use of org.locationtech.jts.algorithm.locate.IndexedPointInAreaLocator in project qupath by qupath.
the class PathObjectTileCache method getLocator.
PointOnGeometryLocator getLocator(ROI roi, boolean addToCache) {
var locator = locatorMap.get(roi);
if (locator == null) {
var geometry = getGeometry(roi);
if (geometry instanceof Polygonal || geometry instanceof LinearRing)
locator = new IndexedPointInAreaLocator(geometry);
else
locator = new SimplePointInAreaLocator(geometry);
// Workaround for multithreading bug in JTS 1.17.0 - see https://github.com/locationtech/jts/issues/571
locator.locate(new Coordinate());
locatorMap.put(roi, locator);
}
return locator;
}
use of org.locationtech.jts.algorithm.locate.IndexedPointInAreaLocator in project qupath by qupath.
the class DistanceTools method centroidToBoundsDistance2D.
/**
* Calculate the distance between source object centroids and the boundary of specified target objects, adding the result to the measurement list of the source objects.
* Calculations are all made in 2D; distances will not be calculated between objects occurring on different z-planes of at different timepoints.
*
* @param sourceObjects source objects; measurements will be added based on centroid distances
* @param targetObjects target objects; no measurements will be added
* @param pixelWidth pixel width to use in Geometry conversion (use 1 for pixel units)
* @param pixelHeight pixel height to use in Geometry conversion (use 1 for pixel units)
* @param measurementName the name of the measurement to add to the measurement list
*/
public static void centroidToBoundsDistance2D(Collection<PathObject> sourceObjects, Collection<PathObject> targetObjects, double pixelWidth, double pixelHeight, String measurementName) {
boolean preferNucleus = true;
var timePoints = new TreeSet<Integer>();
var zSlices = new TreeSet<Integer>();
for (var temp : sourceObjects) {
timePoints.add(temp.getROI().getT());
zSlices.add(temp.getROI().getZ());
}
var transform = pixelWidth == 1 && pixelHeight == 1 ? null : AffineTransformation.scaleInstance(pixelWidth, pixelHeight);
for (int t : timePoints) {
for (int z : zSlices) {
PrecisionModel precision = null;
List<Geometry> areaGeometries = new ArrayList<>();
List<Geometry> lineGeometries = new ArrayList<>();
List<Geometry> pointGeometries = new ArrayList<>();
for (var annotation : targetObjects) {
var roi = annotation.getROI();
if (roi != null && roi.getZ() == z && roi.getT() == t) {
var geom = annotation.getROI().getGeometry();
if (transform != null) {
geom = transform.transform(geom);
if (precision == null)
precision = geom.getPrecisionModel();
}
// var geom = converter.roiToGeometry(annotation.getROI());
if (geom instanceof Puntal)
pointGeometries.add(geom);
else if (geom instanceof Lineal)
lineGeometries.add(geom);
else if (geom instanceof Polygonal)
areaGeometries.add(geom);
else {
for (int i = 0; i < geom.getNumGeometries(); i++) {
var geom2 = geom.getGeometryN(i);
if (geom2 instanceof Puntal)
pointGeometries.add(geom2);
else if (geom2 instanceof Lineal)
lineGeometries.add(geom2);
else if (geom2 instanceof Polygonal)
areaGeometries.add(geom2);
else
logger.warn("Unexpected nested Geometry collection, some Geometries may be ignored");
}
}
}
}
if (areaGeometries.isEmpty() && pointGeometries.isEmpty() && lineGeometries.isEmpty())
continue;
var precisionModel = precision == null ? GeometryTools.getDefaultFactory().getPrecisionModel() : precision;
List<Coordinate> pointCoords = new ArrayList<>();
Geometry temp = null;
if (!areaGeometries.isEmpty())
temp = areaGeometries.size() == 1 ? areaGeometries.get(0) : GeometryCombiner.combine(areaGeometries);
Geometry shapeGeometry = temp;
temp = null;
if (!lineGeometries.isEmpty())
temp = lineGeometries.size() == 1 ? lineGeometries.get(0) : GeometryCombiner.combine(lineGeometries);
Geometry lineGeometry = temp;
// Identify points, and create an STRtree to find nearest neighbors more quickly if there are a lot of them
if (!pointGeometries.isEmpty()) {
for (var geom : pointGeometries) {
for (var coord : geom.getCoordinates()) {
precisionModel.makePrecise(coord);
pointCoords.add(coord);
}
}
}
STRtree pointTree = pointCoords != null && pointCoords.size() > 1000 ? createCoordinateCache(pointCoords) : null;
CoordinateDistance coordinateDistance = new CoordinateDistance();
int zi = z;
int ti = t;
var locator = shapeGeometry == null ? null : new IndexedPointInAreaLocator(shapeGeometry);
// See https://github.com/locationtech/jts/issues/571
if (locator != null)
locator.locate(new Coordinate(0, 0));
sourceObjects.parallelStream().forEach(p -> {
var roi = PathObjectTools.getROI(p, preferNucleus);
if (roi.getZ() != zi || roi.getT() != ti)
return;
Coordinate coord = new Coordinate(roi.getCentroidX() * pixelWidth, roi.getCentroidY() * pixelHeight);
precisionModel.makePrecise(coord);
double pointDistance = pointCoords == null ? Double.POSITIVE_INFINITY : computeCoordinateDistance(coord, pointCoords, pointTree, coordinateDistance);
double lineDistance = lineGeometry == null ? Double.POSITIVE_INFINITY : computeDistance(coord, lineGeometry, null);
double shapeDistance = shapeGeometry == null ? Double.POSITIVE_INFINITY : computeDistance(coord, shapeGeometry, locator);
double distance = Math.min(lineDistance, Math.min(pointDistance, shapeDistance));
try (var ml = p.getMeasurementList()) {
ml.putMeasurement(measurementName, distance);
}
});
}
}
}
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