/**
 * Replace (selected) annotations with ROIs containing holes with filled-in versions.
 *
 * @author Pete Bankhead
 */

import qupath.lib.objects.PathAnnotationObject
import qupath.lib.roi.AreaROI
import qupath.lib.roi.PathROIToolsAwt
import qupath.lib.scripting.QPEx

// Get selected objects
// If you're willing to loop over all annotation objects, for example, then use getAnnotationObjects() instead
def pathObjects = QPEx.getSelectedObjects()

// Create a list of objects to remove, and their replacements
def toRemove = []
def toAdd = []
for (pathObject in pathObjects) {
    def roi = pathObject.getROI()
    // AreaROIs are the only kind that might have holes
    if (roi instanceof AreaROI) {
        // Extract exterior polygons
        def polygons = PathROIToolsAwt.splitAreaToPolygons(roi)[1] as List
        // If we have multiple polygons, merge them
        def roiNew = polygons.remove(0)
        for (temp in polygons)
            roiNew = PathROIToolsAwt.combineROIs(roiNew, temp, PathROIToolsAwt.CombineOp.ADD)
        // Create a new annotation
        toAdd << new PathAnnotationObject(roiNew, pathObject.getPathClass())
        toRemove << pathObject
    }
}

// Remove & add objects as required
def hierarchy = QPEx.getCurrentHierarchy()
hierarchy.getSelectionModel().clearSelection()
hierarchy.removeObjects(toRemove, true)
hierarchy.addPathObjects(toAdd, false)