Stream the field of an RFC-5 displacements or coordinates transform - #695
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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. 📝 WalkthroughWalkthroughRFC-5 displacement and coordinate fields now use shared validation, chunk-wise displacement bounds, block-wise field streaming, and field-aware bounding boxes. Python and TypeScript tests cover chunking, multiscale fields, coordinate fields, restricted reads, and interior displacement extrema. ChangesTransform resampling interoperability
Estimated code review effort: 4 (Complex) | ~60 minutes Merge Risk: ⚪ Minimal · up to The PR streams RFC-5 displacement and coordinate fields while improving transformed-region coverage, with targeted tests and measured memory improvements; no actionable merge-blocking risk remains beyond normal checks and review. Sequence Diagram(s)sequenceDiagram
participant resample
participant resample_bounding_box
participant field_displacement_bound
participant field_array
participant ITK_transform
resample->>resample_bounding_box: compute the moving-image region
resample_bounding_box->>field_displacement_bound: calculate field bounds
field_displacement_bound->>field_array: read intersecting field chunks
field_array-->>field_displacement_bound: return displacement ranges
resample->>field_array: assemble the block field crop
resample->>ITK_transform: create the block-specific field transform
ITK_transform-->>resample: resample the output block
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Full details: Linked Issues checkExplanation The changes satisfy issue Full details: Out of Scope Changes checkExplanation The changes remain within issue ✨ Finishing Touches🧪 Generate unit tests (beta)
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💡 Codex Reviewngff-zarr/py/ngff_zarr/displacement_field_transform.py Lines 679 to 681 in b0d6d08  Include identity displacement when grids cross field edges
When a fixed grid or output block only partially overlaps the field and the in-field displacements are all on one side of zero, clamping the window here loses the fact that some samples are outside the field. ITK applies zero displacement outside the field, but ngff-zarr/ts/src/utils/displacement_field_transform.ts Lines 573 to 578 in b0d6d08 Include zero for partially out-of-field TypeScript grids
When the fixed grid extends both inside and outside a field whose in-field displacements are, for example, a constant positive offset, this clamping makes ngff-zarr/ts/src/io/resample_bounding_box-shared.ts Lines 421 to 425 in b0d6d08  Reject oriented fields before computing an intrinsic box
For a field with a non-identity ngff-zarr/ts/src/utils/ngff_transform_to_itk_transform.ts Lines 315 to 316 in b0d6d08 Reject invalid byDimension axis indices
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Both P1s were real. Reproduced, fixed and pinned in b803885. Zero missing from the range when a grid reaches past the field. A 64x64 grid over a 32x32 field of constant -5, against a single whole-image ITK call: 496 of 4096 output pixels wrong, by up to 100. The window already knew it had clamped; it now says so, and the range takes zero in when it did. The regression test fails without that ( The TypeScript half of the same thing, fixed the same way: The oriented field. Correct, and it was a regression: the refusal used to come from The Suites after the fixes: 1261 Python, 681 TypeScript. |
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In `@py/test/test_resample_field_streaming.py`:
- Around line 23-24: Update the imports for _whole_image_reference and
_interior_bump to use repository-root absolute import paths instead of
package-relative syntax, while preserving their local-test-helper grouping.
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@vboussot can the commits please be squashed into logical commits? 🙏 |
The pipeline sizes a region by walking the boundary of the transformed grid. That reports a linear map exactly and misses whatever a displacement does strictly inside the grid: a bump that is zero on the boundary voxels left the region unchanged, and resample then returned the default value for the pixels it displaces onto. Measured on a 64x64 grid with a 60-pixel bump in the middle: 63 of 4096 output pixels wrong, by up to 213. A displacements or coordinates transform is the identity plus a displacement, so the region is now the grid's own image moved and widened by the range that displacement takes. The range comes from the field itself, read one chunk at a time with two numbers kept per component and the values dropped: a field is read through a kernel that is non-negative and sums to one, so a displacement anywhere is a convex combination of the values around it and lies between their smallest and largest. That is a bound, not a sample. Keeping the range rather than a magnitude means a field that shifts every point the same way moves the region instead of widening it, and the region for a constant field is the affine one to the pixel. Zero joins the range when the grid reaches past the field, where ITK displaces nothing: a field that displaces every point it covers one way otherwise carried the region off the points it does not cover, 496 of 4096 pixels wrong on a half-covered grid. The pass reads only the chunks the caller's window touches, cut on chunk borders, and names the meta its extrema map produces rather than leaning on dask's dtype fallback. The identity's own region is also plain arithmetic; _identity_region computes it for the per-block callers and a property test pins it to the pipeline's answer over randomized geometry, all seven reported fields, while resample_bounding_box itself stays on the pipeline. A field carrying an anatomical orientation is refused in both ports, as the conversion it bypasses already refused it. On a 201 MB field the bounding box held 1508 MB before and 236 MB now.
resample streamed the moving image and nothing else: an RFC-5 displacements or coordinates transform was converted before the graph was built, and that conversion read its field in full and allocated three to five times its size on top. A field the size of the volume had to fit in memory while the moving image did not. Each block now reads the window of the field its own points fall in, and that window becomes the block's ITK transform. What sizes the block's moving read is the range of displacement that window holds, so a quiet slab pays a quiet halo; a block whose window is empty takes the identity, which is what ITK does beyond the field. The field is passed over once when the graph is built, a chunk at a time, to learn the range per chunk, and the per-block region is the arithmetic identity region widened by it: profiled at 256 blocks, the pipeline round trip it replaces was three quarters of the graph build. Measured against the whole-field path on the same inputs, checksums equal: 2D 2048^2 over 256 blocks, 29.4 s and +754 MB there, under a second and flat here; 3D 256^3 over 64 blocks, 45.7 s and +4156 MB there. On float32 the streamed result is the undecomposed result pixel for pixel; a window declares its own origin, which changes the last bits of the continuous index ITK computes from it, so on float64 the two agree to about 1e-13.
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History rewritten into two commits, the bound and the streaming; the tree is byte-identical to the nine-commit head and the branch is rebased onto current main. Each commit stands alone: the first passes 109 Python and 40 TypeScript tests without the second. Full suite on the head: 1464 passed, 3 skipped. |
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@vboussot looks great! Did you re-run the elastix notebook? Are there any changes to the embedded figures there? |
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The notebook registers rigid + affine, so nothing on this branch reaches its path: running that same linear composite through |
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Re-ran it, bbeef02. The geometry is identical to the committed run, the pyramid table, the registration, the output grid and the block/region line all match character for character; what moved is the timings and peak RSS, which are now this machine's. One fix was needed to read the stores at all, and it is independent of this branch: obstore does not resolve the bucket region the way fsspec did, so the anonymous read was going to us-east-1 for a bucket in us-west-2, and it fails the same way on released 0.45.0. |
2 participants
Closes #692.
resamplestreamed the moving image and nothing else. An RFC-5displacementsorcoordinatestransform was converted before the graph was built, and that conversion read its field in full and allocated three to five times its size on top of it. A field the size of the volume had to fit in memory while the moving image did not.While measuring that, a second thing turned up, and it is the one that matters more.
The region misses what a field does inside the grid
resample_bounding_boxsizes a region by walking the boundary of the transformed grid. That reports a linear map exactly and says nothing about what a displacement does strictly inside it. A field that is zero on the boundary voxels and large in the middle left the region covering the grid alone, andresamplethen returned the default value for every pixel the bump displaces onto.Measured on a 64x64 grid, a 160x160 moving image and a bump of 60 pixels in the middle:
The same appears in 3D, and on the ITK-transform branch, so the cause is the boundary walk rather than the RFC-5 conversion. This PR fixes the RFC-5 field path; the ITK-transform branch is #696.
What replaces it
A
displacementsorcoordinatestransform is the identity plus a displacement, so the region is now the grid's own image moved and widened by the range that displacement takes.The range comes from the field itself. A chunk is read, two numbers per component are kept, the values are dropped. A field is read through a kernel that is non-negative and sums to one, so a displacement anywhere is a convex combination of the values around it and lies between their smallest and largest: a bound, not a sample.
The range is kept rather than its magnitude, which matters in practice. A field that shifts every point the same way moves the region instead of widening it, so the region for a constant field is still the affine one to the pixel, and
test_rfc5_displacements_matches_the_itk_field_it_came_frompasses unchanged.What each block reads
Each output block reads the window of the field its own points fall in, and that window becomes the block's ITK transform. What sizes the block's moving read is the range of displacement that window holds, so a quiet slab pays a quiet halo instead of the worst displacement in the volume. The field is passed over once when the graph is built, a chunk at a time, to learn the range per chunk; nothing else about it is held.
A block whose window falls outside the field takes the identity, which is what ITK does there anyway.
Measured
3 x 256^3 float32 field, 201 MB, resident growth over the source buffer:
The streamed result is the undecomposed result pixel for pixel on a float32 image. A window declares its own origin, which changes the last bits of the continuous index ITK computes from it, so on a float64 image the two agree to about 1e-13 rather than exactly. That is recorded in the
resampledocstring.The crop window keeps one lattice point per side. Zero is sufficient and one is safe: checked over about 700 blocks, 2D and 3D, aligned and unaligned, round and non-round field geometry, and a window one point short per side is not sufficient.
Benchmark
Against
main, which converts the whole field once and hands it to the pipeline per block. Same inputs, 4 workers, and the checksums are equal, so the outputs are identical to the bit.On
mainthe whole field crosses into wasm once per block while the graph is built, and again inside each block's resample. Here a block carries only its window, and the region it reads is arithmetic.Profiled after the first round, the remaining build time was three quarters a wasm round trip per block that measured nothing but the identity: a field transform's linear part.
_identity_regioncomputes that region directly inresample's per-block loop, andtest_the_identity_region_is_the_pipelinespins it to the pipeline's own answer over randomized geometry, all seven reported fields. The publicresample_bounding_boxstays on the pipeline: it is called once per invocation, and the pipeline remains the one authority for its answer. What is left of the build is the single pass over the field for the per-chunk ranges, and the compute is the resampling itself: profiled single-threaded, wasm execution takes 0.44 s of a 0.9 s compute, and the Python around it under 0.1 s.TypeScript
TypeScript has no
resample, butresampleBoundingBoxhad the same boundary walk and the same whole-field read, so both halves are mirrored there.fieldImage,fieldWindowandfieldDisplacementRangeare the counterparts of the Python helpers.Design
The shape is KonfAI's
Resample, moved upstream rather than reimplemented: the field is read region by region, the window a region samples is its own box, and the range of the values just read bounds that region's pull. That is the direction of #650 and #667, one streamed resampler upstream instead of a bespoke one downstream.Base
On
main, which carries #674.Summary by CodeRabbit
New Features
Bug Fixes
Tests