handle empty points in the image (#133)

Co-authored-by: Sonja Stockhaus <stockhaus@cip.ifi.lmu.de>
Co-authored-by: Tim Treis <tim.treis@stud.uni-heidelberg.de>

Author: 3 people

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
 ### Fixed
 
 -   Multi-scale images/labels are now correctly substituted and the action is logged (#131).
+-   Empty geometries among the shapes can be handeled (#133).
 
 ## [0.0.2] - 2023-06-25
 

src/spatialdata_plot/pl/basic.py

@@ -195,6 +195,10 @@ def render_shapes(
         kwargs
             Additional arguments to be passed to cmap and norm.
 
+        Notes
+        -------
+            - Empty geometries will be removed at the time of plotting.
+
         Returns
         -------
         None

src/spatialdata_plot/pl/render.py

@@ -121,6 +121,8 @@ def _get_collection_shape(
     ) -> PatchCollection:
         patches = []
         for shape in shapes:
+            # remove empty points/polygons
+            shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
             # We assume that all elements in one collection are of the same type
             if shape["geometry"].iloc[0].geom_type == "Polygon":
                 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]

src/spatialdata_plot/pl/utils.py

@@ -314,11 +314,13 @@ def get_point_bb(
 
                         # Split by Point and Polygon:
                         tmp_points = sdata.shapes[e_id][
-                            sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
+                            sdata.shapes[e_id]["geometry"].apply(
+                                lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
+                            )
                         ]
                         tmp_polygons = sdata.shapes[e_id][
                             sdata.shapes[e_id]["geometry"].apply(
-                                lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
+                                lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
                             )
                         ]
 

tests/_images/Shapes_can_render_empty_geometry.png

@@ -1,3 +1,4 @@
+import geopandas as gpd
 import matplotlib
 import scanpy as sc
 import spatialdata_plot  # noqa: F401
@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
         sdata_blobs.pl.render_shapes(
             elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
         ).pl.show()
+
+    def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
+        sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
+        sdata_blobs.pl.render_shapes().pl.show()