RFC-3: more dimensions for thee #239
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/ome-ngff-update-postponing-transforms-previously-v0-5/95617/5 |
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PS: I asked @joshmoore whether whimsy was allowed and he said yes, hence the title. (This comes after I realised I couldn't have "RFC-2: dimensional hullabaloo" because @normanrz had taken that number already. 😂) |
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full endorsement. While i absolutely recognize the significant challenge that lifting the strict dimensionality model may pose for mapping arbitrary future usage onto legacy code bases that have been built around XYZCT, I fully agree that a true next-generation format is going to have to lift it. I have personally experienced a number of use cases and applications where the current restrictions have led me to delay adopting ngff in my own work, and this RFC would allow me to more enthusiastically consider adoption. I agree with @jni that concerns around communicating the semantics of specific axes (i.e. formally named "X", "Y" and "Z") are better addressed by additional keys in the axis metadata, such as |
For comparison, https://datatracker.ietf.org/doc/html/rfc2549 ("IP over Avian Carriers") |
Would you be able/willing to contribute those, perhaps even for a section in the RFC? |
Sure, the most direct stories I can share are from implementing writers for data coming off microscopes (code in pymmcore-plus/mda/handlers). There I essentially have a |
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it's possible that @nclack and/or @aliddell would have opinions here as well, as I know they've spent a fair amount of time thinking about how to map a variety of custom experiment types to the ngff format in the acquire-python schema |
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@tlambert03 thanks for the links! I'll add these to the background section, but could you point me to where in the code
would fail? The smoking gun would be:
Maybe it's not as easy as that to define these things compactly, but if it is, I think it would be worthwhile detail for this RFC's motivation. |
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A few quick clarifications, @jni:
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Re: NGFF readers: cc @manzt - https://github.com/hms-dbmi/vizarr - Any idea how much work it would be to support n-dimensional NGFF data? cc @dgault - https://github.com/ome/ZarrReader/ - Since the OME data model is very much 5D, this is going to take a bit of thought on how to handle n-dimensional NGFF data? |
The space restrictions, and all other axis restrictions (other than the requirement that axes have unique names) are removed in #235 |
Webknossos already supports an arbitrary number of dimensions. However, it assumes that there are only 3 space dimensions to map to xyz. I think the spec should provide guidance to visualization tools what to do with >3 space dimensions. |
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/request-for-info-ngff-use-cases-that-are-currently-blocked/96641/1 |
rfc/3/index.md
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| As part of the [proposed implementation][implementation], Davis Bennett has | ||
| created pydantic models that validate the proposed schema. These are actually | ||
| new additions to the NGFF specification, surfaced pre-existing errors in the | ||
| schema, and should prevent new errors from appearing. |
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I don't think we need this text. Those pydantic models are merely a convenient way to write JSON schema. They don't express anything that's not already written in the prose of the spec. Also, I am planning on removing those models from the PR, because they add an undocumented build step that I don't have the energy to document.
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as of aa5c953 those models are gone
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@d-v-b I really loved the models! 😭
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they will live here https://github.com/janeliascicomp/pydantic-ome-ngff if 0.5 comes out
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The PR at #235 mentioned above seems to go a bit further than this RFC in that it removes restrictions on ordering of dimensions, whereas this proposal only mentions removing the restriction on the number of dimensions. I imagine that supporting arbitrary dimension order is a fair bit more work for implementers that n-dimensions, so that endorsement of this proposal may not signal endorsement of #235? |
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regarding advice for partial implementations (e.g., implementations that only support a fixed number of dimensions, or a fixed order), I included the following section in the PR: https://github.com/ome/ngff/pull/235/files#diff-ffe6148e5d9f47acc4337bb319ed4503a810214933e51f5f3e46a227b10e3fcdR565-R580, please let me know if this guidance is sufficient or if we should say more (and lets have that conversation over in #235 instead of here, so that we can keep synchronized with the actual changes to the spec) |
I probably need to update the summary at the top, but under "proposal" I write:
If the names are arbitrary, the ordering must also be arbitrary, surely? But I can make it explicit. |
| A draft proposal for [coordinate transformations][trafo spec] already includes | ||
| most of the changes proposed here, so we envision that this RFC is compatible | ||
| with future plans for the format. The proposal does currently limit the number | ||
| of dimensions of type "space" to at most 3, but that limit [could be | ||
| removed][space dims comment]. If this RFC is approved, the transformation | ||
| specification would need to be updated to reflect this. However, that is an easy | ||
| change and there seems to be sufficient support in the community for this idea. |
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Do we need to talk about that (stalled) PR at all? I don't see why it's relevant here
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It's relevant because it speaks to the forward compatibility of this RFC — ie it is in line with existing proposals for the format. That the PR is stalled is not really relevant — it's stalled because of minor details (e.g. array order) that don't have a bearing on this PR. Based on the discussion, other aspects, and certainly the ones relevant to this RFC, have quite broad consensus.
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in that case isn't it sufficient to just state that there are no known conflicts with other active proposals?
in my opinion the spec should leave this question undefined. The mapping can be direct (x=x, y=y, z=z), user defined (give users options of how to map axes), or arbitrary (x=foo, y=bar, z=baz). In practice, I think it is not going to be an issue, I am just wary of restricting the number for the same reason that I was wary of restricting the total number of dimensions, which indeed caused problems. If it helps this RFC move forward, I can bring back the "maximum three spatial dimensions" limit from #138, and we can have the discussion in a later RFC. The unlike the other changes in this RFC, the removal of the maximum number of "space" dimensions is purely speculative on my end, and not motivated from a concrete use case. Action requested:
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Implementations that do not support some aspect of user data should clearly communicate that to users. Users can then decide which implementation use, given the data they have stored. We should not try to limit the data that users can store, simply because some implementations cannot represent that data. This is a broader issue: as of 0.4, there are lots of OME-NGFF tools that don't support big images on cloud storage (of which I have plenty). Should we change the spec to limit the size, or location of images, just because some implementations can't load my big ones? I don't think so. So for the same reason, we should not restrict what axes users have, just because some implementations are opinionated about axes. |
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Thanks for the update, @jni! ❤️ A few TODOs from my side (or even for me) before merging:
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what's the latest recommendation here?
link? |
The format is OME-Zarr. The process/community is NGFF. I'm happy to read through and take care of that though.
Doesn't yet exist. It should really be a RFC in its own right. |
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@joshmoore I believe with the latest changes this should be ready to merge, at least from my end. From your todo from a month ago:
Let me know if there's anything else needed from me, and hopefully I won't take 6 months next time. 😂 |
SHA: 54b146f Reason: push, by @joshmoore Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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RFC-3 is now live under https://ngff.openmicroscopy.org/rfc/3 |
To make sure we have consensus, I'm opening this RFC in the style of RFC-2. (I'm aware that RFC-1 has some pending issues to be resolved, but when consensus is possible 🤞 this is a useful way to document the history of past decisions.) Please add a thumbs up if you want to be listed as an endorser. Please reply if you have concerns.
@d-v-b @joshmoore @normanrz @bogovicj @will-moore @ziw-liu @tlambert03
Please add pings for authors of libraries implementing ome-ngff readers and writers, as the main effect here is not on existing files but on implementations that may implement too-restrictive a spec.
My goal is to get this and #235 merged before the upcoming 0.5 release. 🤞 (I think that is being targeted for late June/early July? @joshmoore?)
Review URL: https://ngff--239.org.readthedocs.build/rfc/3/