feat(geometry): bound a displacement by where it reaches, not how far - #172
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Limit details: You’ve used all 4 included reviews currently available. Your 64 included PR review attempts over the past 7 days set your current allowance at 4 reviews per hour. 📝 WalkthroughWalkthroughThe geometry bounds model now uses signed per-axis displacement intervals. World boxes extend asymmetrically, affine transforms propagate interval bounds, and displacement stages expose cached ranges. OME-Zarr utilities now support remote URI loading, lazy stepped reads, and remote metadata writing. ChangesSigned geometry bounds
URI-aware OME-Zarr access
Estimated code review effort: 4 (Complex) | ~60 minutes Merge Risk: 🟠 High · up to Remote replacement can delete the existing dataset before the replacement is safely ready, which could cause data loss or service unavailability; this should be fixed or explicitly accepted before merging. Sequence Diagram(s)sequenceDiagram
participant OMEZarrUtility
participant FsspecMapper
participant RemoteStore
participant NGFFZarr
OMEZarrUtility->>FsspecMapper: open remote URI mapping
FsspecMapper->>RemoteStore: access store files
RemoteStore->>NGFFZarr: provide OME-Zarr data
OMEZarrUtility->>NGFFZarr: load image and metadata
OMEZarrUtility->>RemoteStore: upload generated metadata skeleton
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🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Description checkExplanation The description is focused and technically detailed. It explains the motivation, interval propagation, compatibility behavior, and measured results. It does not include explicit template sections for change type, test commands, checklist confirmations, or breaking-change status, but the core required context is present. ✨ Finishing Touches 💡 1📝 Generate docstrings 💡
🧪 Generate unit tests (beta)
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Inline comments:
In `@konfai/data/geometry.py`:
- Line 540: Update DisplacementStage.bound() so each returned TransformBound
endpoint is clamped to include zero, preserving identity displacement outside
the grid. Keep range_xyz’s sampled extrema unchanged, and adjust the
one-sided-field test to assert that range_xyz retains those extrema while
bound() includes zero.
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konfai/data/geometry.pytests/unit/test_geometry.pytests/unit/test_warp.py
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In `@konfai/utils/ome_zarr.py`:
- Around line 915-916: Update the replacement flow around filesystem.exists and
filesystem.rm so local metadata generation and uploads complete in a staging
location before modifying target. After the staged replacement succeeds, commit
it using replacement semantics appropriate to the active filesystem backend,
preserving the existing target until the commit is ready.
- Around line 652-654: Update the fallback indexing logic around span and steps
to normalize every slice against data.shape, including negative-step slices with
explicit bounds. Read the enclosing unit-step span using normalized bounds, then
apply each slice’s local step so cases such as slice(10, 2, -2) return the
expected reverse sequence while preserving existing non-slice indexing.
- Line 1131: The pyramid-generation flow around _from_ngff_zarr must preserve
remote store URIs as strings instead of converting store_path to Path. Keep the
original string for store access, group operations, cache invalidation, and
metadata consolidation, while introducing a separate local Path variable only
for scratch-file creation.
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TransformBound carried a symmetric residual, so a map was bounded by affine(p) +/- r. That is the right shape for a wiggle and the wrong one for a field solved between two frames, which carries the offset between them in every voxel: priced as a radius such a field opens a region's window both ways by twice its largest value, where the truth is a window of the same size sitting that far along. It becomes an interval. WorldBox.extended moves each end by its own end of it, DisplacementStage keeps min and max where it kept the larger magnitude -- the same two reductions, measured 79 ms against 80 on a 184 M-value window -- and after() folds through the outer affine by splitting the matrix into its non-negative and non-positive parts, because |A| @ r loses which end a sign flip sends where. Measured on an ExaSPIM field whose z runs [-28.1, -22.2] mm on a volume 20.6 mm thick: as a radius every region pulls the whole volume and the fold refuses, 23.57 GiB held against a 19.01 GiB budget; as an interval a 24-row region pulls 175 source rows of 514. residual_xyz stays as the symmetric envelope, which is what sup |v| already was, so coverage and anything else reading one number per axis is unchanged.
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TransformBound carried a symmetric residual, so a map was bounded by
affine(p) +/- r. That is the right shape for a wiggle and the wrong one for a
field solved between two frames, which carries the offset between them in every
voxel: priced as a radius such a field opens a region's window both ways by
twice its largest value, where the truth is a window of the same size sitting
that far along.
It becomes an interval. WorldBox.extended moves each end by its own end of it,
DisplacementStage keeps min and max where it kept the larger magnitude -- the
same two reductions, measured 79 ms against 80 on a 184 M-value window -- and
after() folds through the outer affine by splitting the matrix into its
non-negative and non-positive parts, because |A| @ r loses which end a sign flip
sends where.
Measured on an ExaSPIM field whose z runs [-28.1, -22.2] mm on a volume 20.6 mm
thick: as a radius every region pulls the whole volume and the fold refuses,
23.57 GiB held against a 19.01 GiB budget; as an interval a 24-row region pulls
175 source rows of 514.
residual_xyz stays as the symmetric envelope, which is what sup |v| already was,
so coverage and anything else reading one number per axis is unchanged.
Summary by CodeRabbit
New Features
Bug Fixes
Tests