Merge remote-tracking branch 'upstream/main' into load_data_in_thread

Author: Czaki

CHANGELOG.md

@@ -8,7 +8,13 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.x.x] - 2024-xx-xx
+## [0.5.3] - 2024-09-25
+
+### Fixed
+
+- Bug table was not reset after an element without table was added #317
+- Bug when changing channel for a multichannel image #301 #302
+- Bug when plotting catgorical annotations on points #304
 
 ## [0.5.2] - 2024-08-16
 

src/napari_spatialdata/_view.py

@@ -137,9 +137,13 @@ def _update_adata(self) -> None:
             )
             layer.metadata["adata"] = table
 
-        if layer is not None and "adata" in layer.metadata:
-            with self.model.events.adata.blocker():
-                self.model.adata = layer.metadata["adata"]
+        if layer is not None:
+            if "adata" in layer.metadata:
+                with self.model.events.adata.blocker():
+                    self.model.adata = layer.metadata["adata"]
+            else:
+                with self.model.events.adata.blocker():
+                    self.model.adata = None
 
         if self.model.adata.shape == (0, 0):
             return
@@ -186,8 +190,8 @@ def _select_layer(self) -> None:
                 self.color_widget.clear()
             return
 
-        if layer is not None and "adata" in layer.metadata:
-            self.model.adata = layer.metadata["adata"]
+        if layer is not None:
+            self.model.adata = layer.metadata.get("adata", None)
 
     def screenshot(self) -> Any:
         return QImg2array(self.grab().toImage())
@@ -384,10 +388,11 @@ def _select_layer(self) -> None:
                 if isinstance(layer, (Points, Shapes)) and (cols_df := layer.metadata.get("_columns_df")) is not None:
                     self.dataframe_columns_widget.addItems(map(str, cols_df.columns))
                     self.model.system_name = layer.metadata.get("name", None)
+            self.model.adata = None
             return
 
-        if layer is not None and "adata" in layer.metadata:
-            self.model.adata = layer.metadata["adata"]
+        if layer is not None:
+            self.model.adata = layer.metadata.get("adata", None)
 
         if self.model.adata.shape == (0, 0):
             return
@@ -418,9 +423,13 @@ def _update_adata(self) -> None:
             )
             layer.metadata["adata"] = table
 
-        if layer is not None and "adata" in layer.metadata:
-            with self.model.events.adata.blocker():
-                self.model.adata = layer.metadata["adata"]
+        if layer is not None:
+            if "adata" in layer.metadata:
+                with self.model.events.adata.blocker():
+                    self.model.adata = layer.metadata["adata"]
+            else:
+                with self.model.events.adata.blocker():
+                    self.model.adata = None
 
         if self.model.adata.shape == (0, 0):
             return
@@ -440,10 +449,12 @@ def _update_adata(self) -> None:
             return
 
     def _get_adata_layer(self) -> Sequence[str | None]:
+        if self.model.adata is None:
+            return [None]
         adata_layers = list(self.model.adata.layers.keys())
-        if len(adata_layers):
-            return adata_layers
-        return [None]
+        if len(adata_layers) == 0:
+            return [None]
+        return adata_layers
 
     def _change_color_by(self) -> None:
         self.color_by.setText(f"Color by: {self.model.color_by}")

src/napari_spatialdata/_viewer.py

@@ -17,6 +17,7 @@
 from shapely import Polygon
 from spatialdata import get_element_annotators, get_element_instances
 from spatialdata._core.query.relational_query import _left_join_spatialelement_table
+from spatialdata._types import ArrayLike
 from spatialdata.models import PointsModel, ShapesModel, TableModel, force_2d, get_channels
 from spatialdata.transformations import Affine, Identity
 from spatialdata.transformations._utils import scale_radii
@@ -162,13 +163,13 @@ def _write_element_to_disk(
         element: tuple[DaskDataFrame | GeoDataFrame | AnnData],
         overwrite: bool,
     ) -> None:
-        if sdata.is_backed:
-            self._delete_from_disk(sdata, element_name, overwrite)
-            sdata[element_name] = element
-            sdata.write_element(element_name)
-        else:
-            sdata[element_name] = element
-            logger.warning("Spatialdata object is not stored on disk, could only add element in memory.")
+        # if sdata.is_backed:
+        #     self._delete_from_disk(sdata, element_name, overwrite)
+        #     sdata[element_name] = element
+        #     sdata.write_element(element_name)
+        # else:
+        sdata[element_name] = element
+        logger.warning("Annotations only added in memory, please manually save to disk.")
 
     def _save_points_to_sdata(
         self, layer_to_save: Points, spatial_element_name: str | None, overwrite: bool
@@ -188,6 +189,8 @@ def _save_points_to_sdata(
             swap_data = swap_data[:, :2]
         parsed = PointsModel.parse(swap_data, transformations=transformation)
 
+        # saving to disk of points temporarily disabled until the interface update that will unify the view widget,
+        # annotation widget and scatterplot widget
         self._write_element_to_disk(sdata, spatial_element_name, parsed, overwrite)
 
         return parsed, coordinate_system
@@ -248,7 +251,18 @@ def _save_shapes_to_sdata(
         if len(layer_to_save.data) == 0:
             raise ValueError("Cannot export a shapes element with no shapes")
 
-        polygons: list[Polygon] = [Polygon(i) for i in _transform_coordinates(layer_to_save.data, f=lambda x: x[::-1])]
+        coords = [
+            np.array([layer_to_save.data_to_world(xy) for xy in shape._data])
+            for shape in layer_to_save._data_view.shapes
+        ]
+
+        def _fix_coords(coords: ArrayLike) -> ArrayLike:
+            remove_z = coords.shape[1] == 3
+            first_index = 1 if remove_z else 0
+            coords = coords[:, first_index::]
+            return np.fliplr(coords)
+
+        polygons: list[Polygon] = [Polygon(_fix_coords(p)) for p in coords]
         gdf = GeoDataFrame({"geometry": polygons})
 
         force_2d(gdf)
@@ -600,6 +614,7 @@ def get_sdata_shapes(self, sdata: SpatialData, key: str, selected_cs: str, multi
             name=key,
             affine=affine,
             shape_type="polygon",
+            face_color="#00000000",
             metadata={
                 "sdata": sdata,
                 "adata": adata,

src/napari_spatialdata/_widgets.py

@@ -135,6 +135,7 @@ def _onAction(self, items: Iterable[str]) -> None:
                         self.model.layer.text = None  # needed because of the text-feature order of updates
                         # self.model.layer.features = properties.get("features", None)
                         self.model.layer.face_color = properties["face_color"]
+                        # self.model.layer.edge_color = properties["face_color"]
                         self.model.layer.text = properties["text"]
                     elif isinstance(self.model.layer, Labels):
                         version = get_napari_version()
@@ -226,7 +227,7 @@ def _(self, vec: pd.Series, **kwargs: Any) -> dict[str, Any]:
                         f"The {vec_color_name} column must have unique values for the each {vec.name} level. Found:\n"
                         f"{unique_colors}"
                     )
-                color_dict = unique_colors.to_dict()["genes_color"]
+                color_dict = unique_colors.to_dict()[f"{vec.name}_color"]
 
         if self.model.instance_key is not None and self.model.instance_key == vec.index.name:
             merge_df = pd.merge(

src/napari_spatialdata/utils/_utils.py

@@ -419,7 +419,7 @@ def get_itemindex_by_text(
     return widget_item
 
 
-def _get_init_table_list(layer: Layer) -> Sequence[str | None] | None:
+def _get_init_table_list(layer: Layer | None) -> Sequence[str | None] | None:
     """
     Get the table names annotating the SpatialElement upon creating the napari layer.
 
@@ -432,6 +432,8 @@ def _get_init_table_list(layer: Layer) -> Sequence[str | None] | None:
     ------
     The list of table names annotating the SpatialElement if any.
     """
+    if layer is None:
+        return None
     table_names: Sequence[str | None] | None
     if table_names := layer.metadata.get("table_names"):
         return table_names  # type: ignore[no-any-return]