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Use the correct image for scatter plots with alternate spatial bases #1032

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Use the correct image for scatter plots with alternate spatial bases #1032

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531bd21
Use the correct image for alternate spatial bases
obriencshl Sep 8, 2025
34b7d6a
Also fix scalefactor key retrieval
obriencshl Sep 8, 2025
79547da
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 8, 2025
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8 changes: 3 additions & 5 deletions src/squidpy/pl/_spatial_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@ def _get_image(
raise KeyError(
f"Image key: `{img_res_key}` does not exist. Available image keys: `{image_mapping.values()}`"
)
img = [adata.uns[Key.uns.spatial][i][Key.uns.image_key][img_res_key] for i in library_id]
img = [adata.uns[spatial_key][i][Key.uns.image_key][img_res_key] for i in library_id]

if img_channel is None:
img = [im[..., :3] for im in img]
Expand Down Expand Up @@ -234,9 +234,7 @@ def _get_scalefactor_size(
if not len(scale_factor_key):
raise ValueError(f"No `scale_factor` found that could match `img_res_key`: {img_res_key}.")
_scale_factor_key = scale_factor_key[0] # get first scale_factor
scale_factor = [
adata.uns[Key.uns.spatial][i][Key.uns.scalefactor_key][_scale_factor_key] for i in library_id
]
scale_factor = [adata.uns[spatial_key][i][Key.uns.scalefactor_key][_scale_factor_key] for i in library_id]
else: # handle case where scale_factor is float or list
scale_factor = _get_list(scale_factor, _type=float, ref_len=len(library_id), name="scale_factor")

Expand All @@ -251,7 +249,7 @@ def _get_scalefactor_size(
if not (len(size) == len(library_id) == len(scale_factor)):
raise ValueError("Len of `size`, `library_id` and `scale_factor` do not match.")
size = [
adata.uns[Key.uns.spatial][i][Key.uns.scalefactor_key][size_key] * s * sf * 0.5
adata.uns[spatial_key][i][Key.uns.scalefactor_key][size_key] * s * sf * 0.5
for i, s, sf in zip(library_id, size, scale_factor, strict=False)
]
return scale_factor, size
Expand Down