Fix render_images(norm=LogNorm()) crash on zero/non-positive data (#672)

Author: timtreis

src/spatialdata_plot/pl/basic.py

@@ -20,7 +20,7 @@
 from geopandas import GeoDataFrame
 from matplotlib.axes import Axes
 from matplotlib.backend_bases import RendererBase
-from matplotlib.colors import Colormap, Normalize
+from matplotlib.colors import Colormap, LogNorm, Normalize
 from matplotlib.figure import Figure
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from spatialdata import get_extent
@@ -1299,6 +1299,18 @@ def _draw_colorbar(
             base_offsets_axes: dict[str, float],
             trackers_axes: dict[str, float],
         ) -> None:
+            norm = spec.mappable.norm
+            if isinstance(norm, LogNorm):
+                vmin, vmax = norm.vmin, norm.vmax
+                if vmin is None or vmax is None or vmin <= 0 or vmin >= vmax:
+                    warnings.warn(
+                        "Data contains zeros or non-positive values; colorbar suppressed for `LogNorm`. "
+                        "Pass `colorbar=False` to silence this warning, or clip the data to positive values.",
+                        UserWarning,
+                        stacklevel=2,
+                    )
+                    return
+
             base_layout = {
                 "location": CBAR_DEFAULT_LOCATION,
                 "fraction": CBAR_DEFAULT_FRACTION,

tests/pl/test_render_images.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 import scanpy as sc
-from matplotlib.colors import Normalize
+from matplotlib.colors import LogNorm, Normalize
 from spatial_image import to_spatial_image
 from spatialdata import SpatialData
 from spatialdata.models import Image2DModel
@@ -682,3 +682,16 @@ def test_channels_as_legend_coexists_with_other_elements(self, sdata_blobs: Spat
         assert "0" in labels
         assert "1" in labels
         plt.close("all")
+
+
+def test_lognorm_with_zeros_suppresses_colorbar_with_warning():
+    # regression test for #604: LogNorm + non-positive data must not raise an opaque
+    # matplotlib ValueError; instead suppress the colorbar with an actionable UserWarning.
+    img = np.zeros((1, 5, 5), dtype=np.float32)
+    sdata = SpatialData(images={"img": Image2DModel.parse(img, c_coords=["DAPI"])})
+    fig, ax = plt.subplots()
+    try:
+        with pytest.warns(UserWarning, match="LogNorm"):
+            sdata.pl.render_images("img", norm=LogNorm()).pl.show(ax=ax)
+    finally:
+        plt.close(fig)