spatialdata
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scverse
CosMx data `render_images` after cropping via `query.bounding_box`
Hi @LucaMarconato
great work on spatialdata! I started playing around with this and noticed and error when cropping an image from the CosMx dataset:
import spatialdata as sd
data = sd.read_zarr("data.zarr")
cur_img = data.filter_by_coordinate_system("10")
cropped_img = cur_img.query.bounding_box(
axes=["x", "y"],
min_coordinate=[1000,1500],
max_coordinate=[1500,2000],
target_coordinate_system="10"
)
cropped_img.pl.render_images().pl.show()
returns
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[119], line 1
----> 1 cropped_img.pl.render_images().pl.show(coordinate_systems="10")
File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/basic.py:645, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
643 if members["has_labels"].values[0]:
644 for key in sdata.labels:
--> 645 sdata.labels[key] = _robust_transform(sdata.labels[key], cs)
647 if members["has_points"].values[0]:
648 for key in sdata.points:
File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py:1145, in _robust_transform(element, cs)
1143 for _, t in enumerate(transformations):
1144 if isinstance(t, sd.transformations.transformations.Translation):
-> 1145 element = _translate_image(image=element, translation=t)
1147 elif isinstance(t, sd.transformations.transformations.Affine):
1148 # edge case, waiting for Luca to decompose affine into components
1149 # element = transform(element, t)
(...)
1156 # element = _robust_transform(element, cs)
1157 # print(element.shape)
1158 pass
File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py:1099, in _translate_image(image, translation)
...
807 )
809 y_axis_name = "y"
810 if axis_names and "y" in axis_names:
IndexError: tuple index out of range
This is my environment:
abseil-cpp 20211102.0 he9d5cce_0
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aiofiles 22.1.0 py39hecd8cb5_0
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Hi Nils, thanks for the kind feedback and for reporting this bug.
I think this behavior is due to this bug that I have reported here: https://github.com/scverse/spatialdata-plot/issues/146. In such a case, we are working on the solution and it should be fixed soon 😊
I just checked, the bug is not present anymore, probably thanks to the fix mentioned above.