feat: RGB support

examples/rgb.py

@@ -0,0 +1,16 @@
+import math
+
+import numpy
+
+import ndv
+
+img = numpy.zeros((256, 256, 4), dtype=numpy.uint8)
+
+for x in range(256):
+    for y in range(256):
+        img[x, y, 0] = x
+        img[x, y, 1] = y
+        img[x, y, 2] = 255 - x
+        img[x, y, 3] = int(math.sqrt((x - 128) ** 2 + (y - 128) ** 2))
+
+n = ndv.imshow(img)

src/ndv/util.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import sys
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any
 
 from qtpy.QtWidgets import QApplication
 
@@ -12,14 +12,16 @@
 if TYPE_CHECKING:
     from qtpy.QtCore import QCoreApplication
 
+    from .viewer._components import ChannelMode
     from .viewer._data_wrapper import DataWrapper
+    from .viewer._viewer import ChannelModeStr
 
 
 def imshow(
     data: Any | DataWrapper,
     cmap: Any | None = None,
     *,
-    channel_mode: Literal["mono", "composite", "auto"] = "auto",
+    channel_mode: ChannelModeStr | ChannelMode = "auto",
 ) -> NDViewer:
     """Display an array or DataWrapper in a new NDViewer window.
 
@@ -29,7 +31,7 @@ def imshow(
         The data to be displayed. If not a DataWrapper, it will be wrapped in one.
     cmap : Any | None, optional
         The colormap(s) to use for displaying the data.
-    channel_mode : Literal['mono', 'composite'], optional
+    channel_mode : Literal['mono', 'composite', 'rgb', 'rgba', 'auto'], optional
         The initial mode for displaying the channels. By default "mono" will be
         used unless a cmap is provided, in which case "composite" will be used.
 
@@ -39,12 +41,8 @@ def imshow(
         The viewer window.
     """
     app, should_exec = _get_app()
-    if cmap is not None:
-        channel_mode = "composite"
-        if not isinstance(cmap, (list, tuple)):
-            cmap = [cmap]
-    elif channel_mode == "auto":
-        channel_mode = "mono"
+    if cmap is not None and not isinstance(cmap, (list, tuple)):
+        cmap = [cmap]
     viewer = NDViewer(data, colormaps=cmap, channel_mode=channel_mode)
     viewer.show()
     viewer.raise_()

src/ndv/viewer/_backends/_pygfx.py

@@ -32,20 +32,31 @@
     )
 
 
+# TODO Combine with similar function in _vispy.py
+def _coerce_rgb(data: np.ndarray | None) -> np.ndarray | None:
+    if data is not None and data.ndim == 3:
+        # PyGFX expects (A)RGB data to be X, Y, C
+        for i, s in enumerate(data.shape):
+            if s in [3, 4]:
+                return np.moveaxis(data, i, -1)
+    return data
+
+
 class PyGFXImageHandle:
     def __init__(self, image: pygfx.Image | pygfx.Volume, render: Callable) -> None:
         self._image = image
         self._render = render
         self._grid = cast("Texture", image.geometry.grid)
         self._material = cast("ImageBasicMaterial", image.material)
+        self._cmap = cmap.Colormap("gray")
 
     @property
     def data(self) -> np.ndarray:
         return self._grid.data  # type: ignore [no-any-return]
 
     @data.setter
     def data(self, data: np.ndarray) -> None:
-        self._grid.data[:] = data
+        self._grid.data[:] = _coerce_rgb(data)
         self._grid.update_range((0, 0, 0), self._grid.size)
 
     @property
@@ -85,7 +96,9 @@
     @cmap.setter
     def cmap(self, cmap: cmap.Colormap) -> None:
         self._cmap = cmap
-        self._material.map = cmap.to_pygfx()
+        # RGB image special case
+        if self.data.ndim != 3:
+            self._material.map = cmap.to_pygfx()
         self._render()
 
     def start_move(self, pos: Sequence[float]) -> None:
@@ -409,7 +422,6 @@
     """pygfx-based canvas wrapper."""
 
     def __init__(self) -> None:
-        self._current_shape: tuple[int, ...] = ()
         self._last_state: dict[Literal[2, 3], Any] = {}
 
         self._canvas = _QWgpuCanvas(size=(600, 600))
@@ -470,6 +482,7 @@
         self, data: np.ndarray | None = None, cmap: cmap.Colormap | None = None
     ) -> PyGFXImageHandle:
         """Add a new Image node to the scene."""
+        data = _coerce_rgb(data)
         tex = pygfx.Texture(data, dim=2)
         image = pygfx.Image(
             pygfx.Geometry(grid=tex),
@@ -479,9 +492,7 @@
         self._scene.add(image)
 
         if data is not None:
-            self._current_shape, prev_shape = data.shape, self._current_shape
-            if not prev_shape:
-                self.set_range()
+            self.set_range()
 
         # FIXME: I suspect there are more performant ways to refresh the canvas
         # look into it.
@@ -504,9 +515,7 @@
 
         if data is not None:
             vol.local_position = [-0.5 * i for i in data.shape[::-1]]
-            self._current_shape, prev_shape = data.shape, self._current_shape
-            if len(prev_shape) != 3:
-                self.set_range()
+            self.set_range()
 
         # FIXME: I suspect there are more performant ways to refresh the canvas
         # look into it.

src/ndv/viewer/_backends/_vispy.py

@@ -29,6 +29,16 @@
 DEFAULT_QUATERNION = Quaternion(turn, turn, 0, 0)
 
 
+# TODO Combine with similar function in _pygfx.py
+def _coerce_rgb(data: np.ndarray | None) -> np.ndarray | None:
+    if data is not None and data.ndim == 3:
+        # PyGFX expects (A)RGB data to be X, Y, C
+        for i, s in enumerate(data.shape):
+            if s in [3, 4]:
+                return np.moveaxis(data, i, -1)
+    return data
+
+
 class Handle(scene.visuals.Markers):
     """A Marker that allows specific ROI alterations."""
 
@@ -248,7 +258,7 @@ def cursor_at(self, pos: Sequence[float]) -> Qt.CursorShape | None:
 class VispyImageHandle:
     def __init__(self, visual: scene.visuals.Image | scene.visuals.Volume) -> None:
         self._visual = visual
-        self._ndim = 2 if isinstance(visual, scene.visuals.Image) else 3
+        self._ndim = self.data.ndim
 
     @property
     def data(self) -> np.ndarray:
@@ -266,7 +276,7 @@ def data(self, data: np.ndarray) -> None:
                 stacklevel=2,
             )
             return
-        self._visual.set_data(data)
+        self._visual.set_data(_coerce_rgb(data))
 
     @property
     def visible(self) -> bool:
@@ -490,6 +500,7 @@ def add_image(
         self, data: np.ndarray | None = None, cmap: cmap.Colormap | None = None
     ) -> VispyImageHandle:
         """Add a new Image node to the scene."""
+        data = _coerce_rgb(data)
         img = scene.visuals.Image(data, parent=self._view.scene)
         img.set_gl_state("additive", depth_test=False)
         img.interactive = True

src/ndv/viewer/_components.py

@@ -2,11 +2,15 @@
 
 from enum import Enum
 from pathlib import Path
+from typing import TYPE_CHECKING
 
-from qtpy.QtCore import QSize
+from qtpy.QtCore import QSize, Qt
 from qtpy.QtGui import QMovie
 from qtpy.QtWidgets import QLabel, QPushButton, QWidget
-from superqt import QIconifyIcon
+from superqt import QEnumComboBox, QIconifyIcon
+
+if TYPE_CHECKING:
+    from qtpy.QtGui import QStandardItem, QStandardItemModel
 
 SPIN_GIF = str(Path(__file__).parent / "spin.gif")
 
@@ -35,35 +39,41 @@
 
 class ChannelMode(str, Enum):
     COMPOSITE = "composite"
+    RGBA = "rgba"
     MONO = "mono"
 
+    @classmethod
+    def _missing_(cls, value: object) -> ChannelMode | None:
+        if value == "rgb":
+            return ChannelMode.RGBA
+        return None
+
     def __str__(self) -> str:
         return self.value
 
 
-class ChannelModeButton(QPushButton):
-    def __init__(self, parent: QWidget | None = None):
-        super().__init__(parent)
-        self.setCheckable(True)
-        self.toggled.connect(self.next_mode)
-
-        # set minimum width to the width of the larger string 'composite'
-        self.setMinimumWidth(92)  # magic number :/
-
-    def next_mode(self) -> None:
-        if self.isChecked():
-            self.setMode(ChannelMode.MONO)
-        else:
-            self.setMode(ChannelMode.COMPOSITE)
-
-    def mode(self) -> ChannelMode:
-        return ChannelMode.MONO if self.isChecked() else ChannelMode.COMPOSITE
-
-    def setMode(self, mode: ChannelMode) -> None:
-        # we show the name of the next mode, not the current one
-        other = ChannelMode.COMPOSITE if mode is ChannelMode.MONO else ChannelMode.MONO
-        self.setText(str(other))
-        self.setChecked(mode == ChannelMode.MONO)
+class ChannelModeCombo(QEnumComboBox):
+    """A ComboBox for ChannelMode, where the RGBA enum can be removed."""
+
+    def __init__(self, parent: QWidget | None = None, allow_rgba: bool = False):
+        super().__init__(parent, enum_class=ChannelMode)
+        # Find the RGBA item
+        idx = list(ChannelMode.__members__.keys()).index("RGBA")
+        model: QStandardItemModel = self.model()
+        self._rgba_item: QStandardItem = model.item(idx)
+
+        self.allow_rgba(allow_rgba)
+
+    def allow_rgba(self, enable: bool) -> None:
+        flags = self._rgba_item.flags()
+        self._rgba_item.setFlags(
+            flags | Qt.ItemFlag.ItemIsEnabled
+            if enable
+            else flags & ~Qt.ItemFlag.ItemIsEnabled
+        )
+        if self.currentEnum() == ChannelMode.RGBA and not enable:
+            # Arbitrary fallback mode
+            self.setCurrentEnum(ChannelMode.COMPOSITE)
 
 
 class ROIButton(QPushButton):

src/ndv/viewer/_data_wrapper.py

@@ -134,19 +134,15 @@ def guess_channel_axis(self) -> Hashable | None:
         """Return the (best guess) axis name for the channel dimension."""
         # for arrays with labeled dimensions,
         # see if any of the dimensions are named "channel"
-        for dimkey, val in self.sizes().items():
+        sizes = self.sizes()
+        for dimkey, val in sizes.items():
             if str(dimkey).lower() in self.COMMON_CHANNEL_NAMES:
                 if val <= self.MAX_CHANNELS:
                     return dimkey
 
         # for shaped arrays, use the smallest dimension as the channel axis
-        shape = getattr(self._data, "shape", None)
-        if isinstance(shape, Sequence):
-            with suppress(ValueError):
-                smallest_dim = min(shape)
-                if smallest_dim <= self.MAX_CHANNELS:
-                    return shape.index(smallest_dim)
-        return None
+        min_key = min(sizes, key=sizes.get)  # type: ignore
+        return min_key if sizes[min_key] <= self.MAX_CHANNELS else None
 
     def save_as_zarr(self, save_loc: str | Path) -> None:
         raise NotImplementedError("save_as_zarr not implemented for this data type.")

src/ndv/viewer/_lut_control.py

@@ -135,3 +135,20 @@ def update_autoscale(self) -> None:
             self._clims.setMinimum(min(mi, self._clims.minimum()))
             self._clims.setMaximum(max(ma, self._clims.maximum()))
             self._clims.setValue((mi, ma))
+
+
+class RGBAControl(LutControl):
+    def __init__(
+        self,
+        name: str = "",
+        handles: Iterable[PImageHandle] = (),
+        parent: QWidget | None = None,
+        cmaplist: Iterable[Any] = (),
+        auto_clim: bool = True,
+    ) -> None:
+        super().__init__("RGB", handles, parent, cmaplist, auto_clim)
+        self._cmap.setVisible(False)
+
+    def _on_cmap_changed(self, cmap: cmap.Colormap) -> None:
+        # NB: No-op
+        pass