Select channels

setup.cfg

@@ -37,7 +37,7 @@ install_requires =
     anndata
     click
     cycler
-    dask>=2024.4.1
+    dask>=2024.4.1,<=2024.11.2
     geopandas
     loguru
     matplotlib

src/napari_spatialdata/_view.py

@@ -41,9 +41,7 @@
 from napari_spatialdata._widgets import (
     AListWidget,
     AnnDataSaveDialog,
-    CBarWidget,
     ComponentWidget,
-    RangeSliderWidget,
     SaveDialog,
     ScatterAnnotationDialog,
 )
@@ -497,13 +495,6 @@ def __init__(self, napari_viewer: Viewer, model: DataModel | None = None) -> Non
         self.color_by = QLabel("Colored by:")
         self.layout().addWidget(self.color_by)
 
-        # scalebar
-        colorbar = CBarWidget(model=self.model)
-        self.slider = RangeSliderWidget(self.viewer, self.model, colorbar=colorbar)
-        self._viewer.window.add_dock_widget(self.slider, area="left", name="slider")
-        self._viewer.window.add_dock_widget(colorbar, area="left", name="colorbar")
-        self.viewer.layers.selection.events.active.connect(self.slider._onLayerChange)
-
         if (layer := self.viewer.layers.selection.active) is not None and layer.metadata.get("adata") is not None:
             self._on_layer_update()
 

src/napari_spatialdata/_viewer.py

@@ -29,6 +29,7 @@
     _get_ellipses_from_circles,
     _get_init_metadata_adata,
     _get_transform,
+    _obtain_channel_image,
     _transform_coordinates,
     get_duplicate_element_names,
     get_napari_version,
@@ -442,10 +443,14 @@ def clean_worker(self) -> None:
         """Clean the worker."""
         self.worker = None
 
-    def add_sdata_image(self, sdata: SpatialData, key: str, selected_cs: str, multi: bool) -> None:
-        self.add_layer(self.get_sdata_image(sdata, key, selected_cs, multi))
+    def add_sdata_image(
+        self, sdata: SpatialData, key: str, selected_cs: str, multi: bool, channel_name: str | None = None
+    ) -> None:
+        self.add_layer(self.get_sdata_image(sdata, key, selected_cs, multi, channel_name))
 
-    def get_sdata_image(self, sdata: SpatialData, key: str, selected_cs: str, multi: bool) -> Image:
+    def get_sdata_image(
+        self, sdata: SpatialData, key: str, selected_cs: str, multi: bool, channel_name: str | None = None
+    ) -> Image:
         """
         Add an image in a spatial data object to the viewer.
 
@@ -465,15 +470,20 @@ def get_sdata_image(self, sdata: SpatialData, key: str, selected_cs: str, multi:
             original_name = original_name[: original_name.rfind("_")]
 
         affine = _get_transform(sdata.images[original_name], selected_cs)
-        rgb_image, rgb = _adjust_channels_order(element=sdata.images[original_name])
+        if channel_name:
+            image = _obtain_channel_image(element=sdata.images[original_name], channel_name=channel_name)
+            rgb = False
+            key = key + f"_ch:{channel_name}"
+        else:
+            image, rgb = _adjust_channels_order(element=sdata.images[original_name])
 
         channels = ("RGB(A)",) if rgb else get_channels(sdata.images[original_name])
 
         adata = AnnData(shape=(0, len(channels)), var=pd.DataFrame(index=channels))
 
         # TODO: type check
         return Image(
-            rgb_image,
+            image,
             rgb=rgb,
             name=key,
             affine=affine,

src/napari_spatialdata/_widgets.py

@@ -19,17 +19,12 @@
 from qtpy import QtCore, QtWidgets
 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 _min_max_norm, get_napari_version
 
-__all__ = ["AListWidget", "CBarWidget", "RangeSliderWidget", "ComponentWidget"]
+__all__ = ["AListWidget", "ComponentWidget"]
 
 # label string: attribute name
 # TODO(giovp): remove since layer controls private?
@@ -409,193 +404,6 @@ def attr(self, field: str | None) -> None:
         self._attr = field
 
 
-class CBarWidget(QtWidgets.QWidget):
-    FORMAT = "{0:0.2f}"
-
-    cmapChanged = Signal(str)
-    climChanged = Signal((float, float))
-
-    def __init__(
-        self,
-        model: DataModel,
-        cmap: str = "viridis",
-        label: str | None = None,
-        width: int | None = 250,
-        height: int | None = 50,
-        **kwargs: Any,
-    ):
-        super().__init__(**kwargs)
-
-        self._model = model
-
-        self._clim = (0.0, 1.0)
-        self._oclim = self._clim
-
-        self._width = width
-        self._height = height
-        self._label = label
-
-        self.__init_UI()
-
-    def __init_UI(self) -> None:
-        self.setFixedWidth(self._width)
-        self.setFixedHeight(self._height)
-
-        # use napari's BG color for dark mode
-        self._canvas = scene.SceneCanvas(
-            size=(self._width, self._height), bgcolor="#262930", parent=self, decorate=False, resizable=False, dpi=150
-        )
-        self._colorbar = ColorBarWidget(
-            self._create_colormap(self.cmap),
-            orientation="top",
-            label=self._label,
-            label_color="white",
-            clim=self.getClim(),
-            border_width=1.0,
-            border_color="black",
-            padding=(0.3, 0.167),
-            axis_ratio=0.05,
-        )
-
-        self._canvas.central_widget.add_widget(self._colorbar)
-
-        self.climChanged.connect(self.onClimChanged)
-        self.cmapChanged.connect(self.onCmapChanged)
-
-    def _create_colormap(self, cmap: str) -> Colormap:
-        ominn, omaxx = self.getOclim()
-        delta = omaxx - ominn + 1e-12
-
-        minn, maxx = self.getClim()
-        minn = (minn - ominn) / delta
-        maxx = (maxx - ominn) / delta
-
-        assert 0 <= minn <= 1, f"Expected `min` to be in `[0, 1]`, found `{minn}`"
-        assert 0 <= maxx <= 1, f"Expected `maxx` to be in `[0, 1]`, found `{maxx}`"
-
-        cm = MatplotlibColormap(cmap)
-
-        return Colormap(cm[np.linspace(minn, maxx, len(cm.colors))], interpolation="linear")
-
-    def getCmap(self) -> str:
-        return self.cmap
-
-    def onCmapChanged(self, value: str) -> None:
-        # this does not trigger update for some reason...
-        self._colorbar.cmap = self._create_colormap(value)
-        self._colorbar._colorbar._update()
-
-    def setClim(self, value: tuple[float, float]) -> None:
-        if value == self._clim:
-            return
-
-        self._clim = value
-        self.climChanged.emit(*value)
-
-    def getClim(self) -> tuple[float, float]:
-        return self._clim
-
-    def getOclim(self) -> tuple[float, float]:
-        return self._oclim
-
-    def setOclim(self, value: tuple[float, float]) -> None:
-        # original color limit used for 0-1 normalization
-        self._oclim = value
-
-    def onClimChanged(self, minn: float, maxx: float) -> None:
-        # ticks are not working with vispy's colorbar
-        self._colorbar.cmap = self._create_colormap(self.cmap)
-        self._colorbar.clim = (self.FORMAT.format(minn), self.FORMAT.format(maxx))
-
-    def getCanvas(self) -> scene.SceneCanvas:
-        return self._canvas
-
-    def getColorBar(self) -> ColorBarWidget:
-        return self._colorbar
-
-    def setLayout(self, layout: QtWidgets.QLayout) -> None:
-        layout.addWidget(self.getCanvas().native)
-        super().setLayout(layout)
-
-    def update_color(self) -> None:
-        # when changing selected layers that have the same limit
-        # could also trigger it as self._colorbar.clim = self.getClim()
-        # but the above option also updates geometry
-        # cbarwidget->cbar->cbarvisual
-        self._colorbar._colorbar._colorbar._update()
-
-    @property
-    def cmap(self) -> str:
-        return self._model.cmap
-
-
-class RangeSliderWidget(QRangeSlider):
-    def __init__(self, viewer: Viewer, model: DataModel, colorbar: CBarWidget, **kwargs: Any):
-        super().__init__(**kwargs)
-
-        self._viewer = viewer
-        self._model = model
-        self._colorbar = colorbar
-        self._cmap = plt.get_cmap(self._colorbar.cmap)
-        self.setValue((0, 100))
-        self.setSliderPosition((0, 100))
-        self.setSingleStep(0.01)
-        self.setOrientation(Qt.Horizontal)
-        self.valueChanged.connect(self._onValueChange)
-
-    def _onLayerChange(self) -> None:
-        layer = self.viewer.layers.selection.active
-        if layer is not None:
-            self._onValueChange((0, 100))
-
-    def _onValueChange(self, percentile: tuple[float, float]) -> None:
-        layer = self.viewer.layers.selection.active
-        # TODO(michalk8): use constants
-        if "data" not in layer.metadata:
-            return None  # noqa: RET501
-        v = layer.metadata["data"]
-        # 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}
-            layer.face_color = "value"
-            layer.properties = {"value": clipped}
-            layer.refresh_colors()
-        elif isinstance(layer, Labels):
-            norm_vec = self._scale_vec(clipped)
-            color_vec = self._cmap(norm_vec)
-            layer.color = dict(zip(layer.color.keys(), color_vec, strict=False))
-            layer.properties = {"value": clipped}
-            layer.refresh()
-
-        self._colorbar.setOclim(layer.metadata["minmax"])
-        self._colorbar.setClim((np.min(layer.properties["value"]), np.max(layer.properties["value"])))
-        self._colorbar.update_color()
-
-    def _scale_vec(self, vec: ArrayLike) -> ArrayLike:
-        ominn, omaxx = self._colorbar.getOclim()
-        delta = omaxx - ominn + 1e-12
-
-        minn, maxx = self._colorbar.getClim()
-        minn = (minn - ominn) / delta
-        maxx = (maxx - ominn) / delta
-        scaler = MinMaxScaler(feature_range=(minn, maxx))
-        return scaler.fit_transform(vec.reshape(-1, 1))
-
-    @property
-    def viewer(self) -> napari.Viewer:
-        """:mod:`napari` viewer."""
-        return self._viewer
-
-    @property
-    def model(self) -> DataModel:
-        """:mod:`napari` viewer."""
-        return self._model
-
-
 class SaveDialog(QtWidgets.QDialog):
     def __init__(self, layer: Layer, table_name: str) -> None:
         super().__init__()

src/napari_spatialdata/utils/_utils.py

@@ -5,7 +5,7 @@
 from contextlib import contextmanager
 from functools import wraps
 from random import randint
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Literal, TypeVar
 
 import numpy as np
 import packaging.version
@@ -44,7 +44,7 @@
     from napari.utils.events import EventedList
     from qtpy.QtWidgets import QListWidgetItem
 
-    from napari_spatialdata._sdata_widgets import CoordinateSystemWidget, ElementWidget
+    from napari_spatialdata._sdata_widgets import ListWidget
 
 from spatialdata._types import ArrayLike
 
@@ -221,6 +221,31 @@
     return out
 
 
+def _datatree_to_dataarray_list(new_raster: DataArray | DataTree) -> DataArray | list[DataArray]:
+    if isinstance(new_raster, DataTree):
+        list_of_xdata = []
+        for k in new_raster:
+            v = new_raster[k].values()
+            assert len(v) == 1
+            xdata = v.__iter__().__next__()
+            list_of_xdata.append(xdata)
+        return list_of_xdata
+    return new_raster
+
+
+def _obtain_channel_image(element: DataArray | DataTree, channel_name: str | int) -> DataArray | list[DataArray]:
+    is_multiscale_int_ch = isinstance(element, DataTree) and np.issubdtype(
+        element["scale0"].c.to_numpy().dtype, np.integer
+    )
+    is_int_ch = isinstance(element, DataArray) and np.issubdtype(element.c.to_numpy().dtype, np.integer)
+    if isinstance(channel_name, str) and (is_multiscale_int_ch or is_int_ch):
+        channel_name = int(channel_name)
+
+    # works for both DataArray and DataTree
+    new_raster = element.sel(c=channel_name)
+    return _datatree_to_dataarray_list(new_raster)
+
+
 def _adjust_channels_order(element: DataArray | DataTree) -> tuple[DataArray | list[DataArray], bool]:
     """Swap the axes to y, x, c and check if an image supports rgb(a) visualization.
 
@@ -264,14 +289,7 @@
         rgb = False
         new_raster = element
 
-    if isinstance(new_raster, DataTree):
-        list_of_xdata = []
-        for k in new_raster:
-            v = new_raster[k].values()
-            assert len(v) == 1
-            xdata = v.__iter__().__next__()
-            list_of_xdata.append(xdata)
-        new_raster = list_of_xdata
+    new_raster = _datatree_to_dataarray_list(new_raster)
 
     return new_raster, rgb
 
@@ -387,9 +405,7 @@
     return adata
 
 
-def get_itemindex_by_text(
-    list_widget: CoordinateSystemWidget | ElementWidget, item_text: str
-) -> None | QListWidgetItem:
+def get_itemindex_by_text(list_widget: ListWidget, item_text: str) -> None | QListWidgetItem:
     """
     Get the item in a listwidget based on its text.
 
@@ -493,3 +509,7 @@
         yield
     finally:
         widget.blockSignals(False)
+
+
+WidgetType = Literal["coordinate_system", "element", "channel"]
+F = TypeVar("F", bound=Callable[..., Any])