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

Example 71 with PathObject

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

the class QP method getAllObjects.

/**
 * Get an array of all objects in the current hierarchy.
 *
 * @param includeRootObject
 * @return
 * @see #getCurrentHierarchy
 */
public static PathObject[] getAllObjects(boolean includeRootObject) {
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return new PathObject[0];
    var objList = hierarchy.getFlattenedObjectList(null);
    if (includeRootObject)
        return objList.toArray(new PathObject[0]);
    return objList.parallelStream().filter(e -> !e.isRootObject()).toArray(PathObject[]::new);
}

Example 72 with PathObject

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

the class QP method clearAllObjects.

/**
 * Remove all the objects of a specified Java class.
 *
 * @param cls the class, e.g. {@code PathAnnotationObject.class}, {@code PathDetectionObject.class}, or
 * 			  {@code null} if all objects should be removed.
 *
 * @see #getCurrentHierarchy
 * @see qupath.lib.objects.hierarchy.PathObjectHierarchy#getObjects
 */
public static void clearAllObjects(final Class<? extends PathObject> cls) {
    if (cls == null) {
        clearAllObjects();
        return;
    }
    PathObjectHierarchy hierarchy = getCurrentHierarchy();
    if (hierarchy == null)
        return;
    Collection<PathObject> pathObjects = hierarchy.getObjects(null, cls);
    hierarchy.removeObjects(pathObjects, true);
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    if (selected != null && selected.getClass().isAssignableFrom(cls))
        hierarchy.getSelectionModel().setSelectedObject(null);
}

Example 73 with PathObject

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

the class QP method makeInverseAnnotation.

/**
 * Make an annotation, for which the ROI is obtained by subtracting the ROIs of the specified objects from the closest
 * common ancestor ROI (or entire image if the closest ancestor is the root).
 * <p>
 * In an inverted annotation can be created, it is added to the hierarchy and set as selected.
 *
 * @param imageData the image containing the annotation
 * @param pathObjects the annotation to invert
 * @return true if an inverted annotation is added to the hierarchy, false otherwise.
 */
public static boolean makeInverseAnnotation(final ImageData<?> imageData, Collection<PathObject> pathObjects) {
    if (imageData == null)
        return false;
    var map = pathObjects.stream().filter(p -> p.hasROI() && p.getROI().isArea()).collect(Collectors.groupingBy(p -> p.getROI().getImagePlane()));
    if (map.isEmpty()) {
        logger.warn("No area annotations available - cannot created inverse ROI!");
        return false;
    }
    if (map.size() > 1) {
        logger.error("Cannot merge annotations from different image planes!");
        return false;
    }
    ImagePlane plane = map.keySet().iterator().next();
    List<PathObject> pathObjectList = map.get(plane);
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    // Try to get the best candidate parent
    Collection<PathObject> parentSet = pathObjectList.stream().map(p -> p.getParent()).collect(Collectors.toCollection(HashSet::new));
    PathObject parent;
    if (parentSet.size() > 1) {
        parentSet.clear();
        boolean firstTime = true;
        for (PathObject temp : pathObjectList) {
            if (firstTime)
                parentSet.addAll(PathObjectTools.getAncestorList(temp));
            else
                parentSet.retainAll(PathObjectTools.getAncestorList(temp));
            firstTime = false;
        }
        List<PathObject> parents = new ArrayList<>(parentSet);
        Collections.sort(parents, Comparator.comparingInt(PathObject::getLevel).reversed().thenComparingDouble(p -> p.hasROI() ? p.getROI().getArea() : Double.MAX_VALUE));
        parent = parents.get(0);
    } else
        parent = parentSet.iterator().next();
    // Get the parent area
    Geometry geometryParent;
    if (parent == null || parent.isRootObject() || !parent.hasROI())
        geometryParent = GeometryTools.createRectangle(0, 0, imageData.getServer().getWidth(), imageData.getServer().getHeight());
    else
        geometryParent = parent.getROI().getGeometry();
    // Get the parent area to use
    var union = GeometryTools.union(pathObjectList.stream().map(p -> p.getROI().getGeometry()).collect(Collectors.toList()));
    var geometry = geometryParent.difference(union);
    // Create the new ROI
    ROI shapeNew = GeometryTools.geometryToROI(geometry, plane);
    PathObject pathObjectNew = PathObjects.createAnnotationObject(shapeNew);
    parent.addPathObject(pathObjectNew);
    hierarchy.fireHierarchyChangedEvent(parent);
    hierarchy.getSelectionModel().setSelectedObject(pathObjectNew);
    return true;
}

Example 74 with PathObject

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

the class ObjectMeasurements method addShapeMeasurements.

/**
 * Add shape measurements for multiple objects. If any of these objects is a cell, measurements will be made for both the
 * nucleus and cell boundary where possible.
 *
 * @param pathObjects the objects for which measurements should be added
 * @param cal pixel calibration, used to determine units and scaling
 * @param features specific features to add; if empty, all available shape features will be added
 */
public static void addShapeMeasurements(Collection<? extends PathObject> pathObjects, PixelCalibration cal, ShapeFeatures... features) {
    PixelCalibration calibration = cal == null || !cal.unitsMatch2D() ? PixelCalibration.getDefaultInstance() : cal;
    Collection<ShapeFeatures> featureCollection = features.length == 0 ? ALL_SHAPE_FEATURES : Arrays.asList(features);
    pathObjects.parallelStream().filter(p -> p.hasROI()).forEach(pathObject -> {
        if (pathObject instanceof PathCellObject) {
            addCellShapeMeasurements((PathCellObject) pathObject, calibration, featureCollection);
        } else {
            try (var ml = pathObject.getMeasurementList()) {
                addShapeMeasurements(ml, pathObject.getROI(), calibration, "", featureCollection);
            }
        }
    });
}

Example 75 with PathObject

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

the class SmoothFeaturesPlugin method getParentObjects.

@Override
protected Collection<PathObject> getParentObjects(final PluginRunner<T> runner) {
    PathObjectHierarchy hierarchy = runner.getImageData().getHierarchy();
    List<PathObject> parents = new ArrayList<>();
    if (hierarchy.getTMAGrid() != null) {
        logger.info("Smoothing using TMA cores");
        for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) {
            if (core.hasChildren())
                parents.add(core);
        }
    } else {
        for (PathObject pathObject : hierarchy.getSelectionModel().getSelectedObjects()) {
            if (pathObject.isAnnotation() && pathObject.hasChildren())
                parents.add(pathObject);
        }
        if (!parents.isEmpty())
            logger.warn("Smoothing using annotations");
    }
    return parents;
}