Fix setting vmin vmax (#307)

Author: LucaMarconato

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning][].
 -   scale parameter was ignored for single-scale images (#301)
 -   Changes to support for dask-expr (#283)
 -   Added error handling for non-existent elements (#305)
+-   Specifying vmin and vmax properly clips image data (#307)
 
 ## [0.2.3] - 2024-07-03
 

src/spatialdata_plot/pl/utils.py

@@ -376,11 +376,11 @@ def _prepare_cmap_norm(
     cmap.set_bad("lightgray" if na_color is None else na_color)
 
     if norm is None:
-        norm = Normalize(vmin=vmin, vmax=vmax)
+        norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
     elif isinstance(norm, Normalize) or not norm:
         pass  # TODO
     elif vcenter is None:
-        norm = Normalize(vmin=vmin, vmax=vmax)
+        norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
     else:
         norm = TwoSlopeNorm(vmin=vmin, vmax=vmax, vcenter=vcenter)
 

tests/_images/Images_can_pass_normalize.png

@@ -3,6 +3,8 @@
 import numpy as np
 import scanpy as sc
 import spatialdata_plot  # noqa: F401
+from matplotlib import pyplot as plt
+from matplotlib.colors import Normalize
 from spatial_image import to_spatial_image
 from spatialdata import SpatialData
 
@@ -68,6 +70,17 @@ def test_plot_can_render_two_channels_str_from_image(self, sdata_blobs_str: Spat
     def test_plot_can_render_two_channels_str_from_multiscale_image(self, sdata_blobs_str: SpatialData):
         sdata_blobs_str.pl.render_images(element="blobs_multiscale_image", channel=["c1", "c2"]).pl.show()
 
+    def test_plot_can_pass_vmin_vmax(self, sdata_blobs: SpatialData):
+        fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+        sdata_blobs.pl.render_images(element="blobs_image", channel=1).pl.show(ax=axs[0])
+        sdata_blobs.pl.render_images(element="blobs_image", channel=1, vmin=0, vmax=0.4).pl.show(ax=axs[1])
+
+    def test_plot_can_pass_normalize(self, sdata_blobs: SpatialData):
+        fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+        norm = Normalize(vmin=0, vmax=0.4, clip=True)
+        sdata_blobs.pl.render_images(element="blobs_image", channel=1).pl.show(ax=axs[0])
+        sdata_blobs.pl.render_images(element="blobs_image", channel=1, norm=norm).pl.show(ax=axs[1])
+
     def test_plot_can_pass_color_to_single_channel(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_images(element="blobs_image", channel=1, palette="red").pl.show()