagePlane.getDefaultPlane()));
        // Create 100 tumor detections
        // ROI emptyROI = ROIs.createEmptyROI();
        ROI smallROI = ROIs.createRectangleROI(500, 500, 1, 1, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) {
            if (i < 25)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(tumorClass)));
            else if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(tumorClass)));
            else if (i < 75)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(tumorClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(tumorClass)));
        }
        // Create 100 stroma detections
        for (int i = 0; i < 100; i++) {
            if (i < 50)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getNegative(stromaClass)));
            else if (i < 60)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getOnePlus(stromaClass)));
            else if (i < 70)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getTwoPlus(stromaClass)));
            else if (i < 100)
                parent.addPathObject(PathObjects.createDetectionObject(smallROI, PathClassFactory.getThreePlus(stromaClass)));
        }
        // Create 50 artefact detections
        for (int i = 0; i < 50; i++) {
            parent.addPathObject(PathObjects.createDetectionObject(smallROI, artefactClass));
        }
        hierarchy.addPathObject(parent);
        ObservableMeasurementTableData model = new ObservableMeasurementTableData();
        model.setImageData(imageData, Collections.singletonList(parent));
        // Check tumor counts
        assertEquals(100, model.getNumericValue(parent, "Num Tumor (base)"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: Negative"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 1+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 2+"), EPSILON);
        assertEquals(25, model.getNumericValue(parent, "Num Tumor: 3+"), EPSILON);
        assertTrue(Double.isNaN(model.getNumericValue(parent, "Num Tumor: 4+")));
        // Check tumor H-score, Allred score & positive %
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        assertEquals(2, model.getNumericValue(parent, "Tumor: Allred intensity"), EPSILON);
        assertEquals(5, model.getNumericValue(parent, "Tumor: Allred proportion"), EPSILON);
        assertEquals(7, model.getNumericValue(parent, "Tumor: Allred score"), EPSILON);
        // Check tumor H-score unaffected when tumor detections added without intensity classification
        for (int i = 0; i < 10; i++) parent.addPathObject(PathObjects.createDetectionObject(smallROI, tumorClass));
        hierarchy.fireHierarchyChangedEvent(this);
        model.refreshEntries();
        // model.setImageData(imageData, Collections.singletonList(parent));
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(50, model.getNumericValue(parent, "Num Stroma: Negative"), EPSILON);
        assertEquals(150, model.getNumericValue(parent, "Tumor: H-score"), EPSILON);
        assertEquals(75, model.getNumericValue(parent, "Tumor: Positive %"), EPSILON);
        // Check stroma scores
        assertEquals(100, model.getNumericValue(parent, "Num Stroma (base)"), EPSILON);
        assertEquals(120, model.getNumericValue(parent, "Stroma: H-score"), EPSILON);
        // Check complete scores
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        // Add a new parent that completely contains the current object, and confirm complete scores agree
        PathObject parentNew = PathObjects.createAnnotationObject(ROIs.createRectangleROI(0, 0, 2000, 2000, ImagePlane.getDefaultPlane()));
        hierarchy.addPathObject(parentNew);
        model.refreshEntries();
        assertEquals(135, model.getNumericValue(parent, "Stroma + Tumor: H-score"), EPSILON);
        assertEquals(135, model.getNumericValue(parentNew, "Stroma + Tumor: H-score"), EPSILON);
        // Create a new object and demonstrate Allred dependence on a single cell
        PathObject parentAllred = PathObjects.createAnnotationObject(ROIs.createRectangleROI(4000, 4000, 1000, 1000, ImagePlane.getDefaultPlane()));
        ROI newROI = ROIs.createEllipseROI(4500, 4500, 10, 10, ImagePlane.getDefaultPlane());
        for (int i = 0; i < 100; i++) parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getNegative(tumorClass)));
        hierarchy.addPathObject(parentAllred);
        model.refreshEntries();
        assertEquals(0, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
        parentAllred.addPathObject(PathObjects.createDetectionObject(newROI, PathClassFactory.getThreePlus(tumorClass)));
        hierarchy.fireHierarchyChangedEvent(parentAllred);
        model.refreshEntries();
        assertEquals(4, model.getNumericValue(parentAllred, "Tumor: Allred score"), EPSILON);
    }
}

Example 25 with PathObjectHierarchy

use of qupath.lib.objects.hierarchy.PathObjectHierarchy in project qupath by qupath.

the class MoveTool method mouseReleased.

@Override
public void mouseReleased(MouseEvent e) {
    super.mouseReleased(e);
    if (e.isConsumed())
        return;
    var viewer = getViewer();
    RoiEditor editor = viewer.getROIEditor();
    if (editor != null && (editor.hasActiveHandle() || editor.isTranslating())) {
        boolean roiChanged = (editor.isTranslating() && editor.finishTranslation()) || editor.hasActiveHandle();
        editor.resetActiveHandle();
        // if (editor.isTranslating())
        // editor.finishTranslation();
        e.consume();
        PathObject pathObject = viewer.getSelectedObject();
        if (requestParentClipping(e) && pathObject instanceof PathAnnotationObject) {
            ROI roiNew = refineROIByParent(pathObject.getROI());
            ((PathAnnotationObject) pathObject).setROI(roiNew);
        }
        if (pathObject != null && pathObject.hasROI() && pathObject.getROI().isEmpty()) {
            if (pathObject.getParent() != null)
                viewer.getHierarchy().removeObject(pathObject, true);
            viewer.setSelectedObject(null);
        } else {
            PathObjectHierarchy hierarchy = viewer.getHierarchy();
            if (pathObject instanceof TMACoreObject) {
                hierarchy.fireHierarchyChangedEvent(pathObject);
            } else if (pathObject != null) {
                // Handle ROI changes only if required
                if (roiChanged) {
                    var updatedROI = editor.getROI();
                    if (pathObject.getROI() != updatedROI && pathObject instanceof PathROIObject)
                        ((PathROIObject) pathObject).setROI(updatedROI);
                    // PathObject parentPrevious = pathObject.getParent();
                    hierarchy.removeObjectWithoutUpdate(pathObject, true);
                    if (getCurrentParent() == null || !PathPrefs.clipROIsForHierarchyProperty().get() || e.isShiftDown())
                        hierarchy.addPathObject(pathObject);
                    else
                        hierarchy.addPathObjectBelowParent(getCurrentParent(), pathObject, true);
                // PathObject parentNew = pathObject.getParent();
                // if (parentPrevious == parentNew)
                // hierarchy.fireHierarchyChangedEvent(this, parentPrevious);
                // else
                // hierarchy.fireHierarchyChangedEvent(this);
                }
            }
            viewer.setSelectedObject(pathObject);
        }
    }
    // Optionally continue a dragging movement until the canvas comes to a standstill
    if (pDragging != null && requestDynamicDragging && System.currentTimeMillis() - lastDragTimestamp < 100 && (dx * dx + dy * dy > viewer.getDownsampleFactor())) {
        mover = new ViewerMover(viewer);
        mover.startMoving(dx, dy, false);
    } else
        viewer.setDoFasterRepaint(false);
    // Make sure we don't have a previous point (to prevent weird dragging artefacts)
    pDragging = null;
// // If we were translating, stop
// if (editor.isTranslating()) {
// editor.finishTranslation();
// // TODO: Make this more efficient!
// viewer.getPathObjectHierarchy().fireHierarchyChangedEvent();
// return;
// }
}