Refuse a transform whose vector does not span its axes - #710
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| (``validate_transform``); this is the same claim for the axes, at both levels and at every | ||
| version, made where the writer already holds them. | ||
| """ | ||
| axes = len(getattr(metadata, "axes", None) or ()) |
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For 0.6/0.9 multiscale-level transforms, the vector applies to the transform's named input/output coordinate systems, not necessarily the intrinsic metadata.axes. A valid two-value scale between two 2D named systems in a store whose intrinsic system is 3D is therefore rejected here. The existing v0.6 structural-validation model explicitly permits those system axis counts to differ, so derive the expected arity from the referenced coordinate systems instead.
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Confirmed and fixed. The layout is one this repository's own field stores produce: a 4-axis intrinsic system (c, z, y, x) beside a 3-axis spatial one. A legal scale between two named 3-axis systems was refused there:
the multiscales coordinateTransformations[0] (scale) gives 3 scale values for the 4 axes it applies to
The count now comes from the systems a transform references, when they resolve, and from the intrinsic axes otherwise, which is every 0.4 and 0.5 transform since none names a system:
named = {
systems[reference.name]
for reference in (
getattr(transform, "input", None),
getattr(transform, "output", None),
)
if reference is not None and reference.name in systems
}
spans = named or inheritedPinned by test_a_transform_spans_the_systems_it_names, which writes that store at 0.6 and reads the entry back; it fails on the pre-fix gate with the refusal above.
| for index, transform in enumerate(transforms): | ||
| for field in ("scale", "translation"): | ||
| vector = getattr(transform, field, None) |
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When writing 0.6/0.9 metadata, dataset transforms are normally TransformSequence objects, with the actual Scale and Translation stored in transform.transformations. Inspecting only attributes of the outer transform means a malformed nested vector still passes this gate and is serialized, leaving the mainstream v0.6 representation unprotected by the validation introduced here.
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Right, and it left the mainstream 0.6 case unprotected rather than only a corner of it. _prepare_metadata(ms, "0.6") puts a dataset's scale and translation inside a single TransformSequence, whose own attributes hold no vector, so a nested [1.0, 2.0, 1.5] over four axes passed the gate untouched and was serialized.
The check now descends, a member inheriting the span of the sequence that holds it, since members name no system of their own:
members = getattr(transform, "transformations", None) or ()
for position, member in enumerate(members):
_gate_spans(member, f"{where}.transformations[{position}]", systems, spans)The error names where it sat: dataset 'scale0/image' coordinateTransformations[0].transformations[0] (scale) gives 3 scale values for the 4 axes it applies to. Pinned by test_a_scale_nested_in_a_sequence_is_checked, which fails on the pre-fix gate because nothing raised.
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Included review availability: 4 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 8 reviews per hour. 📝 WalkthroughWalkthroughThe writer now validates scale and translation vector arity for multiscale-level and dataset-level transformations, including nested sequences, before serialization. Tests cover invalid v0.4 and v0.6 vectors and valid coordinate-system references. ChangesTransform arity validation
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: ⚪ Minimal · up to The change rejects transform vectors whose length does not match the declared axes, preventing invalid metadata from being written; no actionable merge-blocking risk remains beyond normal checks and review. Poem
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Inline comments:
In `@py/ngff_zarr/to_ngff_zarr.py`:
- Around line 310-316: The docstring and error-message fragments in the
transform validation code exceed the 88-character Python line limit. Rewrap the
text at word boundaries, including the documentation near the transform
validation function and the messages around the affected error handling, while
preserving their wording and behavior; ensure the result conforms to ruff
formatting.
- Line 319: Update _gate_transform_arity to resolve each transform’s referenced
coordinate system and use its axis count when validating scale and translation
lengths, rather than relying on metadata.axes. Add a regression test covering
differing intrinsic and named-coordinate-system axis counts.
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A scale of two values over three axes is metadata no consumer can apply, and nothing caught it: the 0.4 and 0.5 models carry no validation of their own, from 0.6 Scale and Translation inherit a validate that checks nothing, and the bundled schemas constrain what these vectors hold rather than how many. Such a store was written and read back as valid at every version, at the multiscales level and the dataset level alike. Which axes a vector spans is the transform's own question. From 0.6 a transform maps between the coordinate systems it names, whose arity need not be the intrinsic one: a spatial system beside a channel axis is what a field transform declares. So the count comes from the systems a transform references when they resolve, and from the intrinsic axes otherwise, which is every 0.4 and 0.5 transform. At 0.6 a dataset's scale and translation sit inside a sequence, so the check descends into one. Refs #667.
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Refs #667 — the arity half of "the data model does not follow the schema of its own version", taken up as offered there.
A
scaleof two values over three axes is metadata no consumer can apply, and nothing caught it. Measured onmainbefore this change, writing a 0.4 store whose scale vector carries two values for three axes:[{'scale': [2.0, 2.0], 'type': 'scale'}], andvalidate(..., version='0.4')passes — the bundled schema constrains what these vectors hold, not how many;From 0.6 a transform is checked against the coordinate systems it names (
validate_transform). Before it, nobody did: the 0.4 and 0.5 models carry no validation of their own._gate_transform_aritymakes the same claim for the axes, at both levels and at every version, where the writer already holds them.Proven
Independent of #708; no rebase needed either way.
Summary by CodeRabbit
Bug Fixes
Tests