Implement to_anndata()

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## 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)

setup.cfg

@@ -69,7 +69,8 @@ exclude =
 # PDF = ReportLab; RXP
 optional =
     pandas
-    requests
+    anndata
+    delayedarray
 
 # Add here test requirements (semicolon/line-separated)
 testing =

src/spatialexperiment/__init__.py

@@ -26,7 +26,6 @@
 )
 
 __all__ = [
-    "ProxySpatialFeatureExperiment",
     "read_tenx_visium",
     "SpatialExperiment",
     "LoadedSpatialImage",

src/spatialexperiment/spatialexperiment.py

@@ -29,7 +29,13 @@
     _validate_spatial_coords,
     _validate_spatial_coords_names,
 )
-from .spatialimage import VirtualSpatialImage, construct_spatial_image_class
+from .spatialimage import (
+    VirtualSpatialImage,
+    StoredSpatialImage,
+    RemoteSpatialImage,
+    LoadedSpatialImage,
+    construct_spatial_image_class,
+)
 
 __author__ = "keviny2"
 __copyright__ = "keviny2"
@@ -1009,6 +1015,46 @@ def mirror_img(self, sample_id=None, image_id=None, axis=("h", "v")):
     def to_spatial_experiment():
         raise NotImplementedError()
 
+    ################################
+    ######>> AnnData interop <<#####
+    ################################
+
+    def to_anndata(self, include_alternative_experiments: bool = False) -> "anndata.AnnData":
+        """Transform :py:class:`~SpatialExperiment`-like into a :py:class:`~anndata.AnnData` representation.
+
+        Args:
+            include_alternative_experiments:
+                Whether to transform alternative experiments.
+
+        Returns:
+            An ``AnnData`` representation of the experiment.
+        """
+        obj, alt_exps = super().to_anndata(include_alternative_experiments=include_alternative_experiments)
+
+        if "spatial" in obj.uns:
+            raise ValueError("'spatial' key already exists in the metadata. Rename to something else.")
+
+        obj.uns["spatial"] = {}
+        for _, row in self.img_data:
+            library_id = row["sample_id"] + "-" + row["image_id"]
+            obj.uns["spatial"][library_id] = {}
+
+            spi = row["data"]
+            if isinstance(spi, LoadedSpatialImage):
+                img = spi.image
+            elif isinstance(spi, (StoredSpatialImage, RemoteSpatialImage)):
+                img = spi.img_source()
+
+            obj.uns["spatial"][library_id]["images"] = {"hires": img}  # default to `hires` for now
+
+            obj.uns["spatial"][library_id]["scalefactors"] = {
+                "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])
+
+        return obj, alt_exps
+
     ################################
     #######>> combine ops <<########
     ################################

src/spatialexperiment/spatialimage.py

@@ -257,8 +257,8 @@ def __str__(self) -> str:
     ######>> img props <<#######
     ############################
 
-    def get_image(self) -> Image.Image:
-        """Get the image as a PIL Image object."""
+    def get_image(self) -> Union[Image.Image, np.ndarray]:
+        """Get the image as a PIL Image object or ndarray."""
 
         return self._image
 

tests/test_to_anndata.py

@@ -0,0 +1,37 @@
+from copy import deepcopy
+from pathlib import Path
+import pytest
+
+__author__ = "keviny2"
+__copyright__ = "keviny2"
+__license__ = "MIT"
+
+
+def test_to_anndata(spe):
+    obj, alt_exps = spe.to_anndata()
+
+    assert obj.shape == (500, 200)
+
+    # check that uns has the correct components
+    assert 'spatial' in obj.uns
+    assert len(obj.uns['spatial']) == 3
+
+    library_id = list(obj.uns['spatial'])[0]
+    assert 'images' in obj.uns['spatial'][library_id]
+    assert 'scalefactors' in obj.uns['spatial'][library_id]
+
+    assert 'hires' in obj.uns['spatial'][library_id]['images']
+    assert isinstance(obj.uns['spatial'][library_id]['images']['hires'], Path)
+
+    # check that obsm has the correct components
+    assert 'spatial' in obj.obsm
+    assert obj.obsm['spatial'].shape == (500, 2)
+
+
+def test_to_anndata_spatial_key_exists(spe):
+    tspe = deepcopy(spe)
+
+    tspe.metadata['spatial'] = "123"
+
+    with pytest.raises(ValueError):
+        tspe.to_anndata()