Delegate to ngff-zarr 0.45, require Python 3.11, and price what a fold pulls - #176
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Limit details: You’ve used all 6 included reviews currently available. Your 41 included PR review attempts over the past 7 days set your current allowance at 6 reviews per hour. 📝 WalkthroughWalkthroughThe pull request raises the minimum Python version to 3.11, updates CI and dependencies, modernizes OME-Zarr storage and displacement handling, revises reduction memory planning, centralizes accumulation markers, and updates runtime compatibility code. ChangesPython support and metadata
OME-Zarr and data processing
Network and runtime behavior
Estimated code review effort: 4 (Complex) | ~60 minutes Merge Risk: 🟡 Moderate · up to Pyramid displacement-field stores may lose their displacement-axis metadata when additional levels are appended, causing them to be read as ordinary three-channel images without an obvious failure. Merge should wait for this path to be fixed and tested, or for explicit owner acceptance of the risk. Sequence Diagram(s)sequenceDiagram
participant Client
participant KonfAI as KonfAI OME-Zarr
participant NGFF as ngff-zarr
participant Store as Zarr store
Client->>KonfAI: Request displacement-field write
KonfAI->>NGFF: Build multiscales metadata and transformations
NGFF->>Store: Create arrays and metadata
KonfAI->>Store: Write component data through the flipping writer
Store-->>Client: Read RFC-5 data remapped to ITK order
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✅ Passed checks (4 passed)
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In `@konfai/utils/ome_zarr.py`:
- Around line 1182-1194: Update append_ome_zarr_levels so the derived images
created by to_multiscales retain the base image’s axes_types, explicitly
reassigning the displacement axis type before passing derived to
ngff_zarr.to_ngff_zarr. Preserve the existing metadata and level-generation
behavior for non-displacement images.
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.github/workflows/konfai_apps_ci.yml.github/workflows/konfai_ci.yml.github/workflows/konfai_mcp_ci.yml.github/workflows/konfai_studio_ci.yml.github/workflows/publish.ymlREADME.mdapps/impact_reg/README.mdapps/impact_reg/pyproject.tomlapps/impact_reg/tests/unit/test_displacement_field_io.pyapps/impact_reg/tests/unit/test_orchestration.pyapps/impact_seg/README.mdapps/impact_seg/pyproject.tomlapps/impact_synth/README.mdapps/impact_synth/pyproject.tomlapps/mrsegmentator/README.mdapps/mrsegmentator/pyproject.tomlapps/totalsegmentator/README.mdapps/totalsegmentator/pyproject.tomldocs/source/development.mddocs/source/getting-started/installation.mddocs/source/index.rstdocs/source/quickstart.rstkonfai-apps/konfai_apps/app_server.pykonfai-apps/pyproject.tomlkonfai-mcp/konfai_mcp/catalog.pykonfai-mcp/konfai_mcp/server_experiments.pykonfai-mcp/pyproject.tomlkonfai-mcp/tests/test_mcp_server_apps.pykonfai/data/case_reduction.pykonfai/data/materialize.pykonfai/data/patching/manager.pykonfai/data/transform/io.pykonfai/network/network/base.pykonfai/network/network/measure.pykonfai/network/network/network.pykonfai/utils/ome_zarr.pykonfai/utils/runtime/distributed.pypyproject.tomlstudio/pyproject.tomlstudio/tests/test_live_feed.pytests/unit/oracle_support.pytests/unit/test_case_reduction.pytests/unit/test_imaging_formats.pytests/unit/test_ome_zarr_data_surface.pytests/unit/test_omezarr_displacement_field.pytests/unit/test_omezarr_store_creation.pytests/unit/test_runtime.pytests/unit/test_sweep_tiling.pytests/unit/test_transformer_workflow.pytests/unit/test_warp.py
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ngff-zarr 0.44/0.45 upstreamed what this backend was compensating for, so the compensation goes: Methods.DASK_BIN_SHRINK replaces the private bin-shrink pyramid (same statistic, and it takes the extents and chunk layouts the wasm one trapped on), to_ngff_zarr(metadata_only=True) replaces the one-voxel stand-in and the hand-built array, start_level=1 replaces the append graft and its scratch store, NgffImage.axes_types replaces the coordinate-system patch, and root_attributes replaces the sidecar's write-ordering hack. ome_zarr.py loses about 200 lines, and four documented traps become upstream's. KonfAI now requires Python 3.11 and zarr 3: ngff-zarr 0.45 does, and the 3.10-era shims go with it (StrEnum, typing_extensions.Self, the GenericAlias guards, the zarr-2 capability checks). Displacement fields are stored the way the specification reads them. An axis-aligned field carries a real RFC-5 displacements transformation, so ngff-zarr alone rebuilds an ITK transform from the store and moves points exactly as the field says; an oriented grid, which the specification cannot express, keeps the typed axis and its Direction in the sidecar. Every field store holds spec-ordered components, marked as such, and one KonfAI wrote before this is refused by name rather than read under a guess. The zarr v2 compressor is pinned to byte-shuffled blosc-lz4: the new writer defaults to zstd-0, which measured +19 % on disk and about +11 % on a streamed read of CT-like uint16. Two fixes ride along, both measured. A Resample before a Reduce is priced for the source window it pulls, which the fold charged nothing for: on the reduction bench the peak above the interpreter floor falls from 664 to 87 MiB against a 256 MiB budget, the plan becomes an upper bound instead of under-stating by 5x, and a budget no region fits is refused rather than run. And the patch-accumulation marker is read in four helpers instead of nine call sites, the two-branch expression that found an accumulator's owner collapsing to one, nesting included.
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Targets 1.8.3. Nothing is tagged here.
The refactor
ngff-zarr 0.44/0.45 absorbed what this backend was compensating for, so the compensation goes:
Methods.DASK_BIN_SHRINKreplaces the private bin-shrink pyramid (same statistic, and it accepts the extents and chunkings the wasm variant tripped on),to_ngff_zarr(metadata_only=True)replaces the one-voxel stand-in and the hand-rolled array creation,start_level=1replaces the append graft and its scratch store,NgffImage.axes_typesreplaces the patch on coordinate systems, androot_attributesreplaces the sidecar write-order hack.ome_zarr.pyloses ~200 lines, and four documented traps become upstream's.KonfAI now requires Python 3.11 and zarr 3 (ngff-zarr 0.45 requires it); the 3.10-era shims go with them (StrEnum,
typing_extensions.Self, theGenericAliasguards, the zarr-2 capability checks).Displacement fields: RFC-5 conformant
An axis-aligned field carries a real
displacementstransformation: ngff-zarr alone rebuilds an ITK transform from the store and displaces points exactly as the field says (tested to 1e-12). An oriented grid, which the spec cannot express, keeps its typed axis and its Direction in the sidecar. Every field store carries its components in spec order, marked as such.Two fixes, measured
Resamplebefore aReduceis finally priced for the source window it pulls. On the reduction bench, the peak above the interpreter floor goes from 664 to 87 MiB for a 256 MiB budget; the plan becomes an upper bound instead of underestimating by a factor of five; a budget no region can hold is refused instead of being started.Validation
Full
pixi run checkgreen; konfai-mcp 218, studio 112+29, apps/impact_reg 38; mypy over 154 files. Non-editable wheel verified in a clean venv (models/python/**PEP 420 plus the 16 catalogue.ymlpresent). Backend A/B against 1.8.2: level 0 and whole pyramids byte-identical. ExaSPIM pipeline replayed: outputs byte-identical (12 stores, diff 0.0).To decide at the tag
The upper bound on
ngff-zarr: their minor versions break (0.44 carries an explicit BREAKING section) and the pin is open (>=0.45).Summary by CodeRabbit
Compatibility
Improvements
Documentation