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Allow shape accessors on X et al. #125

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johnkerl opened this issue May 26, 2022 · 1 comment
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Allow shape accessors on X et al. #125

johnkerl opened this issue May 26, 2022 · 1 comment
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blocked enhancement New feature or request

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@johnkerl
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johnkerl commented May 26, 2022

  • TileDB string-dimensioned sparse arrays don't have a .shape() -- it does not exist (see also .shape attribute of arrays created with from_h5ad generates error #10)
  • People will want to know the 'shape' of X, obsp, varp -- I suspect it will be negative UX if people who are accustomed to getting anndata.X.shape cannot get soma.X.shape()
  • Effectively the shape of soma.X is (soma.obs.shape()[0], soma.var.shape()[0]) and the shape of soma.raw.X is (soma.obs.shape()[0], soma.raw.var.shape()[0])
  • What we can do is within the SOMA class:

Note: On PR #129 we have shape-by-scan which is O(n). For the TileDB core 2.10 timeframe we'll have an O(1) shape accessor.

@johnkerl
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Shape accessors are in place; optimization is a separate task.

nguyenv pushed a commit to nguyenv/TileDB-SOMA that referenced this issue Jan 10, 2024
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