fix(transform): the debts the 1.8.2 stack left, and what measuring them said - #174
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Included review availability: 3 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 4 reviews per hour. 📝 WalkthroughWalkthroughThe change standardizes ChangesDataset processing and storage access
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🟡 Moderate · up to Missing dataset references may be routed to backend readers instead of producing the required structured error, leading to incorrect failure behavior; this should be fixed or explicitly accepted before merging. Sequence Diagram(s)sequenceDiagram
participant Caller
participant OMEZarrLoader
participant fsspecStore
participant RemoteStore
Caller->>OMEZarrLoader: Load URI-backed OME-Zarr
OMEZarrLoader->>fsspecStore: Create remote mapper
fsspecStore->>RemoteStore: Read multiscale metadata and array data
RemoteStore-->>fsspecStore: Return metadata and requested data
fsspecStore-->>OMEZarrLoader: Return loaded image
OMEZarrLoader-->>Caller: Return image or lazy window
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Full details: Description checkExplanation The description provides substantial technical context but omits the required template sections, including Type of change, How has this been tested, Checklist, and Breaking changes or an explicit statement that none apply. Resolution Reformat the description using the repository template. Add the change type, exact test commands and results, completed checklist items, related issue references or state that none apply, and breaking-change information or state that there are none. Also describe the OME-Zarr remote-store changes if they remain in the pull request. Full details: Title checkExplanation The title uses the Conventional Commits format and relates to the fixes, but phrases such as “debts” and “what measuring them said” are indirect. It does not clearly identify the primary changes for a history scan. ✨ Finishing Touches 💡 1📝 Generate docstrings 💡
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Inline comments:
In `@konfai/utils/dataset.py`:
- Around line 3455-3458: Ensure missing groups or entries are converted to
DatasetManagerError before action(...) proceeds, not only missing case files.
Update the lookup flow around _get_dataset(), file_to_data(), and get_infos() so
a None dataset is detected and reported with the existing structured error
instead of dereferencing dataset.shape; preserve normal processing for found
entries.
In `@tests/unit/oracle_support.py`:
- Around line 240-243: The coarse-field geometry setup around
coarse_field_spacing and coarse_field_extents must cover the full target grid,
including FIXED_GEOMETRY along X. Derive spacing from the target world extent
for the selected node count, or remove the three-node extent cap; ensure the
resulting coarse field is large enough for Resample regions at the grid faces.
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AGENTS.mdkonfai/data/case_reduction.pykonfai/data/data_manager.pykonfai/data/sampling.pykonfai/data/transform.pykonfai/utils/dataset.pytests/unit/oracle_support.pytests/unit/test_case_reduction.pytests/unit/test_dataset.pytests/unit/test_transform_working_multiple.py
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Inline comments:
In `@konfai/utils/dataset.py`:
- Line 3460: Update _resolve_entry’s existence guard to resolve wildcard groups
before calling file.is_exist, reusing the existing wildcard-aware behavior from
Dataset.is_dataset_exist or centralizing entry resolution. Ensure groups
containing "*" validate against expanded group names so valid HDF5 entries
proceed to action(...) instead of raising DatasetManagerError.
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Inline comments:
In `@konfai/utils/dataset.py`:
- Line 3454: Update ItkTransformFile’s directory-backed candidate handling to
validate file.is_exist("", entry) before dispatching to action; skip nonexistent
entries and continue searching, then raise the existing structured
DatasetManagerError after all candidates are exhausted instead of passing a
synthesized path to sitk.ReadTransform.
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…em said Six, found by listing what the stack had not closed rather than by waiting for a report. A lookup failure raised a bare NameError in ten places, with five sites catching it and two tests asserting it, against AGENTS.md's rule to use utils/errors.py. Each now carries what to do about it: check the groups_src spelling, check the chain's order, name a reference that is there. The siblings were grepped first, and nothing outside the core depended on the type. transform.py raised DatasetManagerError without importing it, which would have been a NameError at runtime: the very thing being removed. Softmax declared 0.00 and had no integer kernel, so a chain over a stored volume died on torch's message about "host_softmax". It widens an integer input now, measured at 0.00 on float and 1.00 on the int16 a store serves, and the declaration is the worse of the two. It is exercised again rather than named in the test's exclusion list. AGENTS.md described read_granularity as a chunked backend's; a memmap answers it too, anisotropically. The reduction's chain multiple quoted a Resample that declares 3.0 and has declared 6.5 for some time -- a stale figure in a comment that feeds a calculation. _default_walk_budget asks for the chain share the sweep already spends, which reads like double-spending and is not: the walk's target grid IS the sweep's region, and the block price binds first. Measured 0.10x to 0.42x of the declaration across 4 GiB to 256 MiB. Bounding it by the stage's own declaration instead was built and measured WORSE (141 -> 188 MiB at 512 MiB), because that product is the larger of the two. Written down so it is not re-derived. The GLOBAL_STAT route holds 1.19x what the plan announces at 128 MiB. The scan itself is inside its budget above 128 and 1.1x over below; the rest is the sweep peaking on a residue. Not chased, and the reason is the instrument: VmHWM is a high-water mark of the whole resident set and cannot be compared with the instantaneous RssAnon/RssFile split, which is what an OOM kill weighs. The coarse-field case is ported from a worktree it would have died in: a displacement field four times coarser than the case and reversing sign between adjacent nodes, so the interpolated displacement swings its full amplitude across one cell and a region's face cuts through the swing. A region sizes its window from the field values inside its own box; this asks whether that bound holds at the faces, where the interpolator blends nodes from outside it. It does.
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Six, found by listing what the stack had not closed rather than by waiting for
a report.
A lookup failure raised a bare NameError in ten places, with five sites catching
it and two tests asserting it, against AGENTS.md's rule to use utils/errors.py.
Each now carries what to do about it: check the groups_src spelling, check the
chain's order, name a reference that is there. The siblings were grepped first,
and nothing outside the core depended on the type. transform.py raised
DatasetManagerError without importing it, which would have been a NameError at
runtime: the very thing being removed.
Softmax declared 0.00 and had no integer kernel, so a chain over a stored
volume died on torch's message about "host_softmax". It widens an integer input
now, measured at 0.00 on float and 1.00 on the int16 a store serves, and the
declaration is the worse of the two. It is exercised again rather than named in
the test's exclusion list.
AGENTS.md described read_granularity as a chunked backend's; a memmap answers it
too, anisotropically. The reduction's chain multiple quoted a Resample that
declares 3.0 and has declared 6.5 for some time -- a stale figure in a comment
that feeds a calculation.
_default_walk_budget asks for the chain share the sweep already spends, which
reads like double-spending and is not: the walk's target grid IS the sweep's
region, and the block price binds first. Measured 0.10x to 0.42x of the
declaration across 4 GiB to 256 MiB. Bounding it by the stage's own declaration
instead was built and measured WORSE (141 -> 188 MiB at 512 MiB), because that
product is the larger of the two. Written down so it is not re-derived.
The GLOBAL_STAT route holds 1.19x what the plan announces at 128 MiB. The scan
itself is inside its budget above 128 and 1.1x over below; the rest is the sweep
peaking on a residue. Not chased, and the reason is the instrument: VmHWM is a
high-water mark of the whole resident set and cannot be compared with the
instantaneous RssAnon/RssFile split, which is what an OOM kill weighs.
The coarse-field case is ported from a worktree it would have died in: a
displacement field four times coarser than the case and reversing sign between
adjacent nodes, so the interpolated displacement swings its full amplitude
across one cell and a region's face cuts through the swing. A region sizes its
window from the field values inside its own box; this asks whether that bound
holds at the faces, where the interpolator blends nodes from outside it. It
does.
Summary by CodeRabbit
New Features
Bug Fixes
Documentation