get_coords now optionally returns mask or vector of points

lightning/types/images.py

@@ -2,7 +2,7 @@
 
 from lightning.types.base import Base
 from lightning.types.decorators import viztype
-from lightning.types.utils import array_to_im, get_points_from_polygon
+from lightning.types.utils import array_to_im, mask_to_points, polygon_to_mask
 
 
 @viztype
@@ -28,14 +28,33 @@ def clean(imagedata):
 
         return {'images': outdict}
 
-    def get_coords(self, as_points=False):
+    def get_coords(self, return_type='bounds', dims=None):
+        """
+        Get data from polygons drawn on image.
+
+        :param return_type:
+        :return:
+        """
+
         user_data = self.get_user_data()['settings']
-        if 'coords' in user_data.keys():            
+        if 'coords' in user_data.keys():
             coords = user_data['coords']
-            if as_points:
-                return [get_points_from_polygon(x) for x in coords]
+
+            if return_type == 'bounds':
+                return coords
+
+            elif return_type == 'mask':
+                if not dims:
+                    raise Exception('Must provide image dimensions to return mask')
+                return [polygon_to_mask(x, dims) for x in coords]
+
+            elif return_type == 'points':
+                if not dims:
+                    raise Exception('Must provide image dimensions to return inner points')
+                return [mask_to_points(polygon_to_mask(x, dims)) for x in coords]
+
             else:
-                return coords        
+                raise Exception('Option %s is not supported' % return_type)
         else:
             return []
 

lightning/types/utils.py

@@ -208,25 +208,33 @@ def list_to_regions(reg):
             raise Exception("All region names must be two letters (for US) or three letters (for world)")
         return reg
 
-def get_points_from_polygon(coords):
+
+def polygon_to_mask(coords, dims):
+
     """
-    Given a list of pairs of points which define a polygon, return a list of points interior to the polygon
+    Given a list of pairs of points which define a polygon, return a binary
+    mask covering the interior of the polygon
     """
-    
+
     bounds = array(coords).astype('int')
+    path = Path(bounds)
 
-    bMax = bounds.max(0)
-    bMin = bounds.min(0)
+    grid = meshgrid(range(dims[1]), range(dims[0]))
+    grid_flat = zip(grid[0].ravel(), grid[1].ravel())
 
-    path = Path(bounds)
+    mask = path.contains_points(grid_flat).reshape(dims[0:2]).astype('int')
 
-    grid = meshgrid(range(bMin[0],bMax[0]+1),range(bMin[1],bMax[1]+1))
+    return mask
 
-    gridFlat = zip(grid[0].ravel(),grid[1].ravel())
 
-    inside = path.contains_points(gridFlat).reshape(grid[0].shape).astype('int')
-    inside = where(inside)
-    inside = vstack([inside[0],inside[1]]).T + bMin[-1::-1]    
-    inside.tolist()
-
-    return inside
+def mask_to_points(mask):
+
+    """
+    Convert binary mask to a list of (y,x) points for each point where the mask is 1
+    """
+
+    points = where(mask)
+    points = vstack([points[0], points[1]]).T
+    points = points.tolist()
+
+    return points