Preserve points feature_key in queries (#794)

* Preserve points feature_key during queries

* add PR number to changelog

* fix docs; add sphinx-autobuild dep

---------

Co-authored-by: Luca Marconato <[email protected]>

Author: quentinblampey

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning][].
 ### Fixed
 
 -   Updated deprecated default stages of `pre-commit` #771
+-   Preserve points `feature_key` during queries #794
 
 ## [0.2.5] - 2024-06-11
 

pyproject.toml

@@ -55,6 +55,7 @@ dev = [
 ]
 docs = [
     "sphinx>=4.5",
+	"sphinx-autobuild",
     "sphinx-book-theme>=1.0.0",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",

src/spatialdata/_core/query/spatial_query.py

@@ -33,6 +33,7 @@
     points_geopandas_to_dask_dataframe,
 )
 from spatialdata.models._utils import ValidAxis_t, get_spatial_axes
+from spatialdata.models.models import ATTRS_KEY
 from spatialdata.transformations.operations import set_transformation
 from spatialdata.transformations.transformations import (
     Affine,
@@ -712,9 +713,13 @@ def _(
                 points_df = p.compute().iloc[bounding_box_indices]
                 old_transformations = get_transformation(p, get_all=True)
                 assert isinstance(old_transformations, dict)
+                feature_key = p.attrs.get(ATTRS_KEY, {}).get(PointsModel.FEATURE_KEY)
+
                 output.append(
                     PointsModel.parse(
-                        dd.from_pandas(points_df, npartitions=1), transformations=old_transformations.copy()
+                        dd.from_pandas(points_df, npartitions=1),
+                        transformations=old_transformations.copy(),
+                        feature_key=feature_key,
                     )
                 )
     if len(output) == 0:
@@ -925,10 +930,11 @@ def _(
     queried_points = points_gdf.loc[joined["index_right"]]
     ddf = points_geopandas_to_dask_dataframe(queried_points, suppress_z_warning=True)
     transformation = get_transformation(points, target_coordinate_system)
+    feature_key = points.attrs.get(ATTRS_KEY, {}).get(PointsModel.FEATURE_KEY)
     if "z" in ddf.columns:
-        ddf = PointsModel.parse(ddf, coordinates={"x": "x", "y": "y", "z": "z"})
+        ddf = PointsModel.parse(ddf, coordinates={"x": "x", "y": "y", "z": "z"}, feature_key=feature_key)
     else:
-        ddf = PointsModel.parse(ddf, coordinates={"x": "x", "y": "y"})
+        ddf = PointsModel.parse(ddf, coordinates={"x": "x", "y": "y"}, feature_key=feature_key)
     set_transformation(ddf, transformation, target_coordinate_system)
     t = get_transformation(ddf, get_all=True)
     assert isinstance(t, dict)

src/spatialdata/models/_utils.py

@@ -417,8 +417,7 @@ def set_channel_names(element: DataArray | DataTree, channel_names: str | list[s
 
     Returns
     -------
-    element
-        The image `SpatialElement` or parsed `ImageModel` with the channel names set to the `c` dimension.
+    The image `SpatialElement` or parsed `ImageModel` with the channel names set to the `c` dimension.
     """
     from spatialdata.models import Image2DModel, Image3DModel, get_model
 

src/spatialdata/models/models.py

@@ -736,8 +736,11 @@ def _(
         elif isinstance(data, dd.DataFrame):  # type: ignore[attr-defined]
             table = data[[coordinates[ax] for ax in axes]]
             table.columns = axes
-            if feature_key is not None and data[feature_key].dtype.name != "category":
-                table[feature_key] = data[feature_key].astype(str).astype("category")
+            if feature_key is not None:
+                if data[feature_key].dtype.name == "category":
+                    table[feature_key] = data[feature_key]
+                else:
+                    table[feature_key] = data[feature_key].astype(str).astype("category")
         if instance_key is not None:
             table[instance_key] = data[instance_key]
         for c in [X, Y, Z]:

tests/core/query/test_spatial_query.py

@@ -29,6 +29,7 @@
     ShapesModel,
     TableModel,
 )
+from spatialdata.models.models import ATTRS_KEY
 from spatialdata.testing import assert_spatial_data_objects_are_identical
 from spatialdata.transformations import Identity, MapAxis, set_transformation
 from tests.conftest import _make_points, _make_squares
@@ -205,6 +206,21 @@ def test_query_points(is_3d: bool, is_bb_3d: bool, with_polygon_query: bool, mul
     if is_3d:
         np.testing.assert_allclose(points_element["z"].compute(), original_z)
 
+    # the feature_key should be preserved
+    if not multiple_boxes:
+        assert (
+            points_result.attrs[ATTRS_KEY][PointsModel.FEATURE_KEY]
+            == points_element.attrs[ATTRS_KEY][PointsModel.FEATURE_KEY]
+        )
+    else:
+        for result in points_result:
+            if result is None:
+                continue
+            assert (
+                result.attrs[ATTRS_KEY][PointsModel.FEATURE_KEY]
+                == points_element.attrs[ATTRS_KEY][PointsModel.FEATURE_KEY]
+            )
+
 
 def test_query_points_no_points():
     """Points bounding box query with no points in range should