Fix OME-Zarr physical scale metadata

[maxliebscher]

Summary

Fixes OME-Zarr physical scale metadata written by vc_render_tifxyz so rendered output stores the actual physical spacing for the generated Z/Y/X axes.

What changed

• writeZarrAttrs now accepts separate physical sizes for Z and Y/X instead of one isotropic base voxel size.
• vc_render_tifxyz computes output Y/X spacing from the selected source group and --scale.
• Rendered Z spacing uses --slice-step and remains unchanged across output pyramid levels.
• Pyramid metadata doubles only Y/X scale per downsampled output level.
• TIFF DPI uses the rendered Y/X pixel size.
• Added a focused doctest for anisotropic OME-Zarr scale metadata.

Why

The previous metadata path used one base voxel size for all output axes and levels. That loses the distinction between:

• the source OME-Zarr group resolution,
• the render pixel scale,
• the rendered slice spacing along Z,
• and the Y/X-only downsampling applied to output pyramid levels.

This can make downstream OME-Zarr consumers interpret rendered volumes with the wrong physical scale.

Validation

Rebased onto current main and ran in WSL2 Ubuntu 24.04:

git diff --check origin/main...HEAD
cmake -S volume-cartographer -B volume-cartographer/build/wsl-vc-pr845 -GNinja -DCMAKE_BUILD_TYPE=Release -DVC_TESTING=ON -DLAPACKE_INCLUDE_DIRS=/usr/include -DLAPACKE_LIBRARIES=/usr/lib/x86_64-linux-gnu/liblapacke.so
cmake --build volume-cartographer/build/wsl-vc-pr845 --target vc_render_tifxyz test_zarr_attrs -j2
ctest --test-dir volume-cartographer/build/wsl-vc-pr845 -R '^test_zarr_attrs$' --output-on-failure

Result:

100% tests passed, 0 tests failed out of 1

The generated build directory was removed after verification.

[vercel]

@maxliebscher is attempting to deploy a commit to the scroll Team on Vercel.

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[maxliebscher]

Quick note on the Vercel check: this PR only touches volume-cartographer C++/CMake test code. I validated the affected path locally in WSL2 by building vc_render_tifxyz and test_zarr_attrs, then running ctest -R test_zarr_attrs --output-on-failure. The Vercel preview is blocked because this comes from a fork and needs team authorization; I do not think it is relevant for this patch unless you want preview deployments enabled for it.

[giorgioangel]

@codex review

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Preserve existing writeZarrAttrs call sites

With yxVoxelSize inserted before voxelUnit, existing callers that pass only a voxel size and unit no longer compile: I checked repo-wide with rg "writeZarrAttrs\\(", and volume-cartographer/core/test/test_zarr.cpp:119 still calls writeZarrAttrs(..., 7.91, "um"), so the string literal is now bound to this new double parameter. Building the normal test_zarr target will fail unless that call is updated or a compatibility overload keeps the old (baseVoxelSize, voxelUnit) form working.

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