Remove _filter_table_by_element_names and replace with _filter_table_by_elements

The old function filtered only by region name, ignoring instance IDs.
Replace its only caller (filter_tables by coordinate system) with
_filter_table_by_elements, which correctly filters by both region and instance.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: LucaMarconato

src/spatialdata/_core/query/relational_query.py

@@ -59,31 +59,6 @@ def get_element_annotators(sdata: SpatialData, element_name: str) -> set[str]:
     return table_names
 
 
-def _filter_table_by_element_names(table: AnnData | None, element_names: str | list[str]) -> AnnData | None:
-    """
-    Filter an AnnData table to keep only the rows that are in the coordinate system.
-
-    Parameters
-    ----------
-    table
-        The table to filter; if None, returns None
-    element_names
-        The element_names to keep in the tables obs.region column
-
-    Returns
-    -------
-    The filtered table, or None if the input table was None
-    """
-    if table is None or not table.uns.get(TableModel.ATTRS_KEY):
-        return None
-    table_mapping_metadata = table.uns[TableModel.ATTRS_KEY]
-    region_key = table_mapping_metadata[TableModel.REGION_KEY_KEY]
-    table.obs = pd.DataFrame(table.obs)
-    table = table[table.obs[region_key].isin(element_names)].copy()
-    table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY] = table.obs[region_key].unique().tolist()
-    return table
-
-
 @singledispatch
 def get_element_instances(
     element: SpatialElement,

src/spatialdata/_core/spatialdata.py

@@ -691,12 +691,17 @@ def _filter_tables(
                     continue
                 # each mode here requires paths or elements, using assert here to avoid mypy errors.
                 if by == "cs":
-                    from spatialdata._core.query.relational_query import (
-                        _filter_table_by_element_names,
-                    )
+                    from spatialdata._core.query.relational_query import _filter_table_by_elements
 
                     assert element_names is not None
-                    table = _filter_table_by_element_names(table, element_names)
+                    elements_dict = {}
+                    for element_type in ["images", "labels", "shapes", "points"]:
+                        elements = getattr(self, element_type)
+                        if elements:  # Check if the dictionary is not empty
+                            elements_dict[element_type] = {
+                                name: elements[name] for name in element_names if name in elements
+                            }
+                    table = _filter_table_by_elements(table, elements_dict=elements_dict)
                     if table is not None and len(table) != 0:
                         tables[table_name] = table
                 elif by == "elements":