Render constant-value channels as mid-grey with a warning (#636)

Author: timtreis

src/spatialdata_plot/pl/render.py

@@ -1421,7 +1421,15 @@ def _render_images(
             if isinstance(ch_norm, Normalize):
                 ch_norm = copy(ch_norm)
 
-            layers[ch] = ch_norm(layers[ch])
+            ch_arr = np.asarray(layers[ch])
+            ch_min, ch_max = float(ch_arr.min()), float(ch_arr.max())
+            if ch_min == ch_max and not (
+                isinstance(ch_norm, Normalize) and (ch_norm.vmin is not None or ch_norm.vmax is not None)
+            ):
+                logger.warning(f"Channel {ch!r} has a constant value ({ch_min:.6g}).")
+                layers[ch] = np.full(ch_arr.shape, 0.5, dtype=np.float64)
+            else:
+                layers[ch] = ch_norm(layers[ch])
 
         # Colors for the channel legend (set by each branch if applicable)
         legend_colors: list[str] | None = None

tests/_images/Images_constant_channel_renders_as_midgrey.png

@@ -154,6 +154,13 @@ def test_plot_correctly_normalizes_multichannel_images(self, sdata_raccoon: Spat
         axs[1].set_title("two-channel uint16")
         fig.tight_layout()
 
+    def test_plot_constant_channel_renders_as_midgrey(self):
+        h, w = 64, 64
+        data = np.full((1, h, w), 128, dtype=np.uint8)
+        img = Image2DModel.parse(data, dims=("c", "y", "x"))
+        sdata = SpatialData(images={"img": img})
+        sdata.pl.render_images("img").pl.show(title="constant channel: mid-value (not black)")
+
 
 # ---------------------------------------------------------------------------
 # Grayscale + transfunc visual tests