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Conversion between "new transforms" and "ngff transforms" #114

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LucaMarconato opened this issue Jan 25, 2023 · 3 comments
Closed

Conversion between "new transforms" and "ngff transforms" #114

LucaMarconato opened this issue Jan 25, 2023 · 3 comments

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@LucaMarconato
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At the moment the new transformations are being saved with the ngff syntax, but not all the constraints of the ngff specs are respected. For instance we can save an Identity with mismatching input and output coordinate system and we can save a MapAxis that creates new axes that were not present in the input coordinate system.

This is fine for now, but in the future we have to adjust it to the specs. The idea is to for instance save an Identity with mismatching axis as an Affine or better as a Sequence of [Identity, Affine]. When reading we can remove the Affine from the Sequence when we detect that the affine is just permuting the axes (without remapping them).

For instance this affine transformation can be deleted when reading a Sequence of [Identity, Affine]:

  y x
x 0 1 0
y 1 0 0
  0 0 1

but this not (because it's genuinely swapping the axes

  x y
x 0 1 0
y 1 0 0
  0 0 1
@LucaMarconato
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LucaMarconato commented Jan 30, 2023

Also in _overwrite_coordinate_transformations_raster() from spatialdata._io.write.py we need to split coordinate systems and the coordinate transformations as described in the NGFF specs, and avoid writing the implicit coordinate systems.
The reader has to be updated accordingly.

@LucaMarconato
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As discussed #35, we need to wait until the NGFF specs is finalized. So I am closing this issue (marked as stale), until the NGFF specs is merged: ome/ngff#138.

@LucaMarconato LucaMarconato closed this as not planned Won't fix, can't repro, duplicate, stale Jul 9, 2024
@LucaMarconato
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Btw, to search for all the "stale" issues, one can use

sort:updated-desc is:issue is:close reason:"not planned"

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