added warning

Author: timtreis

src/spatialdata_plot/pl/render.py

@@ -17,7 +17,7 @@
 from matplotlib.cm import ScalarMappable
 from matplotlib.colors import ListedColormap, Normalize
 from scanpy._settings import settings as sc_settings
-from spatialdata import get_element_annotators, get_extent, get_values, join_spatialelement_table
+from spatialdata import get_extent, get_values, join_spatialelement_table
 from spatialdata.models import PointsModel, ShapesModel, get_table_keys
 from spatialdata.transformations import get_transformation, set_transformation
 from spatialdata.transformations.transformations import Identity
@@ -73,36 +73,24 @@ def _render_shapes(
     col_for_color = render_params.col_for_color
     groups = render_params.groups
     table_layer = render_params.table_layer
-    table_name = render_params.table_name
 
     sdata_filt = sdata.filter_by_coordinate_system(
         coordinate_system=coordinate_system,
         filter_tables=bool(render_params.table_name),
     )
-    if table_name is None:
+
+    if (table_name := render_params.table_name) is None:
         table = None
         shapes = sdata_filt[element]
     else:
-        # Check if the table actually annotates the element
-        annotating_tables = get_element_annotators(sdata, element)
-        if table_name not in annotating_tables:
-            warnings.warn(
-                f"Table '{table_name}' does not annotate element '{element}'",
-                UserWarning,
-                stacklevel=2,
-            )
-            # Fall back to no table
-            table = None
-            shapes = sdata_filt[element]
-        else:
-            element_dict, joined_table = join_spatialelement_table(
-                sdata, spatial_element_names=element, table_name=table_name, how="inner"
-            )
-            sdata_filt[element] = shapes = element_dict[element]
-            joined_table.uns["spatialdata_attrs"]["region"] = (
-                joined_table.obs[joined_table.uns["spatialdata_attrs"]["region_key"]].unique().tolist()
-            )
-            sdata_filt[table_name] = table = joined_table
+        element_dict, joined_table = join_spatialelement_table(
+            sdata, spatial_element_names=element, table_name=table_name, how="inner"
+        )
+        sdata_filt[element] = shapes = element_dict[element]
+        joined_table.uns["spatialdata_attrs"]["region"] = (
+            joined_table.obs[joined_table.uns["spatialdata_attrs"]["region_key"]].unique().tolist()
+        )
+        sdata_filt[table_name] = table = joined_table
 
     if (
         col_for_color is not None
@@ -502,39 +490,22 @@ def _render_points(
             dtype=points[["x", "y"]].values.dtype,
         )
     else:
-        # Check if the table actually annotates the element
-        annotating_tables = get_element_annotators(sdata, element)
-        if table_name not in annotating_tables:
-            warnings.warn(
-                f"Table '{table_name}' does not annotate element '{element}'",
-                UserWarning,
-                stacklevel=2,
-            )
-            # Fall back to no table
-            adata = AnnData(
-                X=points[["x", "y"]].values,
-                obs=points[coords].reset_index(),
-                dtype=points[["x", "y"]].values.dtype,
-            )
-        else:
-            adata_obs = sdata_filt[table_name].obs
-            # if the points are colored by values in X (or a different layer), add the values to obs
-            if col_for_color in sdata_filt[table_name].var_names:
-                if table_layer is None:
-                    adata_obs[col_for_color] = sdata_filt[table_name][:, col_for_color].X.flatten().copy()
-                else:
-                    adata_obs[col_for_color] = (
-                        sdata_filt[table_name][:, col_for_color].layers[table_layer].flatten().copy()
-                    )
-            if groups is not None:
-                adata_obs = adata_obs[adata_obs[col_for_color].isin(groups)]
-            adata = AnnData(
-                X=points[["x", "y"]].values,
-                obs=adata_obs,
-                dtype=points[["x", "y"]].values.dtype,
-                uns=sdata_filt[table_name].uns,
-            )
-            sdata_filt[table_name] = adata
+        adata_obs = sdata_filt[table_name].obs
+        # if the points are colored by values in X (or a different layer), add the values to obs
+        if col_for_color in sdata_filt[table_name].var_names:
+            if table_layer is None:
+                adata_obs[col_for_color] = sdata_filt[table_name][:, col_for_color].X.flatten().copy()
+            else:
+                adata_obs[col_for_color] = sdata_filt[table_name][:, col_for_color].layers[table_layer].flatten().copy()
+        if groups is not None:
+            adata_obs = adata_obs[adata_obs[col_for_color].isin(groups)]
+        adata = AnnData(
+            X=points[["x", "y"]].values,
+            obs=adata_obs,
+            dtype=points[["x", "y"]].values.dtype,
+            uns=sdata_filt[table_name].uns,
+        )
+        sdata_filt[table_name] = adata
 
     # we can modify the sdata because of dealing with a copy
 
@@ -1080,23 +1051,11 @@ def _render_labels(
         instance_id = np.unique(label)
         table = None
     else:
-        # Check if the table actually annotates the element
-        annotating_tables = get_element_annotators(sdata, element)
-        if table_name not in annotating_tables:
-            warnings.warn(
-                f"Table '{table_name}' does not annotate element '{element}'",
-                UserWarning,
-                stacklevel=2,
-            )
-            # Fall back to no table
-            instance_id = np.unique(label)
-            table = None
-        else:
-            _, region_key, instance_key = get_table_keys(sdata[table_name])
-            table = sdata[table_name][sdata[table_name].obs[region_key].isin([element])]
+        _, region_key, instance_key = get_table_keys(sdata[table_name])
+        table = sdata[table_name][sdata[table_name].obs[region_key].isin([element])]
 
-            # get instance id based on subsetted table
-            instance_id = np.unique(table.obs[instance_key].values)
+        # get instance id based on subsetted table
+        instance_id = np.unique(table.obs[instance_key].values)
 
     _, trans_data = _prepare_transformation(label, coordinate_system, ax)
 

src/spatialdata_plot/pl/utils.py

@@ -1833,7 +1833,8 @@ def _validate_label_render_params(
 
         element_params[el]["table_name"] = None
         element_params[el]["color"] = None
-        if (color := param_dict["color"]) is not None:
+        color = param_dict["color"]
+        if color is not None:
             color, table_name = _validate_col_for_column_table(sdata, el, color, param_dict["table_name"], labels=True)
             element_params[el]["table_name"] = table_name
             element_params[el]["color"] = color
@@ -1995,6 +1996,11 @@ def _validate_col_for_column_table(
         if table_name not in tables or (
             col_for_color not in sdata[table_name].obs.columns and col_for_color not in sdata[table_name].var_names
         ):
+            warnings.warn(
+                f"Table '{table_name}' does not annotate element '{element_name}'.",
+                UserWarning,
+                stacklevel=2,
+            )
             table_name = None
             col_for_color = None
     else: