🐛 Fix Rendering Annotations with Holes (#813)

This PR adds correct rendering of annotations with holes.

Previously, annotations with holes would not be rendered. This PR fixes the issue.

![image](https://github.com/TissueImageAnalytics/tiatoolbox/assets/20169086/a6fb3576-9a58-4416-a676-e2d5d030bedc)

Previously an overlay like the above, with a geometry with holes in it, would not display.

tests/test_annotation_tilerendering.py

@@ -33,7 +33,8 @@
 def cell_grid() -> list[Polygon]:
     """Generate a grid of fake cell boundary polygon annotations."""
     return [
-        cell_polygon(((i + 0.5) * 100, (j + 0.5) * 100)) for i, j in np.ndindex(5, 5)
+        cell_polygon(((i + 0.5) * 100, (j + 0.5) * 100), radius=13)
+        for i, j in np.ndindex(5, 5)
     ]
 
 
@@ -168,7 +169,7 @@ def test_filter_by_expression(fill_store: Callable, tmp_path: Path) -> None:
     tg = AnnotationTileGenerator(wsi.info, store, renderer, tile_size=256)
     thumb = tg.get_thumb_tile()
     _, num = label(np.array(thumb)[:, :, 1])
-    assert num == 25  # expect 25 cell objects, as the added one is too small
+    assert num == 25  # expect 25 cell objects
 
 
 def test_zoomed_out_rendering(fill_store: Callable, tmp_path: Path) -> None:
@@ -190,7 +191,7 @@ def test_zoomed_out_rendering(fill_store: Callable, tmp_path: Path) -> None:
 
     thumb = tg.get_tile(1, 0, 0)
     _, num = label(np.array(thumb)[:, :, 1])  # default color is green
-    assert num == 25  # expect 25 cells in top left quadrant
+    assert num == 25  # expect 25 cells in top left quadrant (added one too small)
 
 
 def test_decimation(fill_store: Callable, tmp_path: Path) -> None:
@@ -434,7 +435,7 @@ def test_unfilled_polys(fill_store: Callable, tmp_path: Path) -> None:
     renderer = AnnotationRenderer(thickness=1)
     tg = AnnotationTileGenerator(wsi.info, store, renderer, tile_size=256)
     tile_outline = np.array(tg.get_tile(1, 0, 0))
-    tg.renderer.edge_thickness = -1
+    tg.renderer.thickness = -1
     tile_filled = np.array(tg.get_tile(1, 0, 0))
     # expect sum of filled polys to be much greater than sum of outlines
     assert np.sum(tile_filled) > 2 * np.sum(tile_outline)

tiatoolbox/utils/visualization.py

@@ -661,7 +661,10 @@ def to_tile_coords(
                 Array of coordinates in tile space in the form [x, y].
 
         """
-        return ((np.reshape(coords, (-1, 2)) - top_left) / scale).astype(np.int32)
+        return [
+            ((np.reshape(ring, (-1, 2)) - top_left) / scale).astype(np.int32)
+            for ring in coords
+        ]
 
     def get_color(
         self: AnnotationRenderer,
@@ -756,19 +759,26 @@ def render_poly(
             scale,
         )
         if self.thickness > -1:
-            cv2.drawContours(
+            cv2.polylines(
                 tile,
-                [cnt],
-                0,
-                col,
-                self.edge_thickness,
+                cnt,
+                isClosed=True,
+                color=col,
+                thickness=self.edge_thickness,
                 lineType=cv2.LINE_8,
             )
         else:
-            cv2.drawContours(tile, [cnt], 0, col, self.thickness, lineType=cv2.LINE_8)
+            cv2.fillPoly(tile, cnt, col)
         if self.thickness == -1 and self.edge_thickness > 0:
             edge_col = self.get_color(annotation, edge=True)
-            cv2.drawContours(tile, [cnt], 0, edge_col, 1, lineType=cv2.LINE_8)
+            cv2.polylines(
+                tile,
+                cnt,
+                isClosed=True,
+                color=edge_col,
+                thickness=1,
+                lineType=cv2.LINE_8,
+            )
 
     def render_multipoly(
         self: AnnotationRenderer,
@@ -782,7 +792,7 @@ def render_multipoly(
         geoms = annotation.coords
         for poly in geoms:
             cnt = self.to_tile_coords(poly, top_left, scale)
-            cv2.drawContours(tile, [cnt], 0, col, self.thickness, lineType=cv2.LINE_8)
+            cv2.fillPoly(tile, cnt, col)
 
     def render_pt(
         self: AnnotationRenderer,
@@ -811,7 +821,7 @@ def render_pt(
                 annotation.coords,
                 top_left,
                 scale,
-            )[0],
+            )[0][0],
             np.maximum(self.edge_thickness, 1),
             col,
             thickness=self.thickness,
@@ -838,15 +848,14 @@ def render_line(
 
         """
         col = self.get_color(annotation, edge=False)
+        cnt = self.to_tile_coords(
+            list(annotation.coords),
+            top_left,
+            scale,
+        )
         cv2.polylines(
             tile,
-            [
-                self.to_tile_coords(
-                    list(annotation.coords),
-                    top_left,
-                    scale,
-                ),
-            ],
+            [np.array(cnt)],
             isClosed=False,
             color=col,
             thickness=3,