fix invalid polygons

Author: Matt Sokoloff

labelbox/data/annotation_types/geometry/mask.py

@@ -38,9 +38,7 @@ class Mask(Geometry):
     @property
     def geometry(self) -> Dict[str, Tuple[int, int, int]]:
         mask = self.draw(color=1)
-        contours, hierarchy = cv2.findContours(image=mask,
-                                               mode=cv2.RETR_TREE,
-                                               method=cv2.CHAIN_APPROX_NONE)
+        contours, hierarchy = cv2.findContours(image=mask,mode=cv2.RETR_TREE, method=cv2.CHAIN_APPROX_NONE)
 
         holes = []
         external_contours = []
@@ -51,9 +49,16 @@ def geometry(self) -> Dict[str, Tuple[int, int, int]]:
             else:
                 external_contours.append(contours[i])
 
-        external_polygons = self._extract_polygons_from_contours(
-            external_contours)
+        external_polygons = self._extract_polygons_from_contours(external_contours)
         holes = self._extract_polygons_from_contours(holes)
+
+
+        if not external_polygons.is_valid:
+            external_polygons = external_polygons.buffer(0)
+
+        if not holes.is_valid:
+            holes = holes.buffer(0)
+
         return external_polygons.difference(holes).__geo_interface__
 
     def draw(self,
@@ -78,7 +83,6 @@ def draw(self,
             np.ndarray representing only this object
                 as opposed to the mask that this object references which might have multiple objects determined by colors
         """
-
         mask = self.mask.value
         mask = np.alltrue(mask == self.color, axis=2).astype(np.uint8)
 

labelbox/data/serialization/coco/instance_dataset.py

@@ -21,7 +21,6 @@ def mask_to_coco_object_annotation(
     # This is going to fill any holes into the multipolygon
     # If you need to support holes use the panoptic data format
     shapely = annotation.value.shapely.simplify(1).buffer(0)
-
     if shapely.is_empty:
         return
 
@@ -42,6 +41,8 @@ def mask_to_coco_object_annotation(
         iscrowd=0)
 
 
+
+
 def vector_to_coco_object_annotation(annotation: ObjectAnnotation,
                                      annot_idx: int, image_id: int,
                                      category_id: int) -> COCOObjectAnnotation:

labelbox/data/serialization/coco/panoptic_dataset.py

@@ -18,11 +18,17 @@
 from .annotation import PanopticAnnotation, SegmentInfo, get_annotation_lookup
 
 
+
+
 def vector_to_coco_segment_info(canvas: np.ndarray,
                                 annotation: ObjectAnnotation,
                                 annotation_idx: int, image: CocoImage,
                                 category_id: int):
+
     shapely = annotation.value.shapely
+    if shapely.is_empty:
+        return
+
     xmin, ymin, xmax, ymax = shapely.bounds
     canvas = annotation.value.draw(height=image.height,
                                    width=image.width,
@@ -40,6 +46,9 @@ def mask_to_coco_segment_info(canvas: np.ndarray, annotation,
     color = id_to_rgb(annotation_idx)
     mask = annotation.value.draw(color=color)
     shapely = annotation.value.shapely
+    if shapely.is_empty:
+        return
+
     xmin, ymin, xmax, ymax = shapely.bounds
     canvas = np.where(canvas == (0, 0, 0), mask, canvas)
     return SegmentInfo(id=annotation_idx,
@@ -70,20 +79,32 @@ def process_label(label: Label,
         for annotation_idx, annotation in enumerate(annotations[class_name]):
             categories[annotation.name] = hash_category_name(annotation.name)
             if isinstance(annotation.value, Mask):
-                segment, canvas = (mask_to_coco_segment_info(
+                coco_segment_info = mask_to_coco_segment_info(
                     canvas, annotation, class_idx + 1,
-                    categories[annotation.name]))
+                    categories[annotation.name])
+
+                if coco_segment_info is None:
+                    # Filter out empty masks
+                    continue
+
+                segment, canvas = coco_segment_info
                 segments.append(segment)
                 is_thing[annotation.name] = 0
 
             elif isinstance(annotation.value, (Polygon, Rectangle)):
-                segment, canvas = vector_to_coco_segment_info(
+                coco_vector_info = vector_to_coco_segment_info(
                     canvas,
                     annotation,
                     annotation_idx=(class_idx if all_stuff else annotation_idx)
                     + 1,
                     image=image,
                     category_id=categories[annotation.name])
+
+                if coco_segment_info is None:
+                    # Filter out empty annotations
+                    continue
+
+                segment, canvas = coco_vector_info
                 segments.append(segment)
                 is_thing[annotation.name] = 1 - int(all_stuff)