Fix/recursion limit (SBU-BMI#208)

* dynamically handled recursion limit

* removed redundant qupath files

* rectified chunksize error

* added return type in function which sets recursionlimit

* yield after setting the recursionlimit

* removed trailing whitespace

wsinfer/patchlib/patch.py

@@ -11,10 +11,23 @@
 from shapely import Point
 from shapely import Polygon
 from shapely import STRtree
+from contextlib import contextmanager
+import sys
+from typing import Iterator
 
 logger = logging.getLogger(__name__)
 
 
+@contextmanager
+def temporary_recursion_limit(limit: int) -> Iterator[None]:
+    old_limit = sys.getrecursionlimit()
+    try:
+        sys.setrecursionlimit(limit)
+        yield
+    finally:
+        sys.setrecursionlimit(old_limit)
+
+
 def get_multipolygon_from_binary_arr(
     arr: npt.NDArray[np.int_], scale: tuple[float, float] | None = None
 ) -> tuple[MultiPolygon, Sequence[npt.NDArray[np.int_]], npt.NDArray[np.int_]]:
@@ -96,8 +109,10 @@ def merge_polygons(polygon: MultiPolygon, idx: int, add: bool) -> MultiPolygon:
 
         return polygon
 
-    # Call the function with an initial empty polygon and start from contour 0
-    polygon = merge_polygons(MultiPolygon(), 0, True)
+    temp_limit = max(sys.getrecursionlimit(), len(contours))
+    with temporary_recursion_limit(temp_limit):
+        # Call the function with an initial empty polygon and start from contour 0
+        polygon = merge_polygons(MultiPolygon(), 0, True)
 
     # Add back the axis in hierarchy because we squeezed it before.
     return polygon, contours_unscaled, hierarchy[np.newaxis]

wsinfer/write_geojson.py

@@ -109,4 +109,4 @@ def write_geojsons(csvs: list[Path], results_dir: Path, num_workers: int) -> Non
         output.mkdir(parents=True, exist_ok=True)
 
     func = partial(make_geojson, results_dir=results_dir)
-    process_map(func, csvs, max_workers=num_workers)
+    process_map(func, csvs, max_workers=num_workers, chunksize=1)