obsm (spatial, spatial_fov) size seems unreasonably large.

[JonatanSahar]

Description

After loading a single FOV (CosMx data), which was saved to h5ad with a sparse X, I noticed the memory required was 13GB(!). Investigating with pymplr.asizeof() revealed that:

f1 size in MB: 13403.45
f1.X size in MB: 1.58
f1.obs size in MB: 91.63
f1.obsm size in MB: 13403.45, flat: 0.00
f1.varm size in MB: 13403.45, flat: 0.00
f1.obsm: AxisArrays with keys: spatial, spatial_fov
f1.obsm['spatial'].shape: (2039, 2)
f1.obsm['spatial_fov'].shape: (2039, 2)
f1.obsm.spatial size in MB: 0.03
f1.obsm.spatial_fov size in MB: 0.03

The difference between the size and the flat size suggests that the 13GB are the size of something obsm is referencing to but I couldn't figure out what that is as I can't look inside the AxisArrays object other than the two keys I inpected.

Is this normal?
Would appreciate any help in the matter, thanks!
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Minimal reproducible example

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Traceback

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[giovp]

mmh @JonatanSahar unfortunately I don't really know, I would transfer this issue to anndata as they might have seen this before