make_tiles now properly copies the transformations from source img

src/squidpy/experimental/im/_make_tiles.py

@@ -228,6 +228,9 @@ def _save_tiles_to_shapes(
     )
 
     sdata.shapes[shapes_key] = ShapesModel.parse(tile_gdf)
+    # we know that a) the element exists and b) it has at least an Identity transformation
+    transformations = get_transformation(sdata.images[image_key], get_all=True)
+    set_transformation(sdata.shapes[shapes_key], transformations, set_all=True)
     logger.info(f"Saved tile grid as 'sdata.shapes[\"{shapes_key}\"]'")
 
 

tests/conftest.py

@@ -48,6 +48,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
 
     warnings.simplefilter("ignore", OldFormatWarning)
     sc.pl.set_rcParams_defaults()
+    sc.set_figure_params(dpi=40, color_map="viridis")
 
 
 @pytest.fixture(scope="session")

tests/experimental/test_make_tiles.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import spatialdata_plot as sdp
+from spatialdata.transformations import Identity, get_transformation, set_transformation
 
 import squidpy as sq
 from tests.conftest import PlotTester, PlotTesterMeta
@@ -104,3 +105,19 @@ def test_plot_make_tiles_center_grid_on_tissue(self):
             center_grid_on_tissue=True,
             preview=True,
         )
+
+
+def test_make_tiles_copies_image_transformations(sdata_hne):
+    """Tiles saved from images inherit the image transformations."""
+    image_key = "hne"
+    custom_cs = Identity()
+    set_transformation(sdata_hne.images[image_key], {"custom_cs": custom_cs}, set_all=True)
+
+    sq.experimental.im.make_tiles(sdata_hne, image_key=image_key, preview=False)
+
+    img_tfs = get_transformation(sdata_hne.images[image_key], get_all=True)
+    tile_tfs = get_transformation(sdata_hne.shapes[f"{image_key}_tiles"], get_all=True)
+
+    assert "custom_cs" in img_tfs and "custom_cs" in tile_tfs
+    assert isinstance(img_tfs["custom_cs"], Identity)
+    assert isinstance(tile_tfs["custom_cs"], Identity)