fix getting mask of tile entirely within annotation

WSI_handling/wsi.py

@@ -144,19 +144,23 @@ def mask_out_tile(self,desired_mpp,coords,wh,colors_to_use=None,annotation_idx=N
         elif annotation_idx is not None:
             points = [points[annotation_idx]]
 
-        outerbounds = [coords[0]+base_wh[0],coords[1]+base_wh[1]]
-        points = [pointSet for pointSet in points if any([((p[0] > coords[0]) and (p[0] < outerbounds[0])) and ((p[1] > coords[1]) and (p[1] < outerbounds[1])) for p in pointSet ])]
+        tile_poly = Polygon([(coords[0],coords[1]),(coords[0],coords[1]+base_wh[1]),(coords[0]+base_wh[0],coords[1]+base_wh[1]),(coords[0]+base_wh[0],coords[1])])
 
-        # this rounding may de-align the mask and RGB image
-        points = self.resize_points(points,resize_factor)
-
-        coords = tuple([int(c * resize_factor) for c in coords])
         mask = np.zeros((wh[1],wh[0]),dtype=np.uint8)
+
+        points_maps = [point_map for point_map in zip(points,map_idx) if tile_poly.intersects(Polygon(point_map[0]))]
+        if points_maps:
+            points,map_idx = zip(*points_maps)        
+
+            # this rounding may de-align the mask and RGB image
+            points = self.resize_points(points,resize_factor)
+
+            coords = tuple([int(c * resize_factor) for c in coords])        
 
-        points = [[(int(p[0] - coords[0]), int(p[1] - coords[1])) for p in pointSet] for pointSet in points]
+            points = [[(int(p[0] - coords[0]), int(p[1] - coords[1])) for p in pointSet] for pointSet in points]
 
-        for annCount, pointSet in enumerate(points):                    
-            cv2.fillPoly(mask,[np.asarray(pointSet).reshape((-1,1,2))],map_idx[annCount])
+            for annCount, pointSet in enumerate(points):                    
+                cv2.fillPoly(mask,[np.asarray(pointSet).reshape((-1,1,2))],map_idx[annCount])
 
         return mask
 

setup.py

@@ -8,15 +8,14 @@
 setup(
   name = 'WSI_handling',         
   packages = ['WSI_handling'],   
-  version = '0.16',
+  version = '0.16.1',
   license='MIT',        
   description = 'Convienent handling of annotated whole slide images',
   long_description=long_description,
   long_description_content_type='text/markdown',
   author = 'Patrick Leo',                   
   author_email = '[email protected]',      
-  url = 'https://github.com/pjl54/WSI_handling',   
-  download_url = 'https://github.com/pjl54/WSI_handling/archive/v0.16.tar.gz',
+  url = 'https://github.com/pjl54/WSI_handling',
   keywords = ['whole slide image', 'digital pathology', 'annotations'],
   install_requires=[
           'numpy',