Examples with Polygonal org.locationtech.jts.geom.Polygonal used on opensource projects

Example 1 with Polygonal

use of org.locationtech.jts.geom.Polygonal 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;
}

Example 2 with Polygonal

use of org.locationtech.jts.geom.Polygonal in project qupath by qupath.

the class DelaunayTools method createGeometryExtractor.

private static Function<PathObject, Collection<Coordinate>> createGeometryExtractor(PixelCalibration cal, boolean preferNucleus, double densifyFactor, double erosion) {
    PrecisionModel precision = calibrated(cal) ? null : GeometryTools.getDefaultFactory().getPrecisionModel();
    AffineTransformation transform = calibrated(cal) ? AffineTransformation.scaleInstance(cal.getPixelWidth().doubleValue(), cal.getPixelHeight().doubleValue()) : null;
    return p -> {
        var roi = PathObjectTools.getROI(p, preferNucleus);
        if (roi == null || roi.isEmpty())
            return Collections.emptyList();
        var geom = roi.getGeometry();
        if (transform != null)
            geom = transform.transform(geom);
        // Shared boundaries can be problematic, so try to buffer away from these
        double buffer = -Math.abs(erosion);
        if (buffer < 0 && geom instanceof Polygonal) {
            var geomBefore = geom;
            geom = GeometryTools.attemptOperation(geom, g -> g.buffer(buffer));
            // Do not permit Geometry to disappear
            if (geom.isEmpty()) {
                geom = geomBefore;
            }
        }
        // Therefore we take extra care in case empty geometries are being generated accidentally.
        if (precision != null) {
            var geom2 = GeometryTools.attemptOperation(geom, g -> GeometryPrecisionReducer.reduce(g, precision));
            if (!geom2.isEmpty())
                geom = geom2;
        }
        if (densifyFactor > 0) {
            var geom2 = GeometryTools.attemptOperation(geom, g -> Densifier.densify(g, densifyFactor));
            if (!geom2.isEmpty())
                geom = geom2;
        }
        // if (!(geom instanceof Polygon))
        // logger.warn("Unexpected Geometry: {}", geom);
        // Making precise is essential! Otherwise there can be small artifacts occurring
        var coords = geom.getCoordinates();
        var output = new LinkedHashSet<Coordinate>();
        var p2 = precision;
        Coordinate lastCoordinate = null;
        if (p2 == null)
            p2 = GeometryTools.getDefaultFactory().getPrecisionModel();
        // Add coordinates, unless they are extremely close to an existing coordinate
        int n = coords.length;
        if (n == 0) {
            logger.warn("Empty Geometry found for {}", p);
            return Collections.emptyList();
        }
        double minDistance = densifyFactor * 0.5;
        var firstCoordinate = coords[0];
        while (n > 2 && firstCoordinate.distance(coords[n - 1]) < minDistance) n--;
        for (int i = 0; i < n; i++) {
            var c = coords[i];
            p2.makePrecise(c);
            if (i == 0 || c.distance(lastCoordinate) > minDistance) {
                output.add(c);
                lastCoordinate = c;
            }
        }
        return output;
    };
}

Example 3 with Polygonal

use of org.locationtech.jts.geom.Polygonal 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);
                }
            });
        }
    }
}

Example 4 with Polygonal

use of org.locationtech.jts.geom.Polygonal in project qupath by qupath.

the class ObjectMeasurements method addShapeMeasurements.

private static void addShapeMeasurements(MeasurementList ml, Geometry geom, String baseName, String units, Collection<ShapeFeatures> features) {
    boolean isArea = geom instanceof Polygonal;
    boolean isLine = geom instanceof Lineal;
    var units2 = units + "^2";
    if (!baseName.isEmpty() && !baseName.endsWith(" "))
        baseName += " ";
    double area = geom.getArea();
    double length = geom.getLength();
    if (isArea && features.contains(ShapeFeatures.AREA))
        ml.putMeasurement(baseName + "Area " + units2, area);
    if ((isArea || isLine) && features.contains(ShapeFeatures.LENGTH))
        ml.putMeasurement(baseName + "Length " + units, length);
    if (isArea && features.contains(ShapeFeatures.CIRCULARITY)) {
        if (geom instanceof Polygon) {
            var polygon = (Polygon) geom;
            double ringArea, ringLength;
            if (polygon.getNumInteriorRing() == 0) {
                ringArea = area;
                ringLength = length;
            } else {
                var ring = ((Polygon) geom).getExteriorRing().getCoordinateSequence();
                ringArea = Area.ofRing(ring);
                ringLength = Length.ofLine(ring);
            }
            double circularity = Math.PI * 4 * ringArea / (ringLength * ringLength);
            ml.putMeasurement(baseName + "Circularity", circularity);
        } else {
            logger.debug("Cannot compute circularity for {}", geom.getClass());
        }
    }
    if (isArea && features.contains(ShapeFeatures.SOLIDITY)) {
        double solidity = area / geom.convexHull().getArea();
        ml.putMeasurement(baseName + "Solidity", solidity);
    }
    if (features.contains(ShapeFeatures.MAX_DIAMETER)) {
        double minCircleRadius = new MinimumBoundingCircle(geom).getRadius();
        ml.putMeasurement(baseName + "Max diameter " + units, minCircleRadius * 2);
    }
    if (features.contains(ShapeFeatures.MIN_DIAMETER)) {
        double minDiameter = new MinimumDiameter(geom).getLength();
        ml.putMeasurement(baseName + "Min diameter " + units, minDiameter);
    }
}