Added parameter to sd.concatenate to control whether to merge coordinate systems with the same name

src/spatialdata/_core/concatenate.py

@@ -13,7 +13,12 @@
 
 from spatialdata._core._utils import _find_common_table_keys
 from spatialdata._core.spatialdata import SpatialData
-from spatialdata.models import SpatialElement, TableModel, get_table_keys
+from spatialdata.models import TableModel, get_table_keys
+from spatialdata.transformations import (
+    get_transformation,
+    remove_transformation,
+    set_transformation,
+)
 
 __all__ = [
     "concatenate",
@@ -81,7 +86,8 @@ def concatenate(
     concatenate_tables: bool = False,
     obs_names_make_unique: bool = True,
     modify_tables_inplace: bool = False,
-    attrs_merge: StrategiesLiteral | Callable[[list[dict[Any, Any]]], dict[Any, Any]] | None = None,
+    merge_coordinate_systems_on_name: bool = False,
+    attrs_merge: (StrategiesLiteral | Callable[[list[dict[Any, Any]]], dict[Any, Any]] | None) = None,
     **kwargs: Any,
 ) -> SpatialData:
     """
@@ -141,6 +147,7 @@ def concatenate(
             rename_tables=not concatenate_tables,
             rename_obs_names=obs_names_make_unique and concatenate_tables,
             modify_tables_inplace=modify_tables_inplace,
+            merge_coordinate_systems_on_name=merge_coordinate_systems_on_name,
         )
 
     ERROR_STR = (
@@ -222,12 +229,14 @@ def _fix_ensure_unique_element_names(
     rename_tables: bool,
     rename_obs_names: bool,
     modify_tables_inplace: bool,
+    merge_coordinate_systems_on_name: bool,
 ) -> list[SpatialData]:
-    elements_by_sdata: list[dict[str, SpatialElement]] = []
-    tables_by_sdata: list[dict[str, AnnData]] = []
+    sdatas_fixed = []
     for suffix, sdata in sdatas.items():
+        # Create new elements dictionary with suffixed names
         elements = {f"{name}-{suffix}": el for _, name, el in sdata.gen_spatial_elements()}
-        elements_by_sdata.append(elements)
+
+        # Handle tables with suffix
         tables = {}
         for name, table in sdata.tables.items():
             if not modify_tables_inplace:
@@ -251,9 +260,27 @@ def _fix_ensure_unique_element_names(
             # fix the table name
             new_name = f"{name}-{suffix}" if rename_tables else name
             tables[new_name] = table
-        tables_by_sdata.append(tables)
-    sdatas_fixed = []
-    for elements, tables in zip(elements_by_sdata, tables_by_sdata, strict=True):
-        sdata = SpatialData.init_from_elements(elements, tables=tables)
-        sdatas_fixed.append(sdata)
+
+        # Create new SpatialData object with suffixed elements and tables
+        sdata_fixed = SpatialData.init_from_elements(elements, tables=tables)
+
+        # Handle coordinate systems and transformations
+        for element_name, element in elements.items():
+            # Get the original element from the input sdata
+            original_name = element_name.replace(f"-{suffix}", "")
+            original_element = sdata.get(original_name)
+
+            # Get transformations from original element
+            transformations = get_transformation(original_element, get_all=True)
+            assert isinstance(transformations, dict)
+
+            # Remove any existing transformations from the new element
+            remove_transformation(element, remove_all=True)
+
+            # Set new transformations with suffixed coordinate system names
+            for cs, t in transformations.items():
+                new_cs = cs if merge_coordinate_systems_on_name else f"{cs}-{suffix}"
+                set_transformation(element, t, to_coordinate_system=new_cs)
+
+        sdatas_fixed.append(sdata_fixed)
     return sdatas_fixed

tests/core/test_concatenate.py

@@ -0,0 +1,36 @@
+import pytest
+
+import spatialdata as sd
+from spatialdata.datasets import blobs
+
+
+@pytest.mark.parametrize("merge_coordinate_systems_on_name", [True, False])
+def test_concatenate_merge_coordinate_systems_on_name(merge_coordinate_systems_on_name):
+    blob1 = blobs()
+    blob2 = blobs()
+
+    sdata_keys = ["blob1", "blob2"]
+    sdata = sd.concatenate(
+        dict(zip(sdata_keys, [blob1, blob2], strict=True)),
+        merge_coordinate_systems_on_name=merge_coordinate_systems_on_name,
+    )
+
+    expected_images = ["blobs_image", "blobs_multiscale_image"]
+    expected_labels = ["blobs_labels", "blobs_multiscale_labels"]
+    expected_points = ["blobs_points"]
+    expected_shapes = ["blobs_circles", "blobs_polygons", "blobs_multipolygons"]
+
+    expected_suffixed_images = [f"{name}-{key}" for key in sdata_keys for name in expected_images]
+    expected_suffixed_labels = [f"{name}-{key}" for key in sdata_keys for name in expected_labels]
+    expected_suffixed_points = [f"{name}-{key}" for key in sdata_keys for name in expected_points]
+    expected_suffixed_shapes = [f"{name}-{key}" for key in sdata_keys for name in expected_shapes]
+
+    assert set(sdata.images.keys()) == set(expected_suffixed_images)
+    assert set(sdata.labels.keys()) == set(expected_suffixed_labels)
+    assert set(sdata.points.keys()) == set(expected_suffixed_points)
+    assert set(sdata.shapes.keys()) == set(expected_suffixed_shapes)
+
+    if merge_coordinate_systems_on_name:
+        assert sdata.coordinate_systems == ["global"]
+    else:
+        assert sdata.coordinate_systems == ["global-blob1", "global-blob2"]