Adding a simplify function to the geometry module

dlup/annotations_experimental.py

@@ -19,7 +19,7 @@
 from dlup._exceptions import AnnotationError
 from dlup._types import PathLike
 from dlup.annotations import CoordinatesDict, GeoJsonDict, _geometry_to_geojson, _get_geojson_color
-from dlup.geometry import DlupGeometryContainer, DlupPoint, DlupPolygon
+from dlup.geometry import GeometryCollection, DlupPoint, DlupPolygon
 
 
 class CoordinatesDict(TypedDict):
@@ -130,7 +130,7 @@ def shape(
 class WsiAnnotationsExperimental:
     """Class that holds all annotations for a specific image"""
 
-    def __init__(self, layers: DlupGeometryContainer):
+    def __init__(self, layers: GeometryCollection):
         self._layers = layers
         self._tags = []
 
@@ -173,7 +173,7 @@ def from_geojson(
                     _geometry = shape(x["geometry"], label=_label, color=_color)
                     geometries += _geometry
 
-        container = DlupGeometryContainer()
+        container = GeometryCollection()
         for layer in geometries:
             if isinstance(layer, DlupPolygon):
                 container.add_polygon(layer)
@@ -189,7 +189,7 @@ def from_asap_xml(
         cls,
         asap_xml: PathLike,
         scaling: float | None = None,
-        sorting: AnnotationSorting | str = AnnotationSorting.AREA,
+        sorting=None,
     ) -> WsiAnnotations:
         pass
 
@@ -198,15 +198,15 @@ def from_halo_xml(
         cls,
         halo_xml: PathLike,
         scaling: float | None = None,
-        sorting: AnnotationSorting | str = AnnotationSorting.NONE,
+        sorting=None,
     ) -> WsiAnnotations:
         pass
 
     @classmethod
     def from_darwin_json(
         cls,
         darwin_json: PathLike,
-        sorting: AnnotationSorting | str = AnnotationSorting.NONE,
+        sorting,
         z_indices: Optional[dict[str, int]] = None,
     ) -> WsiAnnotations:
         pass
@@ -251,6 +251,7 @@ def simplify(self, tolerance: float, *, preserve_topology: bool = True) -> None:
         -------
         None
         """
+        self._layers.simplify(tolerance)
 
     def __contains__(self, item) -> bool:
         pass

dlup/geometry.py

@@ -208,7 +208,7 @@ def dlup_point_factory(point):
 _dg.set_point_factory(dlup_point_factory)
 
 
-class DlupGeometryContainer(_dg.GeometryContainer):
+class GeometryCollection(_dg.GeometryContainer):
     def __init__(self):
         super().__init__()
 
@@ -231,3 +231,20 @@ def color_lut(self):
             LUT[key] = color
 
         return LUT
+
+    def __getstate__(self):
+        state = {
+            "_polygons": [polygon.__getstate__() for polygon in self.polygons],
+            "_points": [point.__getstate__() for point in self.points],
+        }
+        return state
+
+    def __setstate__(self, state):
+        polygons = [DlupPolygon.__setstate__(polygon) for polygon in state["_polygons"]]
+        points = [DlupPoint.__setstate__(point) for point in state["_points"]]
+        self.__init__()
+        for polygon in polygons:
+            self.add_polygon(polygon)
+
+        for point in points:
+            self.add_point(point)

src/geometry.cpp

@@ -112,6 +112,10 @@ std::vector<std::shared_ptr<Polygon>> Polygon::intersection(const BoostPolygon &
     return result;
 }
 
+void Polygon::simplifyPolygons(double tolerance) {
+    bg::simplify(*polygon, *polygon, tolerance);
+}
+
 py::list AnnotationRegion::getPolygons() const {
 #ifdef DLUPDEBUG
     std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now();
@@ -162,6 +166,11 @@ class GeometryCollection {
     void scale(double scaling);
     void setOffset(std::pair<double, double> offset);
     void rebuildRTree() { rtreeWrapper.rebuild(); }
+    void simplifyPolygons(double tolerance) {
+        for (auto &polygon : polygons) {
+            polygon->simplifyPolygons(tolerance);
+        }
+    }
 
     std::uintptr_t getPointerId() const { return reinterpret_cast<std::uintptr_t>(this); }
 
@@ -172,6 +181,8 @@ class GeometryCollection {
 
     // TODO: Rethink the need for this function.
     void reindexPolygons(const std::map<std::string, int> &indexMap);
+
+
 };
 
 GeometryCollection::GeometryCollection() : rtreeWrapper(this) {}
@@ -457,6 +468,7 @@ PYBIND11_MODULE(_geometry, m) {
         .def("set_interiors", &Polygon::setInteriors)
         .def("get_exterior", &Polygon::getExterior)
         .def("get_interiors", &Polygon::getInteriors)
+        .def("simplify", &Polygon::simplifyPolygons)
         .def_property_readonly("wkt", &Polygon::toWkt)
         .def_property_readonly("area", &Polygon::getArea);
 
@@ -482,9 +494,6 @@ PYBIND11_MODULE(_geometry, m) {
         .def("equals", &Point::equals)
         .def("within", &Point::within)
         .def("centroid", &Point::centroid)
-        .def("azimuth", &Point::azimuth)
-        .def("translate", &Point::translate)
-        .def("rotate", &Point::rotate, py::arg("angle"), py::arg("origin") = Point(0, 0))
         .def("scale", &Point::scale, py::arg("scaling"), py::arg("origin") = Point(0, 0))
         .def_property_readonly("wkt", &Point::toWkt);
 

src/geometry.h

@@ -81,6 +81,9 @@ class Polygon : public BaseGeometry {
 
     void setExterior(const std::vector<std::pair<double, double>> &coordinates);
     void setInteriors(const std::vector<std::vector<std::pair<double, double>>> &interiors);
+
+    void simplifyPolygons(double tolerance);
+
 };
 
 class Point : public BaseGeometry {
@@ -119,22 +122,6 @@ class Point : public BaseGeometry {
         return std::make_shared<Point>(centroid);
     }
 
-    double azimuth(const Point &other) const { return bg::azimuth(*point, *(other.point)); }
-
-    std::shared_ptr<Point> translate(double dx, double dy) const {
-        BoostPoint translated;
-        bg::strategy::transform::translate_transformer<double, 2, 2> translate(dx, dy);
-        bg::transform(*point, translated, translate);
-        return std::make_shared<Point>(translated);
-    }
-
-    std::shared_ptr<Point> rotate(double angle, const Point &origin = Point(0, 0)) const {
-        BoostPoint rotated;
-        bg::strategy::transform::rotate_transformer<bg::degree, double, 2, 2> rotate(angle);
-        bg::transform(*point, rotated, rotate);
-        return std::make_shared<Point>(rotated);
-    }
-
     std::shared_ptr<Point> scale(double scaling, const Point &origin = Point(0, 0)) const {
         BoostPoint scaled;
         double dx = getX() - origin.getX();