fix: fix bug in area contours

Author: okunator

cellseg_models_pytorch/inference/_base_inferer.py

@@ -143,10 +143,10 @@ def __init__(
 
             # try loading the weights to the model
             try:
-                msg = self.model.load_state_dict(state_dict, strict=False)
+                msg = self.model.load_state_dict(state_dict, strict=True)
             except RuntimeError:
                 new_ckpt = self._strip_state_dict(state_dict)
-                msg = self.model.load_state_dict(new_ckpt, strict=False)
+                msg = self.model.load_state_dict(new_ckpt, strict=True)
             except BaseException as e:
                 raise RuntimeError(f"Error when loading checkpoint: {e}")
 

cellseg_models_pytorch/utils/file_manager.py

@@ -318,9 +318,6 @@ def get_gson(
                 x-coordinate offset. (to set geojson to .mrxs wsi coordinates)
             y_offset : int, default=0
                 y-coordinate offset. (to set geojson to .mrxs wsi coordinates)
-            geo_format : str, default="qupath"
-                The format for the geo object. "qupath" format allows the result file
-                to be read with QuPath. "simple" format allows for geopandas etc.
 
         Returns
         -------
@@ -357,25 +354,38 @@ def get_gson(
                     inst_type_soft[key] = float(inst_type_soft[key])
 
             # get the cell contour coordinates
-            contours = cv2.findContours(inst, cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
+            contours = cv2.findContours(inst, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
             contours = contours[0] if len(contours) == 2 else contours[1]
 
+            shell = contours[0]  # exterior
+            holes = [cont for cont in contours[1:]]
+
             # got a line instead of a polygon
-            if contours[0].shape[0] < 3:
+            if shell.shape[0] < 3:
                 continue
 
             # shift coordinates based on the offsets
             if x_offset:
-                contours[0][..., 0] += x_offset
+                shell[..., 0] += x_offset
+                if holes:
+                    for cont in holes:
+                        cont[..., 0] += x_offset
+
             if y_offset:
-                contours[0][..., 1] += y_offset
+                shell[..., 1] += y_offset
+                if holes:
+                    for cont in holes:
+                        cont[..., 1] += y_offset
 
-            poly = contours[0].squeeze().tolist()
-            poly.append(poly[0])  # close the polygon
+            # convert to list for shapely Polygon
+            shell = shell.squeeze().tolist()
+            if holes:
+                holes = [cont.squeeze().tolist() for cont in holes]
+            # shell.append(shell[0])  # close the polygon
 
             features.append(
                 FileHandler.geo_obj(
-                    poly=Polygon(poly),
+                    poly=Polygon(shell=shell, holes=holes),
                     uid=inst_id,
                     class_name=inst_type,
                     class_probs=inst_type_soft,
@@ -390,6 +400,7 @@ def to_gson(
         features: List[Dict[str, Any]],
         format: str = ".feather",
         show_bbox: bool = True,
+        silence_warnings: bool = True,
     ) -> None:
         """Write a geojson/feather/parquet file from a list of geojson features.
 
@@ -403,6 +414,8 @@ def to_gson(
             The output format. One of ".feather", ".parquet", ".geojson".
         show_bbox : bool, default=True
             If True, the bbox is added to the geojson object.
+        silence_warnings : bool, default=True
+            If True, warnings are silenced.
         """
         out_fn = Path(out_fn)
         if format not in (".feather", ".parquet", ".geojson"):
@@ -442,7 +455,8 @@ def to_gson(
             if show_bbox:
                 geo["bbox"] = tuple(gdf.total_bounds)
         else:
-            warnings.warn(f"The {out_fn.name} file is empty.")
+            if not silence_warnings:
+                warnings.warn(f"The {out_fn.name} file is empty.")
 
         if format == ".feather":
             gdf.to_feather(out_fn.with_suffix(".feather"))