From 3dc4e5b354288de248a59bb6801659ad4a5d4061 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Wed, 25 Sep 2024 11:39:49 +0300
Subject: [PATCH 1/7] Fix bug adata in model not being reset (#317)

* fix bug adata in model not being reset

* changelog
---
 CHANGELOG.md                           |  4 +++
 src/napari_spatialdata/_view.py        | 37 +++++++++++++++++---------
 src/napari_spatialdata/_viewer.py      |  5 ++--
 src/napari_spatialdata/_widgets.py     |  2 +-
 src/napari_spatialdata/utils/_utils.py |  4 ++-
 5 files changed, 34 insertions(+), 18 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8969d730..afbc7199 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.x.x] - 2024-xx-xx
 
+### Fixed
+
+- Bug table was not reset after an element without table was added #317
+
 ## [0.5.2] - 2024-08-16
 
 ### Minor
diff --git a/src/napari_spatialdata/_view.py b/src/napari_spatialdata/_view.py
index aa6ac626..31e0fb83 100644
--- a/src/napari_spatialdata/_view.py
+++ b/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}")
diff --git a/src/napari_spatialdata/_viewer.py b/src/napari_spatialdata/_viewer.py
index 67ba4201..98dbe123 100644
--- a/src/napari_spatialdata/_viewer.py
+++ b/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
@@ -254,15 +255,13 @@ def _save_shapes_to_sdata(
             for shape in layer_to_save._data_view.shapes
         ]
 
-        def _fix_coords(coords: np.ndarray) -> np.ndarray:
+        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]
-        # polygons: list[Polygon] = [Polygon(i) for i in _transform_coordinates(coords, f=lambda x: x[::-1])]
-        # polygons: list[Polygon] = [Polygon(i) for i in _transform_coordinates(layer_to_save.data, f=lambda x: x[::-1])]
         gdf = GeoDataFrame({"geometry": polygons})
 
         force_2d(gdf)
diff --git a/src/napari_spatialdata/_widgets.py b/src/napari_spatialdata/_widgets.py
index eb18e266..b21d079a 100644
--- a/src/napari_spatialdata/_widgets.py
+++ b/src/napari_spatialdata/_widgets.py
@@ -227,7 +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(
diff --git a/src/napari_spatialdata/utils/_utils.py b/src/napari_spatialdata/utils/_utils.py
index dff137e7..56c503a5 100644
--- a/src/napari_spatialdata/utils/_utils.py
+++ b/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]

From 803c35e632eb17732c17de90d02794f5c2e6065b Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Wed, 25 Sep 2024 11:04:00 +0200
Subject: [PATCH 2/7] Update CHANGELOG.md

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index afbc7199..8dd7d896 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,11 +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
 

From 8df1eb632b4f95042ef9b31d07a4546a97e17680 Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Mon, 30 Sep 2024 14:27:26 +0200
Subject: [PATCH 3/7] fix radii of transformed circles (#318)

* fix radii of transformed circles

* fix pre-commit

* fix mypy

* remove last NDArray, replaced with ArrayLike

* removed another NDArrayA
---
 CHANGELOG.md                                |  6 ++++
 src/napari_spatialdata/_interactive.py      |  4 +--
 src/napari_spatialdata/_model.py            | 11 ++++---
 src/napari_spatialdata/_scatterwidgets.py   | 21 ++++++------
 src/napari_spatialdata/_view.py             |  2 +-
 src/napari_spatialdata/_viewer.py           |  5 +--
 src/napari_spatialdata/_widgets.py          | 20 +++++++-----
 src/napari_spatialdata/utils/_test_utils.py |  9 +++---
 src/napari_spatialdata/utils/_utils.py      | 36 ++++++++-------------
 tests/conftest.py                           |  4 +--
 tests/test_widgets.py                       | 12 +++----
 11 files changed, 65 insertions(+), 65 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8dd7d896..3a5e6320 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,12 @@ 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
 
+## [0.5.4] - 2024-xx-xx
+
+### Fixed
+
+- Bug wrong radii transformed circles (e.g. with Visium lowres)
+
 ## [0.5.3] - 2024-09-25
 
 ### Fixed
diff --git a/src/napari_spatialdata/_interactive.py b/src/napari_spatialdata/_interactive.py
index 2f8b15f2..e515bd61 100644
--- a/src/napari_spatialdata/_interactive.py
+++ b/src/napari_spatialdata/_interactive.py
@@ -4,10 +4,10 @@
 
 import napari
 from napari.utils.events import EventedList
+from spatialdata._types import ArrayLike
 
 from napari_spatialdata._sdata_widgets import SdataWidget
 from napari_spatialdata.utils._utils import (
-    NDArrayA,
     get_duplicate_element_names,
     get_elements_meta_mapping,
     get_itemindex_by_text,
@@ -97,6 +97,6 @@ def run(self) -> None:
         """Run the napari application."""
         napari.run()
 
-    def screenshot(self) -> NDArrayA | Any:
+    def screenshot(self) -> ArrayLike | Any:
         """Take a screenshot of the viewer in its current state."""
         return self._viewer.screenshot(canvas_only=False)
diff --git a/src/napari_spatialdata/_model.py b/src/napari_spatialdata/_model.py
index 6144b8ab..c7a0ca83 100644
--- a/src/napari_spatialdata/_model.py
+++ b/src/napari_spatialdata/_model.py
@@ -9,10 +9,11 @@
 from anndata import AnnData
 from napari.layers import Layer
 from napari.utils.events import EmitterGroup, Event
+from spatialdata._types import ArrayLike
 from spatialdata.models import get_table_keys
 
 from napari_spatialdata.constants._constants import Symbol
-from napari_spatialdata.utils._utils import NDArrayA, _ensure_dense_vector
+from napari_spatialdata.utils._utils import _ensure_dense_vector
 
 __all__ = ["DataModel"]
 
@@ -71,7 +72,7 @@ def get_items(self, attr: str) -> tuple[str, ...] | None:
         return None
 
     @_ensure_dense_vector
-    def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | NDArrayA | None, str]:  # TODO(giovp): fix docstring
+    def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | ArrayLike | None, str]:  # TODO(giovp): fix docstring
         """
         Return an observation.
 
@@ -95,7 +96,7 @@ def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | NDArrayA | None, str
         return obs_column, self._format_key(name)
 
     @_ensure_dense_vector
-    def get_columns_df(self, name: str | int, **_: Any) -> tuple[NDArrayA | None, str]:
+    def get_columns_df(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str]:
         """
         Return a column of the dataframe of the SpatialElement.
 
@@ -113,7 +114,7 @@ def get_columns_df(self, name: str | int, **_: Any) -> tuple[NDArrayA | None, st
         return self.layer.metadata["_columns_df"][name], self._format_key(name)
 
     @_ensure_dense_vector
-    def get_var(self, name: str | int, **_: Any) -> tuple[NDArrayA | None, str]:  # TODO(giovp): fix docstring
+    def get_var(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str]:  # TODO(giovp): fix docstring
         """
         Return a column in anndata.var_names.
 
@@ -135,7 +136,7 @@ def get_var(self, name: str | int, **_: Any) -> tuple[NDArrayA | None, str]:  #
         return self.adata._get_X(layer=self.adata_layer)[ix], self._format_key(name, adata_layer=True)
 
     @_ensure_dense_vector
-    def get_obsm(self, name: str, index: int | str = 0) -> tuple[NDArrayA | None, str]:
+    def get_obsm(self, name: str, index: int | str = 0) -> tuple[ArrayLike | None, str]:
         """
         Return a vector from :attr:`anndata.AnnData.obsm`.
 
diff --git a/src/napari_spatialdata/_scatterwidgets.py b/src/napari_spatialdata/_scatterwidgets.py
index 05885a76..4c188e79 100644
--- a/src/napari_spatialdata/_scatterwidgets.py
+++ b/src/napari_spatialdata/_scatterwidgets.py
@@ -19,12 +19,13 @@
 from pandas.api.types import CategoricalDtype
 from qtpy import QtWidgets
 from qtpy.QtCore import Signal
+from spatialdata._types import ArrayLike
 
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._widgets import AListWidget, ComponentWidget
 from napari_spatialdata.constants.config import POINT_SIZE_SCATTERPLOT_WIDGET
 from napari_spatialdata.utils._categoricals_utils import _add_categorical_legend
-from napari_spatialdata.utils._utils import NDArrayA, _get_categorical, _set_palette
+from napari_spatialdata.utils._utils import _get_categorical, _set_palette
 
 __all__ = [
     "MatplotlibWidget",
@@ -63,7 +64,7 @@ def __init__(
         model: DataModel,
         ax: Axes,
         collection: Collection,
-        data: list[NDArrayA],
+        data: list[ArrayLike],
         alpha_other: float = 0.3,
         viewer: Viewer | None = None,
     ):
@@ -89,7 +90,7 @@ def __init__(
 
         self.selector = LassoSelector(ax, onselect=self.onselect)
 
-        self.ind: NDArrayA | None = None
+        self.ind: ArrayLike | None = None
 
     def export(self, adata: AnnData) -> None:
         model_layer: Layer = self.model.layer
@@ -116,7 +117,7 @@ def export(self, adata: AnnData) -> None:
         sdata[table_name].obs[obs_name] = self.exported_data
         show_info(f"Exported selected coordinates to obs in AnnData as: {obs_name}")
 
-    def onselect(self, verts: list[NDArrayA]) -> None:
+    def onselect(self, verts: list[ArrayLike]) -> None:
         self.path = Path(verts)
         self.ind = np.nonzero(self.path.contains_points(self.xys))[0]
 
@@ -140,7 +141,7 @@ def __init__(self, model: DataModel, attr: str, color: bool, **kwargs: Any):
         AListWidget.__init__(self, None, model, attr, **kwargs)
         self.attrChanged.connect(self._onChange)
         self._color = color
-        self._data: NDArrayA | dict[str, Any] | None = None
+        self._data: ArrayLike | dict[str, Any] | None = None
         self.itemClicked.connect(lambda item: self._onOneClick((item.text(),)))
 
     def _onChange(self) -> None:
@@ -223,11 +224,11 @@ def chosen(self, chosen: str | None) -> None:
         self._chosen = chosen if chosen is not None else None
 
     @property
-    def data(self) -> NDArrayA | dict[str, Any] | None:
+    def data(self) -> ArrayLike | dict[str, Any] | None:
         return self._data
 
     @data.setter
-    def data(self, data: NDArrayA | dict[str, Any]) -> None:
+    def data(self, data: ArrayLike | dict[str, Any]) -> None:
         self._data = data
 
 
@@ -251,9 +252,9 @@ def __init__(self, viewer: Viewer | None, model: DataModel):
 
     def _onClick(
         self,
-        x_data: NDArrayA | pd.Series,
-        y_data: NDArrayA | pd.Series,
-        color_data: NDArrayA | dict[str, NDArrayA | pd.Series | dict[str, str]],
+        x_data: ArrayLike | pd.Series,
+        y_data: ArrayLike | pd.Series,
+        color_data: ArrayLike | dict[str, ArrayLike | pd.Series | dict[str, str]],
         x_label: str | None,
         y_label: str | None,
         color_label: str | None,
diff --git a/src/napari_spatialdata/_view.py b/src/napari_spatialdata/_view.py
index 31e0fb83..94c2850b 100644
--- a/src/napari_spatialdata/_view.py
+++ b/src/napari_spatialdata/_view.py
@@ -97,7 +97,7 @@ def __init__(self, napari_viewer: Viewer, model: DataModel | None = None):
             lambda: self.matplotlib_widget._onClick(
                 self.x_widget.widget.data,
                 self.y_widget.widget.data,
-                self.color_widget.widget.data,  # type:ignore[arg-type]
+                self.color_widget.widget.data,
                 self.x_widget.getFormattedLabel(),
                 self.y_widget.getFormattedLabel(),
                 self.color_widget.getFormattedLabel(),
diff --git a/src/napari_spatialdata/_viewer.py b/src/napari_spatialdata/_viewer.py
index 98dbe123..1cf6c62e 100644
--- a/src/napari_spatialdata/_viewer.py
+++ b/src/napari_spatialdata/_viewer.py
@@ -20,7 +20,6 @@
 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
 
 from napari_spatialdata._model import DataModel
 from napari_spatialdata.constants import config
@@ -741,8 +740,6 @@ def _adjust_radii_of_points_layer(self, layer: Layer, affine: npt.ArrayLike) ->
             raise ValueError(f"Invalid affine shape: {affine.shape}")
         affine_transformation = Affine(affine, input_axes=axes, output_axes=axes)
 
-        new_radii = scale_radii(radii=radii, affine=affine_transformation, axes=axes)
-
         # the points size is the diameter, in "data pixels" of the current coordinate system, so we need to scale by
         # scale factor of the affine transformation. This scale factor is an approximation when the affine
         # transformation is anisotropic.
@@ -751,7 +748,7 @@ def _adjust_radii_of_points_layer(self, layer: Layer, affine: npt.ArrayLike) ->
         modules = np.absolute(eigenvalues)
         scale_factor = np.mean(modules)
 
-        layer.size = 2 * new_radii / scale_factor
+        layer.size = 2 * radii * scale_factor
 
     def _affine_transform_layers(self, coordinate_system: str) -> None:
         for layer in self.viewer.layers:
diff --git a/src/napari_spatialdata/_widgets.py b/src/napari_spatialdata/_widgets.py
index b21d079a..87daf177 100644
--- a/src/napari_spatialdata/_widgets.py
+++ b/src/napari_spatialdata/_widgets.py
@@ -20,13 +20,14 @@
 from qtpy.QtCore import Qt, Signal
 from scanpy.plotting._utils import _set_colors_for_categorical_obs
 from sklearn.preprocessing import MinMaxScaler
+from spatialdata._types import ArrayLike
 from superqt import QRangeSlider
 from vispy import scene
 from vispy.color.colormap import Colormap, MatplotlibColormap
 from vispy.scene.widgets import ColorBarWidget
 
 from napari_spatialdata._model import DataModel
-from napari_spatialdata.utils._utils import NDArrayA, _min_max_norm, get_napari_version
+from napari_spatialdata.utils._utils import _min_max_norm, get_napari_version
 
 __all__ = [
     "AListWidget",
@@ -188,7 +189,7 @@ def _handle_already_present(self, layer_name: str) -> None:
         self.viewer.layers.selection.select_only(self.viewer.layers[layer_name])
 
     @singledispatchmethod
-    def _get_points_properties(self, vec: NDArrayA | pd.Series, **kwargs: Any) -> dict[str, Any]:
+    def _get_points_properties(self, vec: ArrayLike | pd.Series, **kwargs: Any) -> dict[str, Any]:
         raise NotImplementedError(type(vec))
 
     @_get_points_properties.register(pd.Series)
@@ -252,7 +253,7 @@ def _(self, vec: pd.Series, **kwargs: Any) -> dict[str, Any]:
         }
 
     @_get_points_properties.register(np.ndarray)
-    def _(self, vec: NDArrayA, **kwargs: Any) -> dict[str, Any]:
+    def _(self, vec: ArrayLike, **kwargs: Any) -> dict[str, Any]:
         layer = kwargs.pop("layer", None)
 
         # Here kwargs['key'] is actually the column name.
@@ -271,9 +272,9 @@ def _(self, vec: NDArrayA, **kwargs: Any) -> dict[str, Any]:
             layer_meta = self.model.layer.metadata if self.model.layer is not None else None
             element_indices = pd.Series(layer_meta["indices"], name="element_indices")
             if isinstance(layer, Labels):
-                vec = vec.drop(index=0) if 0 in vec.index else vec  # type:ignore[attr-defined]
+                vec = vec.drop(index=0) if 0 in vec.index else vec
             # element_indices = element_indices[element_indices != 0]
-            diff_element_table = set(element_indices).difference(set(vec.index))  # type:ignore[attr-defined]
+            diff_element_table = set(element_indices).difference(set(vec.index))
             merge_vec = pd.merge(element_indices, vec, left_on="element_indices", right_index=True, how="left")[
                 "vec"
             ].fillna(0, axis=0)
@@ -541,7 +542,10 @@ def _onValueChange(self, percentile: tuple[float, float]) -> None:
         if "data" not in layer.metadata:
             return None  # noqa: RET501
         v = layer.metadata["data"]
-        clipped = np.clip(v, *np.percentile(v, percentile))
+        # this code is currently not used since the slider is not enabled; so I silenced the mypy error; 2. there is a
+        # mismatch for this error with the mypy in the CI, so I silenced the unused-ignore from the local mypy.
+        # when this code is re-enabled, let's fix mypy
+        clipped = np.clip(v, *np.percentile(v, percentile))  # type: ignore[misc,unused-ignore]
 
         if isinstance(layer, Points):
             layer.metadata = {**layer.metadata, "perc": percentile}
@@ -559,7 +563,7 @@ def _onValueChange(self, percentile: tuple[float, float]) -> None:
         self._colorbar.setClim((np.min(layer.properties["value"]), np.max(layer.properties["value"])))
         self._colorbar.update_color()
 
-    def _scale_vec(self, vec: NDArrayA) -> NDArrayA:
+    def _scale_vec(self, vec: ArrayLike) -> ArrayLike:
         ominn, omaxx = self._colorbar.getOclim()
         delta = omaxx - ominn + 1e-12
 
@@ -567,7 +571,7 @@ def _scale_vec(self, vec: NDArrayA) -> NDArrayA:
         minn = (minn - ominn) / delta
         maxx = (maxx - ominn) / delta
         scaler = MinMaxScaler(feature_range=(minn, maxx))
-        return scaler.fit_transform(vec.reshape(-1, 1))  # type: ignore[no-any-return]
+        return scaler.fit_transform(vec.reshape(-1, 1))
 
     @property
     def viewer(self) -> napari.Viewer:
diff --git a/src/napari_spatialdata/utils/_test_utils.py b/src/napari_spatialdata/utils/_test_utils.py
index cf9681c7..64242c8b 100644
--- a/src/napari_spatialdata/utils/_test_utils.py
+++ b/src/napari_spatialdata/utils/_test_utils.py
@@ -12,8 +12,7 @@
 import napari
 from loguru import logger
 from PIL import Image
-
-from napari_spatialdata.utils._utils import NDArrayA
+from spatialdata._types import ArrayLike
 
 
 def get_center_pos_listitem(widget: QListWidget, text: str) -> QPoint:
@@ -72,7 +71,7 @@ def click_list_widget_item(
             raise ValueError(f"{click} is not a valid click")
 
 
-def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> NDArrayA | Any:
+def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> ArrayLike | Any:
     """Take screenshot of the Napari viewer.
 
     Parameters
@@ -84,7 +83,7 @@ def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> NDArray
 
     Returns
     -------
-    The screenshot as an NDArray
+    The screenshot as an array.
     """
     logger.info("Taking screenshot of viewer")
     # to distinguish between the black of the image background and the black of the napari background (now white)
@@ -98,7 +97,7 @@ def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> NDArray
     return interactive_screenshot
 
 
-def save_image(image_np: NDArrayA, file_path: str) -> None:
+def save_image(image_np: ArrayLike, file_path: str) -> None:
     """Save image to file.
 
     Parameters
diff --git a/src/napari_spatialdata/utils/_utils.py b/src/napari_spatialdata/utils/_utils.py
index 56c503a5..74d583af 100644
--- a/src/napari_spatialdata/utils/_utils.py
+++ b/src/napari_spatialdata/utils/_utils.py
@@ -47,16 +47,9 @@
 
     from napari_spatialdata._sdata_widgets import CoordinateSystemWidget, ElementWidget
 
-try:
-    from numpy.typing import NDArray
+from spatialdata._types import ArrayLike
 
-    NDArrayA = NDArray[Any]
-except (ImportError, TypeError):
-    NDArray = np.ndarray  # type: ignore[misc]
-    NDArrayA = np.ndarray  # type: ignore[misc]
-
-
-Vector_name_t = tuple[Optional[Union[pd.Series, NDArrayA]], Optional[str]]
+Vector_name_t = tuple[Optional[Union[pd.Series, ArrayLike]], Optional[str]]
 
 
 def _ensure_dense_vector(fn: Callable[..., Vector_name_t]) -> Callable[..., Vector_name_t]:
@@ -137,7 +130,7 @@ def _get_categorical(
     vec: pd.Series | None = None,
     palette: str | None = None,
     colordict: pd.Series | dict[Any, Any] | None = None,
-) -> NDArrayA:
+) -> ArrayLike:
     categorical = vec if vec is not None else adata.obs[key]
     if not isinstance(colordict, dict):
         col_dict = _set_palette(adata, key, palette, colordict)
@@ -155,7 +148,7 @@ def _get_categorical(
     return np.array([col_dict[v] for v in categorical])
 
 
-def _position_cluster_labels(coords: NDArrayA, clusters: pd.Series) -> dict[str, NDArrayA]:
+def _position_cluster_labels(coords: ArrayLike, clusters: pd.Series) -> dict[str, ArrayLike]:
     if clusters is not None and not isinstance(clusters.dtype, pd.CategoricalDtype):
         raise TypeError(f"Expected `clusters` to be `categorical`, found `{infer_dtype(clusters)}`.")
     coords = coords[:, 1:]
@@ -170,7 +163,7 @@ def _position_cluster_labels(coords: NDArrayA, clusters: pd.Series) -> dict[str,
     return {"clusters": clusters}
 
 
-def _min_max_norm(vec: spmatrix | NDArrayA) -> NDArrayA:
+def _min_max_norm(vec: spmatrix | ArrayLike) -> ArrayLike:
     if issparse(vec):
         if TYPE_CHECKING:
             assert isinstance(vec, spmatrix)
@@ -179,18 +172,17 @@ def _min_max_norm(vec: spmatrix | NDArrayA) -> NDArrayA:
     if vec.ndim != 1:
         raise ValueError(f"Expected `1` dimension, found `{vec.ndim}`.")
 
-    maxx, minn = np.nanmax(vec), np.nanmin(vec)
+    maxx: ArrayLike = np.nanmax(vec)
+    minn: ArrayLike = np.nanmin(vec)
 
-    return (  # type: ignore[no-any-return]
-        np.ones_like(vec) if np.isclose(minn, maxx) else ((vec - minn) / (maxx - minn))
-    )
+    return np.ones_like(vec) if np.isclose(minn, maxx) else ((vec - minn) / (maxx - minn))
 
 
 def _transform_coordinates(data: list[Any], f: Callable[..., Any]) -> list[Any]:
     return [[f(xy) for xy in sublist] for sublist in data]
 
 
-def _get_transform(element: SpatialElement, coordinate_system_name: str | None = None) -> None | NDArrayA:
+def _get_transform(element: SpatialElement, coordinate_system_name: str | None = None) -> None | ArrayLike:
     if not isinstance(element, (DataArray, DataTree, DaskDataFrame, GeoDataFrame)):
         raise RuntimeError("Cannot get transform for {type(element)}")
 
@@ -198,12 +190,12 @@ def _get_transform(element: SpatialElement, coordinate_system_name: str | None =
     cs = transformations.keys().__iter__().__next__() if coordinate_system_name is None else coordinate_system_name
     ct = transformations.get(cs)
     if ct:
-        return ct.to_affine_matrix(input_axes=("y", "x"), output_axes=("y", "x"))  # type: ignore
+        return ct.to_affine_matrix(input_axes=("y", "x"), output_axes=("y", "x"))
     return None
 
 
 @njit(cache=True, fastmath=True)
-def _point_inside_triangles(triangles: NDArrayA) -> np.bool_:
+def _point_inside_triangles(triangles: ArrayLike) -> np.bool_:
     # modified from napari
     AB = triangles[:, 1, :] - triangles[:, 0, :]
     AC = triangles[:, 2, :] - triangles[:, 0, :]
@@ -217,7 +209,7 @@ def _point_inside_triangles(triangles: NDArrayA) -> np.bool_:
 
 
 @njit(parallel=True)
-def _points_inside_triangles(points: NDArrayA, triangles: NDArrayA) -> NDArrayA:
+def _points_inside_triangles(points: ArrayLike, triangles: ArrayLike) -> ArrayLike:
     out = np.empty(
         len(
             points,
@@ -459,7 +451,7 @@ def generate_random_color_hex() -> str:
     return f"#{randint(0, 255):02x}{randint(0, 255):02x}{randint(0, 255):02x}ff"
 
 
-def _get_ellipses_from_circles(yx: NDArrayA, radii: NDArrayA) -> NDArrayA:
+def _get_ellipses_from_circles(yx: ArrayLike, radii: ArrayLike) -> ArrayLike:
     """Convert circles to ellipses.
 
     Parameters
@@ -471,7 +463,7 @@ def _get_ellipses_from_circles(yx: NDArrayA, radii: NDArrayA) -> NDArrayA:
 
     Returns
     -------
-    NDArrayA
+    ArrayLike
         Ellipses.
     """
     ndim = yx.shape[1]
diff --git a/tests/conftest.py b/tests/conftest.py
index 77bf8024..de7732de 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -13,10 +13,10 @@
 from loguru import logger
 from matplotlib.testing.compare import compare_images
 from napari_spatialdata.utils._test_utils import save_image, take_screenshot
-from napari_spatialdata.utils._utils import NDArrayA
 from scipy import ndimage as ndi
 from skimage import data
 from spatialdata import SpatialData
+from spatialdata._types import ArrayLike
 from spatialdata.datasets import blobs
 
 HERE: Path = Path(__file__).parent
@@ -118,7 +118,7 @@ def labels():
     return blobs
 
 
-def _get_blobs_galaxy() -> tuple[NDArrayA, NDArrayA]:
+def _get_blobs_galaxy() -> tuple[ArrayLike, ArrayLike]:
     blobs = data.binary_blobs(rng=SEED)
     blobs = ndi.label(blobs)[0]
     return blobs, data.hubble_deep_field()[: blobs.shape[0], : blobs.shape[0]]
diff --git a/tests/test_widgets.py b/tests/test_widgets.py
index 00ee6021..b27bb634 100644
--- a/tests/test_widgets.py
+++ b/tests/test_widgets.py
@@ -10,8 +10,8 @@
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._sdata_widgets import SdataWidget
 from napari_spatialdata._view import QtAdataScatterWidget, QtAdataViewWidget
-from napari_spatialdata.utils._utils import NDArrayA
 from spatialdata import SpatialData
+from spatialdata._types import ArrayLike
 
 
 # make_napari_viewer is a pytest fixture that returns a napari viewer object
@@ -51,7 +51,7 @@ def test_creating_widget_with_no_adata(make_napari_viewer: Any, widget: Any) ->
 def test_model(
     make_napari_viewer: Any,
     widget: Any,
-    labels: NDArrayA,
+    labels: ArrayLike,
     sdata_blobs: SpatialData,
 ) -> None:
     # make viewer and add an image layer using our fixture
@@ -121,7 +121,7 @@ def test_scatterlistwidget(
     make_napari_viewer: Any,
     widget: Any,
     adata_labels: AnnData,
-    image: NDArrayA,
+    image: ArrayLike,
     attr: str,
     item: str,
     text: Union[str, int, None],
@@ -162,7 +162,7 @@ def test_categorical_and_error(
     make_napari_viewer: Any,
     widget: Any,
     adata_labels: AnnData,
-    image: NDArrayA,
+    image: ArrayLike,
     attr: str,
     item: str,
 ) -> None:
@@ -200,7 +200,7 @@ def test_component_widget(
     make_napari_viewer: Any,
     widget: Any,
     adata_labels: AnnData,
-    image: NDArrayA,
+    image: ArrayLike,
 ) -> None:
     viewer = make_napari_viewer()
     layer_name = "labels"
@@ -243,7 +243,7 @@ def test_component_widget(
 
 
 @pytest.mark.parametrize("widget", [QtAdataViewWidget, QtAdataScatterWidget])
-def test_layer_selection(make_napari_viewer: Any, image: NDArrayA, widget: Any, sdata_blobs: SpatialData):
+def test_layer_selection(make_napari_viewer: Any, image: ArrayLike, widget: Any, sdata_blobs: SpatialData):
     viewer = make_napari_viewer()
     sdata_widget = SdataWidget(viewer, EventedList([sdata_blobs]))
     sdata_widget.viewer_model.add_sdata_labels(sdata_blobs, "blobs_labels", "global", False)

From f84b79bcbc2616ecf1736720f4ed029724b3d10c Mon Sep 17 00:00:00 2001
From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
Date: Tue, 1 Oct 2024 13:18:17 +0200
Subject: [PATCH 4/7] Fix instance id shift bug; fix obsm viz; fix background
 color labels (#320)

---
 README.md                                 |  2 +-
 docs/index.md                             |  1 +
 docs/limitations.md                       |  8 +++++
 src/napari_spatialdata/_model.py          | 38 ++++++++++++++---------
 src/napari_spatialdata/_scatterwidgets.py | 10 +++---
 src/napari_spatialdata/_widgets.py        | 22 ++++++++-----
 src/napari_spatialdata/utils/_utils.py    | 20 ++++++------
 tests/conftest.py                         | 11 +++++--
 tests/test_spatialdata.py                 |  2 +-
 tests/test_widgets.py                     |  6 ++--
 10 files changed, 75 insertions(+), 45 deletions(-)
 create mode 100644 docs/limitations.md

diff --git a/README.md b/README.md
index bcbd85c2..8ff45493 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
 
-This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [documentation](https://spatialdata.scverse.org/).
+This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
 
 ## Installation
 
diff --git a/docs/index.md b/docs/index.md
index 431a7edc..dad71f37 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,6 +9,7 @@
 api.md
 cli.md
 contributing.md
+limitations.md
 references.md
 ```
 
diff --git a/docs/limitations.md b/docs/limitations.md
new file mode 100644
index 00000000..e211ef3e
--- /dev/null
+++ b/docs/limitations.md
@@ -0,0 +1,8 @@
+# Limitations
+
+Contributions are welcomed!
+
+- On macOS, the maximum point size is constrained ([details in the Vispy issue tracker](https://github.com/vispy/vispy/issues/2078));
+  it is important to keep this in mind when zooming in on points to [explore the points property on mouse hover](https://github.com/scverse/napari-spatialdata/issues/35#issuecomment-2383792431).
+- 3D data representation is supported in `spatialdata`; 3D data visualization is supported in `napari`.
+  Still, in `napari-spatialdata` we currently don't support 3D data visualization.
diff --git a/src/napari_spatialdata/_model.py b/src/napari_spatialdata/_model.py
index c7a0ca83..835b90e3 100644
--- a/src/napari_spatialdata/_model.py
+++ b/src/napari_spatialdata/_model.py
@@ -72,7 +72,9 @@ def get_items(self, attr: str) -> tuple[str, ...] | None:
         return None
 
     @_ensure_dense_vector
-    def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | ArrayLike | None, str]:  # TODO(giovp): fix docstring
+    def get_obs(
+        self, name: str, **_: Any
+    ) -> tuple[pd.Series | ArrayLike | None, str, pd.Index]:  # TODO(giovp): fix docstring
         """
         Return an observation.
 
@@ -83,7 +85,7 @@ def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | ArrayLike | None, st
 
         Returns
         -------
-        The values and the formatted ``name``.
+        The values, the formatted ``name`` and the `instance_key` values.
         """
         if name not in self.adata.obs.columns:
             raise KeyError(f"Key `{name}` not found in `adata.obs`.")
@@ -93,10 +95,10 @@ def get_obs(self, name: str, **_: Any) -> tuple[pd.Series | ArrayLike | None, st
         else:
             obs_column = self.adata.obs[name].copy()
             obs_column.index = self.adata.obs[self.instance_key]
-        return obs_column, self._format_key(name)
+        return obs_column, self._format_key(name), obs_column.index
 
     @_ensure_dense_vector
-    def get_columns_df(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str]:
+    def get_columns_df(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str, pd.Index]:
         """
         Return a column of the dataframe of the SpatialElement.
 
@@ -107,14 +109,17 @@ def get_columns_df(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, s
 
         Returns
         -------
-        The dataframe column of interest and the formatted name of the column.
+        The dataframe column of interest, the formatted name of the column and the `instance_key` valus.
         """
         if self.layer is None:
             raise ValueError("Layer must be present")
-        return self.layer.metadata["_columns_df"][name], self._format_key(name)
+        column = self.layer.metadata["_columns_df"][name]
+        return column, self._format_key(name), column.index
 
     @_ensure_dense_vector
-    def get_var(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str]:  # TODO(giovp): fix docstring
+    def get_var(
+        self, name: str | int, **_: Any
+    ) -> tuple[ArrayLike | None, str, pd.Index]:  # TODO(giovp): fix docstring
         """
         Return a column in anndata.var_names.
 
@@ -126,17 +131,19 @@ def get_var(self, name: str | int, **_: Any) -> tuple[ArrayLike | None, str]:  #
 
         Returns
         -------
-        The values and the formatted ``name``.
+        The values, the formatted ``name`` and the `instance_key` values.
         """
         try:
             ix = self.adata._normalize_indices((slice(None), name))
         except KeyError:
             raise KeyError(f"Key `{name}` not found in `adata.var_names`.") from None
 
-        return self.adata._get_X(layer=self.adata_layer)[ix], self._format_key(name, adata_layer=True)
+        column = self.adata._get_X(layer=self.adata_layer)[ix]
+        index = self.adata.obs[[self.instance_key]].set_index(self.instance_key).index
+        return column, self._format_key(name, adata_layer=True), index
 
     @_ensure_dense_vector
-    def get_obsm(self, name: str, index: int | str = 0) -> tuple[ArrayLike | None, str]:
+    def get_obsm(self, name: str, index: int | str = 0) -> tuple[ArrayLike | None, str, pd.Index]:
         """
         Return a vector from :attr:`anndata.AnnData.obsm`.
 
@@ -149,19 +156,20 @@ def get_obsm(self, name: str, index: int | str = 0) -> tuple[ArrayLike | None, s
 
         Returns
         -------
-        The values and the formatted ``name``.
+        The values, the formatted ``name`` and the `instance_key` values.
         """
         if name not in self.adata.obsm:
             raise KeyError(f"Unable to find key `{name!r}` in `adata.obsm`.")
         res = self.adata.obsm[name]
         pretty_name = self._format_key(name, index=index)
 
+        adata_index = self.adata.obs[[self.instance_key]].set_index(self.instance_key).index
         if isinstance(res, pd.DataFrame):
             try:
                 if isinstance(index, str):
-                    return res[index], pretty_name
+                    return res[index], pretty_name, adata_index
                 if isinstance(index, int):
-                    return res.iloc[:, index], self._format_key(name, index=res.columns[index])
+                    return res.iloc[:, index], self._format_key(name, index=res.columns[index]), adata_index
             except KeyError:
                 raise KeyError(f"Key `{index}` not found in `adata.obsm[{name!r}].`") from None
 
@@ -173,8 +181,8 @@ def get_obsm(self, name: str, index: int | str = 0) -> tuple[ArrayLike | None, s
                     f"Unable to convert `{index}` to an integer when accessing `adata.obsm[{name!r}]`."
                 ) from None
         res = np.asarray(res)
-
-        return (res if res.ndim == 1 else res[:, index]), pretty_name
+        column = res if res.ndim == 1 else res[:, index]
+        return column, pretty_name, adata_index
 
     def _format_key(self, key: str | int, index: int | str | None = None, adata_layer: bool = False) -> str:
         if index is not None:
diff --git a/src/napari_spatialdata/_scatterwidgets.py b/src/napari_spatialdata/_scatterwidgets.py
index 4c188e79..1800bf25 100644
--- a/src/napari_spatialdata/_scatterwidgets.py
+++ b/src/napari_spatialdata/_scatterwidgets.py
@@ -152,11 +152,11 @@ def _onChange(self) -> None:
 
     def _onAction(self, items: Iterable[str]) -> None:
         for item in sorted(set(items)):
-            try:
-                vec, _ = self._getter(item, index=self.getIndex())
-            except Exception as e:  # noqa: BLE001
-                logger.error(e)
-                continue
+            # try:
+            vec, _, index = self._getter(item, index=self.getIndex())
+            # except Exception as e:  # noqa: BLE001
+            #     logger.error(e)
+            #     continue
             self.chosen = item
             if isinstance(vec, np.ndarray):
                 self.data = vec
diff --git a/src/napari_spatialdata/_widgets.py b/src/napari_spatialdata/_widgets.py
index 87daf177..3b07face 100644
--- a/src/napari_spatialdata/_widgets.py
+++ b/src/napari_spatialdata/_widgets.py
@@ -127,14 +127,22 @@ def _onAction(self, items: Iterable[str]) -> None:
                 i = self.model.layer.metadata["adata"].var.index.get_loc(item)
                 self.viewer.dims.set_point(0, i)
             else:
-                vec, name = self._getter(item, index=self.getIndex())
+                vec, name, index = self._getter(item, index=self.getIndex())
 
                 if self.model.layer is not None:
+                    # update the features (properties for each instance displayed on mouse hover in the bottom bar)
+                    self.getIndex()
+                    features_name = f"{item}_{self.getIndex()}" if self._attr == "obsm" else item
+                    features = pd.DataFrame({features_name: vec})
+                    # we need this secret column "index", as explained here
+                    # https://forum.image.sc/t/napari-labels-layer-properties/57649/2
+                    features["index"] = index
+                    self.model.layer.features = features
+
                     properties = self._get_points_properties(vec, key=item, layer=self.model.layer)
                     self.model.color_by = "" if self.model.system_name is None else item
                     if isinstance(self.model.layer, (Points, Shapes)):
                         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"]
@@ -200,7 +208,7 @@ def _(self, vec: pd.Series, **kwargs: Any) -> dict[str, Any]:
         if isinstance(layer, Labels):
             element_indices = element_indices[element_indices != 0]
         # When merging if the row is not present in the other table it will be nan so we can give it a default color
-        vec_color_name = vec.name + "_color"
+        vec_color_name = vec.name + "_colors"
         if self._attr != "columns_df":
             if vec_color_name not in self.model.adata.uns:
                 colorer = AnnData(shape=(len(vec), 0), obs=pd.DataFrame(index=vec.index, data={"vec": vec}))
@@ -228,7 +236,7 @@ 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()[f"{vec.name}_color"]
+                color_dict = unique_colors.to_dict()[f"{vec.name}_colors"]
 
         if self.model.instance_key is not None and self.model.instance_key == vec.index.name:
             merge_df = pd.merge(
@@ -240,7 +248,6 @@ def _(self, vec: pd.Series, **kwargs: Any) -> dict[str, Any]:
         merge_df["color"] = merge_df[vec.name].map(color_dict)
         if layer is not None and isinstance(layer, Labels):
             index_color_mapping = dict(zip(merge_df["element_indices"], merge_df["color"]))
-            index_color_mapping[0] = "#000000ff"
             return {
                 "color": index_color_mapping,
                 "properties": {"value": vec},
@@ -262,6 +269,7 @@ def _(self, vec: ArrayLike, **kwargs: Any) -> dict[str, Any]:
             (adata := self.model.adata) is not None
             and kwargs["key"] not in adata.obs.columns
             and kwargs["key"] not in adata.var.index
+            and kwargs["key"] not in adata.obsm
         ) or adata is None:
             merge_vec = layer.metadata["_columns_df"][kwargs["key"]]
             element_indices = merge_vec.index
@@ -290,8 +298,6 @@ def _(self, vec: ArrayLike, **kwargs: Any) -> dict[str, Any]:
                     element_indices_list = element_indices.to_list()
                 change_index = element_indices_list.index(i)
                 color_vec[change_index] = np.array([0.5, 0.5, 0.5, 1.0])
-            if isinstance(layer, Labels):
-                color_vec[0] = np.array([0.0, 0.0, 0.0, 1.0])
 
         if layer is not None and isinstance(layer, Labels):
             return {
@@ -441,7 +447,7 @@ def __init_UI(self) -> None:
             clim=self.getClim(),
             border_width=1.0,
             border_color="black",
-            padding=(0.33, 0.167),
+            padding=(0.3, 0.167),
             axis_ratio=0.05,
         )
 
diff --git a/src/napari_spatialdata/utils/_utils.py b/src/napari_spatialdata/utils/_utils.py
index 74d583af..f8b664c9 100644
--- a/src/napari_spatialdata/utils/_utils.py
+++ b/src/napari_spatialdata/utils/_utils.py
@@ -49,29 +49,29 @@
 
 from spatialdata._types import ArrayLike
 
-Vector_name_t = tuple[Optional[Union[pd.Series, ArrayLike]], Optional[str]]
+Vector_name_index_t = tuple[Optional[Union[pd.Series, ArrayLike]], Optional[str], Optional[pd.Index]]
 
 
-def _ensure_dense_vector(fn: Callable[..., Vector_name_t]) -> Callable[..., Vector_name_t]:
+def _ensure_dense_vector(fn: Callable[..., Vector_name_index_t]) -> Callable[..., Vector_name_index_t]:
     @wraps(fn)
-    def decorator(self: Any, *args: Any, **kwargs: Any) -> Vector_name_t:
+    def decorator(self: Any, *args: Any, **kwargs: Any) -> Vector_name_index_t:
         normalize = kwargs.pop("normalize", False)
-        res, fmt = fn(self, *args, **kwargs)
+        res, name, index = fn(self, *args, **kwargs)
         if res is None:
-            return None, None
+            return None, None, None
 
         if isinstance(res, pd.Series):
             if isinstance(res.dtype, pd.CategoricalDtype):
-                return res, fmt
+                return res, name, index
             if is_string_dtype(res) or is_object_dtype(res) or is_bool_dtype(res):
-                return res.astype("category"), fmt
+                return res.astype("category"), name, index
             if is_integer_dtype(res):
                 unique = res.unique()
                 n_uniq = len(unique)
                 if n_uniq <= 2 and (set(unique) & {0, 1}):
-                    return res.astype(bool).astype("category"), fmt
+                    return res.astype(bool).astype("category"), name, index
                 if len(unique) <= len(res) // 100:
-                    return res.astype("category"), fmt
+                    return res.astype("category"), name, index
             elif not is_numeric_dtype(res):
                 raise TypeError(f"Unable to process `pandas.Series` of type `{infer_dtype(res)}`.")
             res = res.to_numpy()
@@ -86,7 +86,7 @@ def decorator(self: Any, *args: Any, **kwargs: Any) -> Vector_name_t:
         if res.ndim != 1:
             raise ValueError(f"Expected 1-dimensional array, found `{res.ndim}`.")
 
-        return (_min_max_norm(res) if normalize else res), fmt
+        return (_min_max_norm(res) if normalize else res), name, index
 
     return decorator
 
diff --git a/tests/conftest.py b/tests/conftest.py
index de7732de..de166f82 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -18,6 +18,7 @@
 from spatialdata import SpatialData
 from spatialdata._types import ArrayLike
 from spatialdata.datasets import blobs
+from spatialdata.models import TableModel
 
 HERE: Path = Path(__file__).parent
 
@@ -42,7 +43,8 @@ def adata_labels() -> AnnData:
         {
             "a": rng.normal(size=(n_obs_labels,)),
             "categorical": pd.Categorical(rng.integers(0, 2, size=(n_obs_labels,))),
-            "cell_id": pd.Categorical(seg),
+            "cell_id": seg,
+            "region": ["labels" for _ in range(n_obs_labels)],
         },
         index=np.arange(n_obs_labels),
     )
@@ -58,7 +60,12 @@ def adata_labels() -> AnnData:
         }
     }
     obsm_labels = {"spatial": rng.integers(0, blobs.shape[0], size=(n_obs_labels, 2))}
-    return generate_adata(n_var, obs_labels, obsm_labels, uns_labels)
+    return TableModel.parse(
+        generate_adata(n_var, obs_labels, obsm_labels, uns_labels),
+        region="labels",
+        region_key="region",
+        instance_key="cell_id",
+    )
 
 
 @pytest.fixture
diff --git a/tests/test_spatialdata.py b/tests/test_spatialdata.py
index ce6d5cf7..ba17d5d1 100644
--- a/tests/test_spatialdata.py
+++ b/tests/test_spatialdata.py
@@ -73,7 +73,7 @@ def test_sdatawidget_images(make_napari_viewer: Any, blobs_extra_cs: SpatialData
     del blobs_extra_cs.images["image"]
 
 
-def test_sdatawidget_labels(make_napari_viewer: Any, blobs_extra_cs: SpatialData):
+def test_sdatawidget_labels(qtbot, make_napari_viewer: Any, blobs_extra_cs: SpatialData):
     viewer = make_napari_viewer()
     widget = SdataWidget(viewer, EventedList([blobs_extra_cs]))
     assert len(widget.viewer_model.viewer.layers) == 0
diff --git a/tests/test_widgets.py b/tests/test_widgets.py
index b27bb634..157c9f81 100644
--- a/tests/test_widgets.py
+++ b/tests/test_widgets.py
@@ -132,7 +132,7 @@ def test_scatterlistwidget(
     viewer.add_labels(
         image,
         name=layer_name,
-        metadata={"adata": adata_labels, "region_key": "cell_id"},
+        metadata={"adata": adata_labels},
     )
     model = DataModel()
     widget = widget(viewer, model)
@@ -173,7 +173,7 @@ def test_categorical_and_error(
     viewer.add_labels(
         image,
         name=layer_name,
-        metadata={"adata": adata_labels, "region_key": "cell_id"},
+        metadata={"adata": adata_labels},
     )
 
     # widget._select_layer()
@@ -208,7 +208,7 @@ def test_component_widget(
     viewer.add_labels(
         image,
         name=layer_name,
-        metadata={"adata": adata_labels, "region_key": "cell_id"},
+        metadata={"adata": adata_labels},
     )
     model = DataModel()
     widget = widget(viewer, model)

From 9b8bb4a9465c5b0ce8b1d4d69c269cd8d3f9ae37 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 2 Oct 2024 20:31:32 +0200
Subject: [PATCH 5/7] [pre-commit.ci] pre-commit autoupdate (#300)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.11.2)
- [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.7...v0.6.8)

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml                  |  4 +--
 benchmarks/benchmark_qt_widget.py        |  1 +
 docs/notebooks/mibitof_analysis.ipynb    | 21 ++++++-------
 docs/notebooks/nanostring_analysis.ipynb | 22 ++++++-------
 docs/notebooks/scatterwidget.ipynb       | 39 ++++++++++++------------
 docs/notebooks/spatialdata.ipynb         | 23 +++++++-------
 examples/spatialdata_visium.py           |  3 +-
 tests/conftest.py                        |  3 +-
 tests/test_cli.py                        |  3 +-
 tests/test_interactive.py                |  2 +-
 tests/test_scatterwidgets.py             |  1 +
 tests/test_spatialdata.py                |  9 +++---
 tests/test_utils.py                      |  3 +-
 tests/test_view.py                       |  5 +--
 tests/test_viewer.py                     |  9 +++---
 tests/test_widgets.py                    |  5 +--
 16 files changed, 82 insertions(+), 71 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 96a9f72a..899506b7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/benchmarks/benchmark_qt_widget.py b/benchmarks/benchmark_qt_widget.py
index d09973db..684e23ff 100644
--- a/benchmarks/benchmark_qt_widget.py
+++ b/benchmarks/benchmark_qt_widget.py
@@ -2,6 +2,7 @@
 from napari import Viewer
 from napari.layers import Image
 from napari.utils.events import EventedList
+
 from napari_spatialdata._sdata_widgets import SdataWidget
 
 
diff --git a/docs/notebooks/mibitof_analysis.ipynb b/docs/notebooks/mibitof_analysis.ipynb
index 624faa71..d5981515 100644
--- a/docs/notebooks/mibitof_analysis.ipynb
+++ b/docs/notebooks/mibitof_analysis.ipynb
@@ -46,12 +46,11 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
     "from spatialdata import SpatialData\n",
-    "import squidpy as sq\n",
-    "import scanpy as sc\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)"
+    "from napari_spatialdata import Interactive\n",
+    "\n",
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)"
    ]
   },
   {
@@ -205,7 +204,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -254,7 +253,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -295,7 +294,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -347,7 +346,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -398,7 +397,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -439,7 +438,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -480,7 +479,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],
diff --git a/docs/notebooks/nanostring_analysis.ipynb b/docs/notebooks/nanostring_analysis.ipynb
index 8b1ec202..3923b775 100644
--- a/docs/notebooks/nanostring_analysis.ipynb
+++ b/docs/notebooks/nanostring_analysis.ipynb
@@ -46,12 +46,12 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
-    "from spatialdata import SpatialData\n",
-    "import squidpy as sq\n",
     "import scanpy as sc\n",
+    "from spatialdata import SpatialData\n",
+    "\n",
+    "from napari_spatialdata import Interactive\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)"
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)"
    ]
   },
   {
@@ -278,7 +278,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -327,7 +327,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -390,7 +390,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -431,7 +431,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -483,7 +483,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -572,7 +572,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -613,7 +613,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],
diff --git a/docs/notebooks/scatterwidget.ipynb b/docs/notebooks/scatterwidget.ipynb
index bbe8611a..d0205346 100644
--- a/docs/notebooks/scatterwidget.ipynb
+++ b/docs/notebooks/scatterwidget.ipynb
@@ -41,12 +41,13 @@
    "cell_type": "code",
    "execution_count": 10,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "from napari_spatialdata import QtAdataScatterWidget\n",
+    "import matplotlib.pyplot as plt\n",
     "import squidpy as sq\n",
-    "import matplotlib.pyplot as plt"
-   ],
-   "outputs": []
+    "\n",
+    "from napari_spatialdata import QtAdataScatterWidget"
+   ]
   },
   {
    "attachments": {},
@@ -60,10 +61,10 @@
    "cell_type": "code",
    "execution_count": 11,
    "metadata": {},
+   "outputs": [],
    "source": [
     "adata = sq.datasets.visium_hne_adata()"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -77,10 +78,10 @@
    "cell_type": "code",
    "execution_count": 13,
    "metadata": {},
+   "outputs": [],
    "source": [
     "%gui qt5"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -94,11 +95,11 @@
    "cell_type": "code",
    "execution_count": 14,
    "metadata": {},
+   "outputs": [],
    "source": [
     "widget = QtAdataScatterWidget(adata)\n",
     "widget.show()"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -112,11 +113,11 @@
    "cell_type": "code",
    "execution_count": 15,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   },
   {
    "attachments": {},
@@ -130,21 +131,21 @@
    "cell_type": "code",
    "execution_count": 19,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 21,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   }
  ],
  "metadata": {
diff --git a/docs/notebooks/spatialdata.ipynb b/docs/notebooks/spatialdata.ipynb
index 540714a2..30dcbace 100644
--- a/docs/notebooks/spatialdata.ipynb
+++ b/docs/notebooks/spatialdata.ipynb
@@ -66,10 +66,11 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
     "from spatialdata import SpatialData\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)\n",
+    "from napari_spatialdata import Interactive\n",
+    "\n",
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)\n",
     "\n",
     "FILE_PATH = \"../../../data/cosmx/data.zarr\" # Change this\n",
     "sdata = SpatialData.read(FILE_PATH)"
@@ -156,7 +157,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -246,7 +247,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -299,7 +300,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -358,7 +359,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -401,7 +402,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -459,7 +460,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -502,7 +503,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -543,7 +544,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -584,7 +585,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],
diff --git a/examples/spatialdata_visium.py b/examples/spatialdata_visium.py
index 52e97db8..1b0cb6af 100644
--- a/examples/spatialdata_visium.py
+++ b/examples/spatialdata_visium.py
@@ -3,9 +3,10 @@
 
 # The dataset can be downloaded from https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html
 
-from napari_spatialdata import Interactive
 from spatialdata import SpatialData
 
+from napari_spatialdata import Interactive
+
 if __name__ == "__main__":
     sdata = SpatialData.read("../data/visium/data.zarr")  # Change this path!
     i = Interactive(sdata)
diff --git a/tests/conftest.py b/tests/conftest.py
index de166f82..531d8d10 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -12,7 +12,6 @@
 from anndata import AnnData
 from loguru import logger
 from matplotlib.testing.compare import compare_images
-from napari_spatialdata.utils._test_utils import save_image, take_screenshot
 from scipy import ndimage as ndi
 from skimage import data
 from spatialdata import SpatialData
@@ -20,6 +19,8 @@
 from spatialdata.datasets import blobs
 from spatialdata.models import TableModel
 
+from napari_spatialdata.utils._test_utils import save_image, take_screenshot
+
 HERE: Path = Path(__file__).parent
 
 SEED = 42
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 6f889ae5..617a122d 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -2,9 +2,10 @@
 
 from click.testing import CliRunner
 from napari.viewer import Viewer
-from napari_spatialdata.__main__ import cli
 from spatialdata.datasets import blobs
 
+from napari_spatialdata.__main__ import cli
+
 
 def test_view_exists():
     runner = CliRunner()
diff --git a/tests/test_interactive.py b/tests/test_interactive.py
index 9a465d15..88ed8d18 100644
--- a/tests/test_interactive.py
+++ b/tests/test_interactive.py
@@ -1,7 +1,7 @@
-from napari_spatialdata._interactive import Interactive
 from spatialdata import SpatialData
 from spatialdata.models import Image2DModel
 
+from napari_spatialdata._interactive import Interactive
 from tests.conftest import PlotTester, PlotTesterMeta
 
 
diff --git a/tests/test_scatterwidgets.py b/tests/test_scatterwidgets.py
index 1cbbff3e..0fe80652 100644
--- a/tests/test_scatterwidgets.py
+++ b/tests/test_scatterwidgets.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 import pandas as pd
+
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import MatplotlibWidget
 
diff --git a/tests/test_spatialdata.py b/tests/test_spatialdata.py
index ba17d5d1..18d68ce0 100644
--- a/tests/test_spatialdata.py
+++ b/tests/test_spatialdata.py
@@ -12,10 +12,6 @@
 from multiscale_spatial_image import to_multiscale
 from napari.layers import Image, Labels, Points
 from napari.utils.events import EventedList
-from napari_spatialdata import QtAdataViewWidget
-from napari_spatialdata._sdata_widgets import CoordinateSystemWidget, ElementWidget, SdataWidget
-from napari_spatialdata.constants import config
-from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
 from numpy import int64
 from spatialdata import SpatialData, deepcopy
 from spatialdata._core.query.relational_query import get_element_instances
@@ -25,6 +21,11 @@
 from spatialdata.transformations.operations import set_transformation
 from xarray import DataArray
 
+from napari_spatialdata import QtAdataViewWidget
+from napari_spatialdata._sdata_widgets import CoordinateSystemWidget, ElementWidget, SdataWidget
+from napari_spatialdata.constants import config
+from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
+
 RNG = np.random.default_rng(seed=0)
 
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index d4f16f05..428aedc5 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -4,6 +4,8 @@
 import numpy as np
 import pytest
 from anndata import AnnData
+from spatialdata.datasets import blobs
+
 from napari_spatialdata.utils._utils import (
     _adjust_channels_order,
     _get_categorical,
@@ -13,7 +15,6 @@
     _position_cluster_labels,
     _set_palette,
 )
-from spatialdata.datasets import blobs
 
 
 def test_get_categorical(adata_labels: AnnData):
diff --git a/tests/test_view.py b/tests/test_view.py
index 61b9f3d5..6d373d92 100644
--- a/tests/test_view.py
+++ b/tests/test_view.py
@@ -3,11 +3,12 @@
 import numpy as np
 import pytest
 from napari.utils.events import EventedList
+from spatialdata.datasets import blobs
+from spatialdata.transformations import Affine, set_transformation
+
 from napari_spatialdata._sdata_widgets import SdataWidget
 from napari_spatialdata._view import QtAdataViewWidget
 from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
-from spatialdata.datasets import blobs
-from spatialdata.transformations import Affine, set_transformation
 
 
 @pytest.mark.parametrize("widget", [QtAdataViewWidget])
diff --git a/tests/test_viewer.py b/tests/test_viewer.py
index d5405bc4..d66a5b7f 100644
--- a/tests/test_viewer.py
+++ b/tests/test_viewer.py
@@ -4,15 +4,16 @@
 import numpy as np
 import pytest
 from napari.utils.events import EventedList
-from napari_spatialdata import QtAdataViewWidget
-from napari_spatialdata._sdata_widgets import SdataWidget
-from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
-from napari_spatialdata.utils._utils import _get_transform
 from qtpy.QtCore import Qt
 from spatialdata.datasets import blobs
 from spatialdata.models import Image2DModel
 from spatialdata.transformations import Scale, Translation, set_transformation
 
+from napari_spatialdata import QtAdataViewWidget
+from napari_spatialdata._sdata_widgets import SdataWidget
+from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
+from napari_spatialdata.utils._utils import _get_transform
+
 sdata = blobs(extra_coord_system="space")
 
 
diff --git a/tests/test_widgets.py b/tests/test_widgets.py
index 157c9f81..82b2779d 100644
--- a/tests/test_widgets.py
+++ b/tests/test_widgets.py
@@ -7,11 +7,12 @@
 from anndata.tests.helpers import assert_equal
 from napari.layers import Image, Labels
 from napari.utils.events import EventedList
+from spatialdata import SpatialData
+from spatialdata._types import ArrayLike
+
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._sdata_widgets import SdataWidget
 from napari_spatialdata._view import QtAdataScatterWidget, QtAdataViewWidget
-from spatialdata import SpatialData
-from spatialdata._types import ArrayLike
 
 
 # make_napari_viewer is a pytest fixture that returns a napari viewer object

From 7d49c2388850b1aff7d2bac2ab1ef3f22c45b88b Mon Sep 17 00:00:00 2001
From: Grzegorz Bokota <bokota+github@gmail.com>
Date: Thu, 3 Oct 2024 18:07:11 +0200
Subject: [PATCH 6/7] Add teardown steep for example benchamark (#311)

Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>
---
 benchmarks/benchmark_qt_widget.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/benchmarks/benchmark_qt_widget.py b/benchmarks/benchmark_qt_widget.py
index 684e23ff..b3c91fec 100644
--- a/benchmarks/benchmark_qt_widget.py
+++ b/benchmarks/benchmark_qt_widget.py
@@ -18,3 +18,6 @@ def time_create_widget(self) -> None:
 
     def time_layer_added(self) -> None:
         self.viewer.add_layer(self.image)
+
+    def teardown(self) -> None:
+        self.viewer.close()

From a38e2866c9195866fecf1eca0f911d52587b163a Mon Sep 17 00:00:00 2001
From: Minh Trinh <159905267+minhtien-trinh@users.noreply.github.com>
Date: Wed, 9 Oct 2024 15:39:34 +0200
Subject: [PATCH 7/7] Add functions to interactive (#315)

* Add functions to interactive

In this commit two functions are added to the interactive class.
get_layer grabs the layer name and returns the layer if it matches the user input.
add_text_to_polygons adds annotations to the chosen polygons/shapes layer

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

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

* Add tests for new functions in interactive

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

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

* Loosen tests for interactive

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

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

* Edit interactive polygon tests to use correct example dataset

* Fix interactive test

* Fix mixed line endings

* trigger ci

* Apply suggestions from code review

improve readability

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>
Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>
---
 CHANGELOG.md                           |  7 +++++++
 src/napari_spatialdata/_interactive.py | 25 ++++++++++++++++++++++
 tests/test_interactive.py              | 29 ++++++++++++++++++++++++++
 3 files changed, 61 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3a5e6320..b2cb8710 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +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
 
+## [0.5.5] - 2024-10-07
+
+### Added
+
+- New function to grab layer by name #315 @minhtien-trinh
+- New annotation function to add text to polygons #315 @minhtien-trinh
+
 ## [0.5.4] - 2024-xx-xx
 
 ### Fixed
diff --git a/src/napari_spatialdata/_interactive.py b/src/napari_spatialdata/_interactive.py
index e515bd61..91bd5a8d 100644
--- a/src/napari_spatialdata/_interactive.py
+++ b/src/napari_spatialdata/_interactive.py
@@ -3,6 +3,7 @@
 from typing import TYPE_CHECKING, Any
 
 import napari
+from napari.layers import Image, Labels, Points, Shapes
 from napari.utils.events import EventedList
 from spatialdata._types import ArrayLike
 
@@ -100,3 +101,27 @@ def run(self) -> None:
     def screenshot(self) -> ArrayLike | Any:
         """Take a screenshot of the viewer in its current state."""
         return self._viewer.screenshot(canvas_only=False)
+
+    def get_layer(self, layer_name: str) -> Image | Labels | Points | Shapes | None:
+        """Get a layer by name."""
+        try:
+            return self._viewer.layers[layer_name]
+        except KeyError:
+            return None
+
+    def add_text_to_polygons(self, layer_name: str, text_annotations: list[str]) -> None:
+        """Add text annotations to a polygon layer."""
+        polygon_layer = self.get_layer(layer_name)
+        if not polygon_layer:
+            raise ValueError(f"Polygon layer '{layer_name}' not found.")
+        if len(text_annotations) != len(polygon_layer.data):
+            raise ValueError(
+                f"The number of text annotations must match the number of polygons. "
+                f"Polygons: {len(polygon_layer.data)}, Text: {len(text_annotations)}."
+            )
+        polygon_layer.text = {
+            "string": text_annotations,
+            "size": 10,
+            "color": "red",
+            "anchor": "center",
+        }
diff --git a/tests/test_interactive.py b/tests/test_interactive.py
index 88ed8d18..ecb74fd6 100644
--- a/tests/test_interactive.py
+++ b/tests/test_interactive.py
@@ -44,3 +44,32 @@ def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     assert i._sdata_widget.coordinate_system_widget._system == "global"
     assert i._viewer.layers[-1].visible
     i._viewer.close()
+
+
+class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
+    def test_get_layer_existing(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        i.add_element(element="blobs_image", element_coordinate_system="global")
+        layer = i.get_layer("blobs_image")
+        assert layer is not None, "Expected to retrieve the blobs_image layer, but got None"
+        assert layer.name == "blobs_image", f"Expected layer name 'blobs_image', got {layer.name}"
+        i._viewer.close()
+
+    def test_get_layer_non_existing(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        layer = i.get_layer("non_existing_layer")
+        assert layer is None, "Expected None for a non-existing layer, but got a layer"
+        i._viewer.close()
+
+    def test_add_text_to_polygons(self, sdata_blobs: SpatialData):
+        i = Interactive(sdata=sdata_blobs, headless=True)
+        i.add_element(element="blobs_polygons", element_coordinate_system="global")
+
+        # Mock polygon layer with some polygon data
+        text_annotations = ["Label 1", "Label 2", "Label 3", "Label 4", "Label 5"]
+        polygon_layer = i.get_layer("blobs_polygons")
+
+        # Verify that text is added
+        i.add_text_to_polygons(layer_name="blobs_polygons", text_annotations=text_annotations)
+        assert polygon_layer.text is not None, "Text annotations were not added to the polygon layer"
+        i._viewer.close()