Reformat

.spin/cmds.py

@@ -1,8 +1,9 @@
+import os
 import site
 import subprocess
 import webbrowser
 from pathlib import Path
-import os
+
 import click
 from spin.cmds import meson
 

dlup/annotations_experimental.py

@@ -845,7 +845,7 @@ def as_dlup_xml(
             extra_annotation_params["tags"] = tags
 
         dlup_annotations = XMLDlupAnnotations(metadata=metadata, geometries=geometries, **extra_annotation_params)
-        config = SerializerConfig(indent=indent)
+        config = SerializerConfig(pretty_print=True)
         serializer = XmlSerializer(config=config)
         return serializer.render(dlup_annotations)
 

examples/annotations_to_mask.py

@@ -2,7 +2,9 @@
 """This code provides an example of how to convert annotations to a mask."""
 import json
 from pathlib import Path
+
 import PIL.Image
+
 from dlup.annotations_experimental import SlideAnnotations
 
 d_fn = Path("TCGA-E9-A1R4-01Z-00-DX1.B04D5A22-8CE5-49FD-8510-14444F46894D.json")
@@ -36,10 +38,18 @@
 region = annotations.read_region((0, 0), scaling, bbox[1])
 LUT = annotations.color_lut
 print(region.polygons)
+
+print("Getting geometries")
+
+for polygon in region.polygons.get_geometries():
+    print(polygon)
+
 mask = LUT[region.polygons.to_mask()]
 PIL.Image.fromarray(mask).save("mask.png")
 
-for polygon in region.polygons.as_geometries():
+print("Getting geometries")
+
+for polygon in region.polygons.get_geometries():
     print(polygon)
 
 with open("test.xml", "w") as f:

src/geometry.cpp

@@ -154,7 +154,6 @@ PYBIND11_MODULE(_geometry, m) {
       .def_property_readonly("boxes", &AnnotationRegion::getBoxes)
       .def_property_readonly("points", &AnnotationRegion::getPoints);
 
-
   py::register_exception<GeometryError>(m, "GeometryError");
   py::register_exception<GeometryIntersectionError>(m, "GeometryIntersectionError");
   py::register_exception<GeometryTransformationError>(m, "GeometryTransformationError");

src/geometry/polygon_collection.h

@@ -0,0 +1,44 @@
+#ifndef DLUP_POLYGON_COLLECTION_H
+#define DLUP_POLYGON_COLLECTION_H
+#pragma once
+
+#include "factory.h"
+#include <mutex>
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <vector>
+
+class Polygon;
+class Box;
+class Point;
+
+class PolygonCollection {
+  public:
+  PolygonCollection(std::vector<std::shared_ptr<Polygon>> polygons, std::tuple<int, int> mask_size)
+      : polygons_(std::move(polygons)), mask_size_(std::move(mask_size)) {}
+
+  std::vector<py::object> getGeometries() const {
+    std::vector<py::object> py_objects;
+    py_objects.reserve(polygons_.size());
+    for (const auto &polygon : polygons_) {
+      py_objects.push_back(FactoryManager<Polygon>::callFactoryFunction(polygon));
+    }
+    return py_objects;
+  }
+
+  py::array_t<int> toMask(int default_value = 0) const {
+    auto mask = generateMaskFromAnnotations(polygons_, mask_size_, default_value);
+
+    int width = std::get<0>(mask_size_);
+    int height = std::get<1>(mask_size_);
+
+    return py::array_t<int>({height, width}, mask->data());
+  }
+
+  private:
+  std::vector<std::shared_ptr<Polygon>> polygons_;
+  std::tuple<int, int> mask_size_;
+};
+
+#endif // DLUP_POLYGON_COLLECTION_H

src/geometry/region.h

@@ -3,6 +3,7 @@
 #pragma once
 
 #include "factory.h"
+#include "polygon_collection.h"
 #include <mutex>
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
@@ -13,34 +14,6 @@ class Polygon;
 class Box;
 class Point;
 
-class PolygonCollection {
-  public:
-  PolygonCollection(std::vector<std::shared_ptr<Polygon>> polygons, std::tuple<int, int> mask_size)
-      : polygons_(std::move(polygons)), mask_size_(std::move(mask_size)) {}
-
-  std::vector<py::object> getGeometries() const {
-    std::vector<py::object> py_objects;
-    py_objects.reserve(polygons_.size());
-    for (const auto &polygon : polygons_) {
-      py_objects.push_back(FactoryManager<Polygon>::callFactoryFunction(polygon));
-    }
-    return py_objects;
-  }
-
-  py::array_t<int> toMask(int default_value = 0) const {
-    auto mask = generateMaskFromAnnotations(polygons_, mask_size_, default_value);
-
-    int width = std::get<0>(mask_size_);
-    int height = std::get<1>(mask_size_);
-
-    return py::array_t<int>({height, width}, mask->data());
-  }
-
-  private:
-  std::vector<std::shared_ptr<Polygon>> polygons_;
-  std::tuple<int, int> mask_size_;
-};
-
 template <typename T>
 class AnnotationRegionBase {
   public:
@@ -64,17 +37,17 @@ class AnnotationRegionBase {
 class AnnotationRegion {
   public:
   AnnotationRegion(std::function<AnnotationRegion()> region_generator)
-      : region_generator_(region_generator), initialized_(false), polygon_region_({}, {0, 0}), point_region_({}),
+      : region_generator_(region_generator), initialized_(false), polygon_collection_({}, {0, 0}), point_region_({}),
         box_region_({}) {}
 
   AnnotationRegion(std::vector<std::shared_ptr<Polygon>> polygons, std::vector<std::shared_ptr<Box>> boxes,
                    std::vector<std::shared_ptr<Point>> points, std::tuple<int, int> mask_size)
-      : polygon_region_(std::move(polygons), std::move(mask_size)), box_region_(std::move(boxes)),
+      : polygon_collection_(std::move(polygons), std::move(mask_size)), box_region_(std::move(boxes)),
         point_region_(std::move(points)), initialized_(true) {}
 
   PolygonCollection getPolygons() {
     ensureInitialized();
-    return polygon_region_;
+    return polygon_collection_;
   }
 
   std::vector<py::object> getPoints() {
@@ -91,7 +64,7 @@ class AnnotationRegion {
   void ensureInitialized() {
     if (!initialized_) {
       AnnotationRegion generated_region = region_generator_();
-      polygon_region_ = std::move(generated_region.polygon_region_);
+      polygon_collection_ = std::move(generated_region.polygon_collection_);
       point_region_ = std::move(generated_region.point_region_);
       box_region_ = std::move(generated_region.box_region_);
       initialized_ = true;
@@ -100,7 +73,7 @@ class AnnotationRegion {
 
   std::function<AnnotationRegion()> region_generator_;
   bool initialized_;
-  PolygonCollection polygon_region_;
+  PolygonCollection polygon_collection_;
   AnnotationRegionBase<Point> point_region_;
   AnnotationRegionBase<Box> box_region_;
 };

src/opencv.h

@@ -10,7 +10,6 @@
 #include <unordered_map>
 #include <vector>
 
-
 std::shared_ptr<std::vector<int>> generateMaskFromAnnotations(const std::vector<std::shared_ptr<Polygon>> &annotations,
                                                               const std::tuple<int, int> &mask_size,
                                                               int default_value) {