RFC-5: Transformations and Coordinate systems by bogovicj · Pull Request #255 · ome/ngff

bogovicj · 2024-08-14T20:26:04Z

No description provided.

* mostly removing irrelevant links and bikeshed stuff

* store as 2d only

* reorder sections

github-actions · 2024-08-14T20:26:17Z

Automated Review URLs

normanrz · 2024-08-22T09:55:46Z

Thanks for your continued work on the transformations proposal and for writing it up as an RFC.
OME-Zarr really needs expanded transformation capabilities and I like this proposal! Happy to endorse it.

One issue that I see is the use of absolute paths in the path attribute (i.e. starting with /). This seems somewhat ill-defined to me. The example in the RFC shows that "store.zarr" is the root, which I assume would be the starting point for the absolute paths. However, any group in a Zarr hierarchy is a valid hierarchy on its own and there is no mandate for a .zarr suffix to denote a root. Therefore, I would advocate for restricting paths to relative paths, which would be relative to the folder that holds the zarr.json.

Also, I want to mention that there is interest in the community to create a "collections" proposal for OME-Zarr. I haven't gotten the time to write an RFC yet but I think that could integrate nicely with this transformations proposal and might provide solutions for the path issue as well.

d-v-b · 2024-08-26T13:52:32Z

+### Array coordinate systems
+
+Every array has a default coordinate system whose parameters need not be explicitly defined.  Its name is the path to the array
+in the container, its axes have `"type":"array"`, are unitless, and have default "name"s. The ith axis has `"name":"dim_i"`


Why make the default name require information about where the array is stored in the container? This means that accessing the default coordinate system requires accessing the storage layer for the array, which rules out anything that acts exclusively on metadata.

Perhaps it would be simpler to reserve a string like "default" for the default coordinate system.

Because the coordinate systems of different arrays need to be different by default.

d-v-b · 2024-08-26T13:58:41Z

+### "coordinateTransformations" metadata
+
+"coordinateTransformations" describe the mapping between two coordinate systems (defined by "axes").
+For example, to map an array's discrete coordinate system to its corresponding physical coordinates.


Suggested change

For example, to map an array's discrete coordinate system to its corresponding physical coordinates.

For example, coordinate transforms can be used to map an array's discrete coordinate system to its corresponding physical coordinates.

typo Co-authored-by: Davis Bennett <[email protected]>

add comma Co-authored-by: Davis Bennett <[email protected]>

emphasize axis types are strings Co-authored-by: Davis Bennett <[email protected]>

rephrase Co-authored-by: Davis Bennett <[email protected]>

spelling Co-authored-by: Davis Bennett <[email protected]>

rm zarr2 specific phrasing Co-authored-by: Davis Bennett <[email protected]>

spelling Co-authored-by: Davis Bennett <[email protected]>

@d-v-b

thanks @d-v-b

LucaMarconato · 2024-09-04T16:22:11Z

Thanks @bogovicj for opening the draft for the RFC, I have added my review. The points are mostly minor and I have only two more small comments, here below. After the above is resolved and the comments are addressed, for me we are good to go to officially submit the RFC.

I find this example of multiscale transformations vs "standard" transformations, very useful: https://github.com/bogovicj/ngff/blob/coord-transforms/latest/examples/multiscales_strict/multiscales_example_relative.json. I would stress this example more in the specs text.
Some things are not clear to me from the example above:
2.1 are we allowed to use just scale, scale+translation or any transformation for the multiscale images? I am not sure what's the best here
2.2 related to the point above is this issue of "what is a multiscale image and what not" Clarifying that multiscale images can only be the same image downscaled #260. I opened it outside the context of this PR, but I think it is still useful to decide how to proceed.

Regarding 2.1, I think that we should allow for scale + translation and not general transformations. Also, I think a scale alone is now enough because we may need small translations depending of the downsampling algorithm because the pixel 0 of a downscaled image may not correspond to the pixel 0 of the original image. Also some people may find useful to define a image origin.

@LucaMarconato

thanks @LucaMarconato

@LucaMarconato

thanks @LucaMarconato

* and clean up table

bogovicj · 2024-09-25T18:22:58Z

Thanks @LucaMarconato and @d-v-b ,

I address most of your comments. While there are few left, I'll get to them soon, and they're more minor. So I'm going to take this PR off of draft status.

- In HTML sections, replace `` with <code> blocks - Replace div notes with MyST directives

joshmoore · 2024-10-08T08:24:25Z

Assigned RFC-5
Added navigation links and changelog
Corrected some minor formatting issues

Merging and sending for review once the build is green. If you would like to be added as an Endorser, please comment below or as always, PRs welcome.

Thanks to everyone involved! 🎉

@joshmoore

RFC-5: Transformations and Coordinate systems SHA: 5fd56e0 Reason: push, by @joshmoore Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

tischi · 2024-11-22T17:34:40Z

I endorse this RFC

imagesc-bot · 2025-11-14T14:27:51Z

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/rfc-5-coordinate-systems-and-transformations/117658/1

bogovicj added 9 commits July 30, 2024 13:46

wip: start of transforms RFC

bd45021

stage D2 + clean up author table

20a0d25

overview and background

ce42618

fixes to proposal section

5c603a6

* mostly removing irrelevant links and bikeshed stuff

update tform rfc authors

2723c7c

updates matrix/affine/rotation

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* store as 2d only

add abandoned ideas section. rm some TODOs

ebe3cd8

write "Drawbacks, risks, alternatives, and unknowns"

e95eaf6

* reorder sections

request some specific feedback

d1a5367

d-v-b reviewed Aug 26, 2024

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Comment thread rfc/wip-tform/index.md Resolved

d-v-b reviewed Aug 26, 2024

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Comment thread rfc/wip-tform/index.md Resolved

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Comment thread rfc/wip-tform/index.md Resolved

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Comment thread rfc/wip-tform/index.md Resolved

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Comment thread rfc/wip-tform/index.md Resolved

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Comment thread rfc/wip-tform/index.md Resolved

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Comment thread rfc/wip-tform/index.md Resolved

bogovicj and others added 8 commits August 28, 2024 13:08

Update rfc/wip-tform/index.md

9cb6ae4

typo Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

6c42692

add comma Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

df16040

emphasize axis types are strings Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

139264d

rephrase Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

9c66c3f

spelling Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

3c3ff8e

rm zarr2 specific phrasing Co-authored-by: Davis Bennett <[email protected]>

Update rfc/wip-tform/index.md

69b6f57

spelling Co-authored-by: Davis Bennett <[email protected]>

rephrase paragraph on discrete/continuous axes

dadff02

thanks @d-v-b

LucaMarconato reviewed Sep 4, 2024

View reviewed changes

Comment thread rfc/wip-tform/index.md Resolved

LucaMarconato mentioned this pull request Sep 4, 2024

Coordinate transformations refactoring scverse/spatialdata#308

Open

bogovicj added 6 commits September 20, 2024 12:02

typo and other minor fixes

b1e0cc8

thanks @LucaMarconato

fix affine matrix size, and other small fixes

77a7db7

thanks @LucaMarconato

clarify invertibility of sequence

cae3490

add @normanrz as endorser

3659933

* and clean up table

fix spelling

9c18d4d

flesh out coordinates + displacements description

8368cae

bogovicj marked this pull request as ready for review September 25, 2024 18:23

joshmoore added 4 commits October 8, 2024 09:40

RFC-5: assign number

6a02c6a

Merge remote-tracking branch 'origin/main' into tform-rfc

8037848

Minor navigation improvements

7979256

Update to long-form status table

08d6a61

joshmoore changed the title ~~RFC: Transformations and Coordinate systems~~ RFC-5: Transformations and Coordinate systems Oct 8, 2024

joshmoore added 5 commits October 8, 2024 09:59

Remove reference to missing example 'above'

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Fix markdown for rendering of `` blocks

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- In HTML sections, replace `` with <code> blocks - Replace div notes with MyST directives

Simplify deflist where possible

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Fix stakeholders links

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Add changelog

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Minor index/changelog adjustments

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joshmoore merged commit 5fd56e0 into ome:main Oct 8, 2024

constantinpape mentioned this pull request Oct 9, 2024

Support for light-sheet (meta) data #264

Open

This was referenced Nov 21, 2024

Track status of OME-NGFF coordinate transformations vitessce/vitessce#1978

Open

Support coordinate transformations and coordinate systems NGFF spec hms-dbmi/viv#841

Open

lubianat added the rfc-5 label Dec 11, 2025

	For example, to map an array's discrete coordinate system to its corresponding physical coordinates.
	For example, coordinate transforms can be used to map an array's discrete coordinate system to its corresponding physical coordinates.

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