add support for layer selection of get_values method (#818)

* add support for layer selection of get_values method

* adding file formatted with wrong prettier

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* ignoring markdown files in prettier

* add test for get_values(table_layer=...)

* using different prettier mirror

---------

Co-authored-by: Sonja Stockhaus <[email protected]>
Co-authored-by: Luca Marconato <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/spatialdata/_core/query/relational_query.py

@@ -841,6 +841,7 @@ def get_values(
     sdata: SpatialData | None = None,
     element_name: str | None = None,
     table_name: str | None = None,
+    table_layer: str | None = None,
     return_obsm_as_is: bool = False,
 ) -> pd.DataFrame | ArrayLike:
     """
@@ -860,6 +861,8 @@ def get_values(
         annotating the element_name.
     table_name
         Name of the table to get the values from.
+    table_layer
+        Layer of the table to get the values from. If None, the values are taken from X.
     return_obsm_as_is
         In case the value is in obsm the value of the key can be returned as is if return_obsm_as_is is True, otherwise
         creates a dataframe and returns it.
@@ -930,7 +933,12 @@ def get_values(
             df = obs[value_key_values].copy()
         if origin == "var":
             matched_table.obs = pd.DataFrame(obs)
-            x = matched_table[:, value_key_values].X
+            if table_layer is None:
+                x = matched_table[:, value_key_values].X
+            else:
+                if table_layer not in matched_table.layers:
+                    raise ValueError(f"Layer {table_layer} was not found.")
+                x = matched_table[:, value_key_values].layers[table_layer]
             import scipy
 
             if isinstance(x, scipy.sparse.csr_matrix | scipy.sparse.csc_matrix | scipy.sparse.coo_matrix):

tests/core/query/test_relational_query.py

@@ -717,6 +717,13 @@ def test_get_values_table(sdata_blobs):
     assert len(df) == 26
 
 
+def test_get_values_table_different_layer(sdata_blobs):
+    sdata_blobs["table"].layers["layer"] = np.log1p(sdata_blobs["table"].X)
+    df = get_values(value_key="channel_0_sum", element=sdata_blobs["table"])
+    df_layer = get_values(value_key="channel_0_sum", element=sdata_blobs["table"], table_layer="layer")
+    assert np.allclose(np.log1p(df), df_layer)
+
+
 def test_get_values_table_element_name(sdata_blobs):
     sdata_blobs["table"].obs["region"] = sdata_blobs["table"].obs["region"].cat.add_categories("another_region")
     sdata_blobs["table"].obs.loc["1", "region"] = "another_region"