Only populate obsm if spatial coordinates exist

CHANGELOG.md

@@ -1,7 +1,10 @@
 # Changelog
 
-## Version 0.0.10
+## Version 0.0.11
+- BUGFIX: `to_anndata()` only populates `obsm` with spatial coordinates if the original `SpatialExperiment` has spatial coordinates (PR #53)
+
 
+## Version 0.0.10
 - Add an affine function that computes a `rasterio.Affine` object given a `scale_factor`. This assumes a simple scaling where the origin is (0,0) in the spatial coordinate system corresponding to the top-left pixel (0,0). More complex alignments would require explicit affine transforms.
 - Ensure img_raster() consistently returns a PIL.Image.Image.
 - Add to_numpy() method.
@@ -11,30 +14,33 @@
 ## Version 0.0.9
 - Added `to_anndata()` in main `SpatialExperiment` class (PR #50)
 
+
 ## Version 0.0.8
 - Set the expected column names for image data slot (PR #46)
 
+
 ## Version 0.0.7
 - Added `img_source` function in main SpatialExperiment class and child classes of VirtualSpatialExperiment (PR #36)
 - Added `remove_img` function (PR #34)
 - Refactored `get_img_idx` for improved maintainability
 - Disambiguated `get_img_data` between `_imgutils.py` and `SpatialExperiment.py`
 - Moved `SpatialFeatureExperiment` into its own package
 
+
 ## Version 0.0.6
 - Added `read_tenx_visium()` function to load 10x Visium data as SpatialExperiment
 - Added `combine_columns` function
 - Implemented `__eq__` override for `SpatialImage` subclasses
 
-## Version 0.0.5
 
+## Version 0.0.5
 - Implementing a placeholder `SpatialFeatureExperiment` class. This version only implements the data structure to hold various geometries but none of the methods except for slicing.
 
-## Version 0.0.3 - 0.0.4
 
+## Version 0.0.3 - 0.0.4
 - Streamlining the `SpatialImage` class implementations.
 
-## Version 0.0.1 - 0.0.2
 
+## Version 0.0.1 - 0.0.2
 - Initial version of the SpatialExperiment class with the additional slots.
 - Allow spatial coordinates to be a numpy array

src/spatialexperiment/spatialexperiment.py

@@ -1051,7 +1051,9 @@ def to_anndata(self, include_alternative_experiments: bool = False) -> "anndata.
                 "tissue_hires_scalef": row["scale_factor"]
             }  # default to `tissue_hires_scalef` for now
 
-        obj.obsm["spatial"] = np.column_stack([self.spatial_coordinates[axis] for axis in self.spatial_coords_names])
+        if len(self.spatial_coordinates) > 0:
+            coords_by_axis = [self.spatial_coordinates[axis] for axis in self.spatial_coords_names]
+            obj.obsm["spatial"] = np.column_stack(coords_by_axis)
 
         return obj, alt_exps
 

tests/test_to_anndata.py

@@ -1,6 +1,9 @@
+import pytest
 from copy import deepcopy
 from pathlib import Path
-import pytest
+import anndata as ad
+
+from spatialexperiment import SpatialExperiment
 
 __author__ = "keviny2"
 __copyright__ = "keviny2"
@@ -28,6 +31,14 @@ def test_to_anndata(spe):
     assert obj.obsm['spatial'].shape == (500, 2)
 
 
+def test_to_anndata_empty():
+    tspe = SpatialExperiment()
+
+    obj, alt_exps = tspe.to_anndata()
+
+    assert isinstance(obj, ad.AnnData)
+
+
 def test_to_anndata_spatial_key_exists(spe):
     tspe = deepcopy(spe)