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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
The text was updated successfully, but these errors were encountered:
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.
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.
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 aMapAxis
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 anAffine
or better as aSequence
of[Identity, Affine]
. When reading we can remove theAffine
from theSequence
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]
:but this not (because it's genuinely swapping the axes
The text was updated successfully, but these errors were encountered: