Labels support for 0.4.19, points support for > 0.4.19

setup.cfg

@@ -36,11 +36,11 @@ install_requires =
     anndata
     click
     cycler
-    dask
+    dask<=2024.2.1
     geopandas
     loguru
     matplotlib
-    napari>=0.4.19
+    napari>=0.4.19.post1
     napari-matplotlib
     numba
     numpy

src/napari_spatialdata/_model.py

@@ -85,11 +85,12 @@ def get_obs(
         if name not in self.adata.obs.columns:
             raise KeyError(f"Key `{name}` not found in `adata.obs`.")
         if name != self.instance_key:
-            adata_obs = self.adata.obs[[self.instance_key, name]]
-            adata_obs.set_index(self.instance_key, inplace=True)
+            obs_column = self.adata.obs[[self.instance_key, name]]
+            obs_column = obs_column.set_index(self.instance_key)[name]
         else:
-            adata_obs = self.adata.obs
-        return adata_obs[name], self._format_key(name)
+            obs_column = self.adata.obs[name].copy()
+            obs_column.index = self.adata.obs[self.instance_key]
+        return obs_column, self._format_key(name)
 
     @_ensure_dense_vector
     def get_columns_df(self, name: Union[str, int], **_: Any) -> Tuple[Optional[NDArrayA], str]:

src/napari_spatialdata/_viewer.py

@@ -4,6 +4,7 @@
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
+import packaging.version
 from anndata import AnnData
 from dask.dataframe.core import DataFrame as DaskDataFrame
 from geopandas import GeoDataFrame
@@ -30,6 +31,7 @@
     _get_transform,
     _transform_coordinates,
     get_duplicate_element_names,
+    get_napari_version,
 )
 from napari_spatialdata.utils._viewer_utils import _get_polygons_properties
 
@@ -372,29 +374,36 @@ def add_sdata_circles(self, sdata: SpatialData, key: str, selected_cs: str, mult
         }
 
         CIRCLES_AS_POINTS = True
+        version = get_napari_version()
+        kwargs: dict[str, Any] = (
+            {"edge_width": 0.0} if version <= packaging.version.parse("0.4.20") else {"border_width": 0.0}
+        )
         if CIRCLES_AS_POINTS:
             layer = self.viewer.add_points(
                 yx,
                 name=key,
                 affine=affine,
                 size=1,  # the sise doesn't matter here since it will be adjusted in _adjust_radii_of_points_layer
-                edge_width=0.0,
                 metadata=metadata,
+                **kwargs,
             )
             assert affine is not None
             self._adjust_radii_of_points_layer(layer=layer, affine=affine)
         else:
+            if version <= packaging.version.parse("0.4.20"):
+                kwargs |= {"edge_color": "white"}
+            else:
+                kwargs |= {"border_color": "white"}
             # useful code to have readily available to debug the correct radius of circles when represented as points
             ellipses = _get_ellipses_from_circles(yx=yx, radii=radii)
             self.viewer.add_shapes(
                 ellipses,
                 shape_type="ellipse",
                 name=key,
-                edge_color="white",
                 face_color="white",
-                edge_width=0.0,
                 affine=affine,
                 metadata=metadata,
+                **kwargs,
             )
 
     def add_sdata_shapes(self, sdata: SpatialData, key: str, selected_cs: str, multi: bool) -> None:
@@ -539,12 +548,13 @@ def add_sdata_points(self, sdata: SpatialData, key: str, selected_cs: str, multi
         np.fliplr(xy)
         # radii_size = _calc_default_radii(self.viewer, sdata, selected_cs)
         radii_size = 3
+        version = get_napari_version()
+        kwargs = {"edge_width": 0.0} if version <= packaging.version.parse("0.4.20") else {"border_width": 0.0}
         layer = self.viewer.add_points(
             xy,
             name=key,
             size=radii_size * 2,
             affine=affine,
-            edge_width=0.0,
             metadata={
                 "sdata": sdata,
                 "adata": adata,
@@ -562,6 +572,7 @@ def add_sdata_points(self, sdata: SpatialData, key: str, selected_cs: str, multi
                     else None
                 ),
             },
+            **kwargs,
         )
         assert affine is not None
         self._adjust_radii_of_points_layer(layer=layer, affine=affine)

src/napari_spatialdata/_widgets.py

@@ -1,16 +1,19 @@
 from __future__ import annotations
 
 from abc import abstractmethod
+from collections import defaultdict
 from functools import singledispatchmethod
 from typing import TYPE_CHECKING, Any, Iterable, Sequence
 
 import matplotlib.pyplot as plt
 import napari
 import numpy as np
+import packaging.version
 import pandas as pd
 from anndata import AnnData
 from loguru import logger
 from napari.layers import Labels, Points, Shapes
+from napari.utils import DirectLabelColormap
 from napari.viewer import Viewer
 from qtpy import QtCore, QtWidgets
 from qtpy.QtCore import Qt, Signal
@@ -22,10 +25,7 @@
 from vispy.scene.widgets import ColorBarWidget
 
 from napari_spatialdata._model import DataModel
-from napari_spatialdata.utils._utils import (
-    NDArrayA,
-    _min_max_norm,
-)
+from napari_spatialdata.utils._utils import NDArrayA, _min_max_norm, get_napari_version
 
 __all__ = [
     "AListWidget",
@@ -121,11 +121,7 @@ def _onChange(self) -> None:
 
     def _onAction(self, items: Iterable[str]) -> None:
         for item in sorted(set(items)):
-            try:
-                vec, name = self._getter(item, index=self.getIndex())
-            except Exception as e:  # noqa: BLE001
-                logger.error(e)
-                continue
+            vec, name = self._getter(item, index=self.getIndex())
 
             if self.model.layer is not None:
                 properties = self._get_points_properties(vec, key=item, layer=self.model.layer)
@@ -136,8 +132,14 @@ def _onAction(self, items: Iterable[str]) -> None:
                     self.model.layer.face_color = properties["face_color"]
                     self.model.layer.text = properties["text"]
                 elif isinstance(self.model.layer, Labels):
-                    self.model.layer.color = properties["color"]
-                    self.model.layer.properties = properties.get("properties", None)
+                    version = get_napari_version()
+                    if version < packaging.version.parse("0.4.20"):
+                        self.model.layer.color = properties["color"]
+                        self.model.layer.properties = properties.get("properties", None)
+                    else:
+                        ddict = defaultdict(lambda: np.zeros(4), properties["color"])
+                        cmap = DirectLabelColormap(color_dict=ddict)
+                        self.model.layer.colormap = cmap
                 else:
                     raise ValueError("TODO")
                 # TODO(michalk8): add contrasting fg/bg color once https://github.com/napari/napari/issues/2019 is done

src/napari_spatialdata/utils/_utils.py

@@ -6,6 +6,7 @@
 from typing import TYPE_CHECKING, Any, Callable, Iterable, Optional, Sequence, Union
 
 import numpy as np
+import packaging.version
 import pandas as pd
 from anndata import AnnData
 from dask.dataframe.core import DataFrame as DaskDataFrame
@@ -14,6 +15,7 @@
 from loguru import logger
 from matplotlib.colors import is_color_like, to_rgb
 from multiscale_spatial_image.multiscale_spatial_image import MultiscaleSpatialImage
+from napari import __version__
 from napari.layers import Layer
 from numba import njit, prange
 from pandas.api.types import CategoricalDtype, infer_dtype
@@ -86,7 +88,7 @@ def decorator(self: Any, *args: Any, **kwargs: Any) -> Vector_name_t:
         elif not isinstance(res, (np.ndarray, Sequence)):
             raise TypeError(f"Unable to process result of type `{type(res).__name__}`.")
 
-        res = np.asarray(np.squeeze(res))
+        res = np.atleast_1d(np.squeeze(res))
         if res.ndim != 1:
             raise ValueError(f"Expected 1-dimensional array, found `{res.ndim}`.")
 
@@ -483,3 +485,7 @@ def _get_ellipses_from_circles(yx: NDArrayA, radii: NDArrayA) -> NDArrayA:
     ellipses = np.stack([lower_left, lower_right, upper_right, upper_left], axis=1)
     assert isinstance(ellipses, np.ndarray)
     return ellipses
+
+
+def get_napari_version() -> packaging.version.Version:
+    return packaging.version.parse(__version__)

tests/test_viewer.py

@@ -84,6 +84,7 @@ def test_layer_transform(qtbot, make_napari_viewer: any):
 
     assert np.array_equal(viewer.layers[0].affine.affine_matrix, affine_transform)
     assert np.array_equal(viewer.layers[1].affine.affine_matrix, no_transform)
+    viewer.close()
 
 
 def test_adata_metadata(qtbot, make_napari_viewer: any):