🐛 Fix Invalid Geometry in JSON Outputs (#1057)

- Replace direct `Polygon` construction with validated geometry via `feature2geometry` and `make_valid_poly`.
- Ensure all shapes are repaired and valid before JSON export.
- Prevents malformed or invalid polygons from breaking QuPath JSON outputs.

---------

Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

tiatoolbox/models/engine/multi_task_segmentor.py

@@ -131,7 +131,6 @@
 import zarr
 from dask import delayed
 from matplotlib import pyplot as plt
-from shapely import Polygon
 from shapely.geometry import mapping
 from shapely.geometry import shape as feature2geometry
 from shapely.strtree import STRtree
@@ -3535,12 +3534,16 @@ def _build_single_qupath_feature(
                 to QuPath JSON.
 
         """
-        contour = np.array(self._contours[i], dtype=float)
-        contour[:, 0] = contour[:, 0] * scale_factor[0] + origin[0]
-        contour[:, 1] = contour[:, 1] * scale_factor[1] + origin[1]
-
-        poly = Polygon(contour)
-        poly_geo = mapping(poly)
+        geom = make_valid_poly(
+            feature2geometry(
+                {
+                    "type": self._processed_predictions.get("geom_type", "Polygon"),
+                    "coordinates": scale_factor * np.array([self._contours[i]]),
+                }
+            ),
+            tuple(origin),
+        )
+        geo_map = mapping(geom)
 
         props = {}
         class_value = None
@@ -3584,7 +3587,7 @@ def _build_single_qupath_feature(
         return {
             "type": "Feature",
             "id": f"object_{i}",
-            "geometry": poly_geo,
+            "geometry": geo_map,
             "properties": props,
             "objectType": "annotation",
             "name": class_name if class_name is not None else "object",