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feat(registration): DeepALI closed-form point reg + template pre-registration hook - #139

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Hendrik-code merged 13 commits into
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Point-Reg
Sep 2, 2026
Merged

feat(registration): DeepALI closed-form point reg + template pre-registration hook#139
Hendrik-code merged 13 commits into
mainfrom
Point-Reg

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@robert-graf

@robert-graf robert-graf commented Aug 26, 2026 •
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Summary

Adds a DeepALI-based closed-form rigid point registration, teaches General_Registration to work when fixed/moving live on different grids and to accept POI landmark sets directly, and introduces Template_Registration2 which composes those pieces so the atlas no longer has to be resampled between the rigid and deformable stages. Optional-dependency handling is tightened along the way and the whole subsystem is documented in CLAUDE_reg.md.

New public surface

  • Deepali_Point_Registration (_ridged_points/deepali_point_registration.py)
    • Kabsch/Horn SVD fit on paired POIs; result exposed as a DeepALI HomogeneousTransform on the target grid so it plugs directly into DeepALI pipelines.
    • Full parity with the SITK Point_Registration API: transform_nii, transform_poi, transform_poi_inverse, transform_cord(+inverse), get_affine, pickle save/load, apply() dispatch, deepali_transform property.
    • _horn_rigid handles the degenerate N == 1 case as a pure translation (R = I, t = q − p) instead of erroring out.
    • Helpers ridged_points_from_poi_deepali / ridged_points_from_subreg_vert_deepali mirroring the SITK counterparts.
  • General_Registration (_deepali/deepali_model.py)
    • New same_space=True flag (default = old behaviour). When False, transform_nii threads the true moving grid into TransformImage, so fixed and moving can differ in shape / spacing / orientation.
    • source_landmarks / target_landmarks now accept POI or POI_Global. Shared IDs are matched automatically and converted to target-grid cube-coordinate tensors for LandmarkPointDistance.
    • get_dump / load_ include the new flag; legacy 4-tuple dumps still load and default to same_space=True.
  • Template_Registration2 (_deformable/multilabel_segmentation.py)
    • Same shape as Template_Registration (rigid → deformable, optional crop, optional side-flip) but uses Deepali_Pod stage and accepts a pre_registration= argument. When supplied, no landmarks/centroids are computed internally.
    • save/load take gpu/ddevice so a round-trip on CPU no longer forces the deformable transform onto CUDA.

Refactor

  • Extracted a module-level _flip_r_axis(x) (with a _r_axis_slicer(axis) helper) in multilabel_segmentation.py. Replnching flip blocks in Template_Registration.init / transform_nii / transform_poi / transform_poi_inverse and the
    same pattern in Template_Registration2. Typed with a TypeVar so callers get their own subtype back; explicitly renstead of silently returning garbage — this fixed a latent bug in Template_Registration.transform_poi_inverse.

Optional-dependency UX

  • TPTBox.registration/init now imports each deepali-backed class in its own try/except. On failure a stub builtb / _make_missing_deepali_func replaces the name. Any use raises a clear ImportError with pip install torch
    hf-deepali. SITK Point_Registration stays fully usable when deepali is absent.
  • TPTBox.core.internal.elastic_deform.py no longer imports elasticdeform bare — it raises an ImportError whose messlled NumPy version at runtime and, on NumPy 2.x, prints the exact source-tarball command that fixes the broken PyPIwheel:
    pip install --no-binary :all: --no-build-isolation --force-reinstall --no-deps
    https://github.com/gvtulder/elasticdeform/archive/refs/tags/v0.5.1.tar.gz

Tests (unit_tests/test_registration_deepali.py)

27 tests, all pass on CPU in ~20 s:Deepali_Point_Registration — identity, translation, full-reorientation numerics; transform_nii matches ground trusform_poi_inverse round-trip; transform_cord/_inverse round-trip; apply() dispatch; deepali_transform type;save/load; too-few-points → ValueError at 0, translation at 1.General_Registration — same_space=False smoke, POI landmark shape/matching, real POI-driven landmark loss actuall) → source residual < 0.02 in cube coords), POI_Global path, save/load round-trip preserving same_space, legacy4-tuple load.

  • Template_Registration2 — pipeline w/ pre-registration, only_rigid=True, transform_poi, auto-fit path when pre_registration=None, save/load round-trip, and — using elasticdeform with fixed small params — a real "deformable stage improves overlap vs. rigid-only" assertion (IoU 0.74 → 0.98).
  • _flip_r_axis — involution on NII and voxel POI, R-axis is the only coordinate that changes, POI_Global explicitly
  • Optional-import stubs — pin the wording of the missing-deepali ImportError.
  • Speed / memory bench — logs a summary line comparing SITK vs. DeepALI on both fit and warp.

Benchmarks (CPU, py3.12)

┌─────────────────────────────┬─────────┬──────────┐
│ │ SITK │ Deepali │
├─────────────────────────────┼─────────┼──────────┤
│ fit (73³) │ ~7.3 ms │ ~1.4 ms │
├─────────────────────────────┼─────────┼──────────┤
│ warp (73³) │ ~9.6 ms │ ~19.7 ms │
├─────────────────────────────┼─────────┼──────────┤
│ fit (270×220×72) │ ~87 ms │ ~1.4 ms │
├─────────────────────────────┼─────────┼──────────┤
│ warp (270×220×72) │ ~131 ms │ ~243 ms │
├─────────────────────────────┼─────────┼──────────┤
│ mean voxel err (270×220×72) │ 6.53 │ 0.0002 │
└─────────────────────────────┴─────────┴──────────┘

Deepali's fit is ~5–60× faster (Kabsch stays constant with N); warp is 1.5–2× slower on CPU but drastically more accurate (SITK BSpline shows heavy ringing). GPU flips the warp comparison.

Non-goals / follow-ups

  • SITK Point_Registration still requires ≥ 2 landmarks (the single-point relaxation is DeepALI-only for now — LandmarkBasedTransformInitializer would need an equivalent manual fallback).
  • No user-facing changes to Rigid_Elements_Registration.

Test plan

  • pytest unit_tests/test_registration_deepali.py — 27 passed
  • ruff check TPTBox/registration/ TPTBox/core/internal/elastic_deform.py unit_tests/test_registration_deepali.p
  • Verified import graceful-degradation with deepali blocked on the meta path
  • Verified elasticdeform dynamic error message on both NumPy 1.x and 2.x branches

🤖 Generated with Claude Code

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github-actions Bot commented Aug 26, 2026 •
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Benchmark comparison

Speed (wall time per call)

baseline ab4d843 vs head ab4d843 · python 3.11.16 · 5 repeats + 1 warmup

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 ms are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_save 9.32 ±0.30 9.05 ±0.14 -2.9% 0.102
nii_rescale 31.23 ±0.14 31.96 ±0.68 +2.3% 0.053
nii_dilate_msk 95.88 ±0.20 93.96 ±0.42 -2.0% 0.000
nii_fill_holes 3.79 ±0.04 3.72 ±0.07 -1.6% 0.164
nii_load_img 9.35 ±0.09 9.22 ±0.03 -1.4% 0.077
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_erode_msk 4.90 ±0.05 4.84 ±0.06 -1.1% 0.178
poi_calc_centroids_nocrop 3.42 ±0.03 3.45 ±0.04 +1.0% 0.422
nii_filter_connected_components 3.36 ±0.04 3.33 ±0.05 -0.7% 0.368
nii_resample_from_to 32.57 ±0.14 32.66 ±0.56 +0.3% 0.251
poi_calc_poi_from_subreg_vert 9.12 ±0.16 9.12 ±0.11 -0.0% 0.431
metric_voxels 250463.00 ±0.00 250463.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 14.51 ±0.00 14.51 ±0.00 +0.0% —
nii_get_array 0.05 ±0.01 0.03 ±0.00 -39.9% (noise) 0.000
nii_reorient 0.71 ±0.02 0.52 ±0.03 -26.7% (noise) 0.000
nii_extract_label 0.33 ±0.04 0.25 ±0.02 -23.6% (noise) 0.026
nii_pad_to 0.56 ±0.05 0.43 ±0.03 -23.5% (noise) 0.004
nii_apply_crop 0.59 ±0.06 0.47 ±0.06 -20.6% (noise) 0.015
nii_set_dtype 0.41 ±0.06 0.33 ±0.05 -19.3% (noise) 0.048
poi_to_global 0.14 ±0.01 0.16 ±0.01 +14.9% (noise) 0.018
poi_map_labels 0.13 ±0.01 0.12 ±0.01 -7.7% (noise) 0.321
nii_compute_crop 0.29 ±0.02 0.27 ±0.01 -7.7% (noise) 0.048
poi_resample_from_to 0.45 ±0.01 0.42 ±0.01 -7.1% (noise) 0.008
poi_local_to_global_arr 0.20 ±0.00 0.21 ±0.02 +6.0% (noise) 0.240
nii_map_labels 0.68 ±0.04 0.64 ±0.08 -5.4% (noise) 0.889
poi_load 0.69 ±0.01 0.67 ±0.02 -2.4% (noise) 0.062
poi_reorient 0.27 ±0.01 0.26 ±0.02 -2.2% (noise) 0.555
nii_center_of_masses 1.39 ±0.01 1.42 ±0.02 +1.9% (noise) 0.052
poi_rescale 0.14 ±0.00 0.14 ±0.01 -1.7% (noise) 0.926
nii_get_connected_components 1.61 ±0.09 1.58 ±0.02 -1.4% (noise) 0.156
nii_load_seg 2.39 ±0.07 2.35 ±0.08 -1.3% (noise) 0.663
poi_save 0.32 ±0.02 0.32 ±0.03 +1.1% (noise) 0.377
nii_unique 0.46 ±0.01 0.46 ±0.02 -0.9% (noise) 0.692
nii_rescale_seg 2.57 ±0.01 2.59 ±0.44 +0.8% (noise) 0.278
nii_volumes 1.52 ±0.02 1.51 ±0.04 -0.4% (noise) 0.808
poi_calc_centroids 1.92 ±0.03 1.92 ±0.04 -0.2% (noise) 0.910

ct_2d — shape (73, 47, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_resample_from_to 6.02 ±0.17 5.67 ±0.18 -5.7% 0.101
nii_dilate_msk 11.10 ±0.13 10.80 ±0.05 -2.7% 0.003
nii_rescale 4.47 ±0.15 4.49 ±0.19 +0.3% 0.979
metric_voxels 3431.00 ±0.00 3431.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
metric_foreground_pct 37.60 ±0.00 37.60 ±0.00 +0.0% —
poi_to_global 0.25 ±0.01 0.22 ±0.01 -11.0% (noise) 0.002
poi_resample_from_to 0.67 ±0.04 0.61 ±0.01 -9.5% (noise) 0.031
nii_unique 0.13 ±0.00 0.12 ±0.01 -9.0% (noise) 0.016
nii_reorient 0.68 ±0.02 0.74 ±0.04 +8.3% (noise) 0.052
poi_save 0.47 ±0.04 0.44 ±0.02 -8.3% (noise) 0.114
nii_extract_label 0.40 ±0.01 0.37 ±0.01 -8.2% (noise) 0.001
poi_calc_centroids_nocrop 0.97 ±0.03 0.90 ±0.02 -6.9% (noise) 0.004
nii_get_connected_components 0.61 ±0.02 0.57 ±0.08 -6.7% (noise) 0.733
poi_map_labels 0.20 ±0.01 0.19 ±0.00 -6.5% (noise) 0.001
nii_save 1.14 ±0.06 1.21 ±0.05 +6.3% (noise) 0.293
nii_erode_msk 0.83 ±0.03 0.78 ±0.02 -6.1% (noise) 0.031
poi_calc_centroids 0.82 ±0.02 0.77 ±0.02 -5.6% (noise) 0.006
nii_center_of_masses 0.20 ±0.00 0.19 ±0.01 -4.9% (noise) 0.019
poi_local_to_global_arr 0.23 ±0.00 0.25 ±0.01 +4.5% (noise) 0.039
nii_fill_holes 0.74 ±0.01 0.70 ±0.01 -4.3% (noise) 0.002
nii_load_seg 1.45 ±0.06 1.39 ±0.03 -3.9% (noise) 0.028
poi_rescale 0.23 ±0.01 0.22 ±0.01 -3.6% (noise) 0.075
nii_apply_crop 0.62 ±0.02 0.61 ±0.01 -2.9% (noise) 0.051
nii_get_array 0.02 ±0.00 0.02 ±0.01 -2.8% (noise) 0.643
poi_reorient 0.39 ±0.01 0.40 ±0.01 +2.3% (noise) 0.012
nii_map_labels 0.45 ±0.02 0.44 ±0.02 -2.1% (noise) 0.791
nii_pad_to 0.51 ±0.05 0.52 ±0.01 +1.8% (noise) 0.838
nii_volumes 0.26 ±0.45 0.26 ±0.01 -1.8% (noise) 0.367
nii_load_img 1.22 ±0.05 1.20 ±0.05 -1.4% (noise) 0.594
nii_set_dtype 0.38 ±0.02 0.38 ±0.01 -1.4% (noise) 0.683
nii_rescale_seg 0.68 ±0.02 0.69 ±0.04 +1.3% (noise) 0.456
nii_compute_crop 0.14 ±0.00 0.14 ±0.01 -1.1% (noise) 0.396
poi_load 0.82 ±0.01 0.81 ±0.01 -0.8% (noise) 0.349
nii_filter_connected_components 0.79 ±0.03 0.79 ±0.12 -0.7% (noise) 0.651

mri_3d — shape (68, 52, 67)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_fill_holes 4.83 ±0.09 4.71 ±0.03 -2.4% 0.046
nii_dilate_msk 124.20 ±0.47 121.33 ±0.82 -2.3% 0.001
nii_load_img 7.45 ±0.06 7.55 ±0.05 +1.3% 0.178
nii_save 7.50 ±0.06 7.45 ±0.06 -0.7% 0.122
nii_resample_from_to 30.60 ±0.39 30.42 ±0.13 -0.6% 0.282
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
poi_calc_poi_from_subreg_vert 8.49 ±0.12 8.54 ±0.09 +0.6% 0.954
nii_rescale 29.21 ±0.10 29.07 ±0.10 -0.5% 0.167
nii_filter_connected_components 3.67 ±0.04 3.66 ±0.04 -0.4% 0.508
nii_erode_msk 6.39 ±0.19 6.41 ±0.04 +0.3% 0.880
poi_calc_centroids_nocrop 7.13 ±0.02 7.14 ±0.06 +0.1% 0.379
metric_voxels 236912.00 ±0.00 236912.00 ±0.00 +0.0% —
metric_labels 8.00 ±0.00 8.00 ±0.00 +0.0% —
metric_foreground_pct 18.21 ±0.00 18.21 ±0.00 +0.0% —
poi_save 0.50 ±0.01 0.48 ±0.01 -5.4% (noise) 0.017
poi_map_labels 0.22 ±0.00 0.21 ±0.00 -5.4% (noise) 0.000
nii_extract_label 0.42 ±0.01 0.41 ±0.01 -2.6% (noise) 0.236
nii_unique 0.51 ±0.02 0.50 ±0.01 -2.5% (noise) 0.305
nii_get_array 0.05 ±0.00 0.05 ±0.00 +2.4% (noise) 0.178
nii_reorient 0.76 ±0.04 0.75 ±0.01 -2.3% (noise) 0.487
poi_resample_from_to 0.66 ±0.01 0.64 ±0.02 -2.3% (noise) 0.116
poi_local_to_global_arr 0.25 ±0.01 0.25 ±0.04 +1.9% (noise) 0.273
nii_rescale_seg 2.51 ±0.05 2.46 ±0.03 -1.7% (noise) 0.128
nii_load_seg 2.26 ±0.11 2.29 ±0.04 +1.6% (noise) 0.631
nii_get_connected_components 1.67 ±0.02 1.70 ±0.03 +1.6% (noise) 0.260
poi_reorient 0.43 ±0.02 0.42 ±0.01 -1.4% (noise) 0.177
nii_set_dtype 0.47 ±0.03 0.46 ±0.02 -1.3% (noise) 0.448
poi_to_global 0.25 ±0.01 0.25 ±0.01 +1.1% (noise) 0.815
poi_rescale 0.26 ±0.01 0.26 ±0.01 +0.9% (noise) 0.586
nii_map_labels 0.83 ±0.02 0.84 ±0.02 +0.9% (noise) 0.937
nii_volumes 1.64 ±0.02 1.63 ±0.01 -0.7% (noise) 0.098
nii_compute_crop 0.32 ±0.00 0.32 ±0.01 +0.6% (noise) 0.934
poi_calc_centroids 2.27 ±0.02 2.28 ±0.01 +0.5% (noise) 0.645
nii_apply_crop 0.62 ±0.01 0.62 ±0.01 +0.4% (noise) 0.820
poi_load 1.67 ±0.01 1.66 ±0.02 -0.2% (noise) 0.917
nii_pad_to 0.65 ±0.02 0.65 ±0.02 +0.2% (noise) 1.000
nii_center_of_masses 1.65 ±0.01 1.65 ±0.01 -0.1% (noise) 0.163

mri_2d — shape (68, 52, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_rescale 4.52 ±0.20 4.25 ±0.03 -5.9% 0.144
nii_resample_from_to 5.82 ±0.16 5.59 ±0.08 -4.0% 0.111
nii_dilate_msk 14.69 ±0.13 14.16 ±0.10 -3.6% 0.000
metric_voxels 3536.00 ±0.00 3536.00 ±0.00 +0.0% —
metric_labels 7.00 ±0.00 7.00 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
metric_foreground_pct 50.17 ±0.00 50.17 ±0.00 +0.0% —
nii_get_array 0.02 ±0.00 0.02 ±0.00 -12.2% (noise) 0.115
nii_set_dtype 0.39 ±0.03 0.36 ±0.01 -9.0% (noise) 0.062
nii_pad_to 0.53 ±0.03 0.49 ±0.01 -6.4% (noise) 0.020
nii_apply_crop 0.61 ±0.03 0.58 ±0.01 -6.2% (noise) 0.033
nii_rescale_seg 0.70 ±0.04 0.66 ±0.01 -5.5% (noise) 0.072
poi_save 0.50 ±0.03 0.48 ±0.01 -5.0% (noise) 0.090
nii_save 1.20 ±0.03 1.15 ±0.02 -4.2% (noise) 0.023
nii_load_img 1.23 ±0.04 1.18 ±0.03 -4.0% (noise) 0.028
nii_volumes 0.39 ±0.01 0.38 ±0.01 -4.0% (noise) 0.008
nii_fill_holes 0.87 ±0.02 0.84 ±0.01 -3.5% (noise) 0.038
poi_calc_centroids_nocrop 1.14 ±0.04 1.10 ±0.02 -3.5% (noise) 0.036
poi_reorient 0.43 ±0.03 0.42 ±0.01 -3.1% (noise) 0.539
nii_map_labels 0.45 ±0.03 0.44 ±0.01 -3.1% (noise) 0.735
poi_map_labels 0.22 ±0.00 0.22 ±0.01 +3.0% (noise) 0.070
poi_load 1.51 ±0.02 1.56 ±0.12 +3.0% (noise) 0.138
nii_unique 0.13 ±0.01 0.12 ±0.01 -2.7% (noise) 0.421
nii_erode_msk 1.00 ±0.02 0.97 ±0.05 -2.7% (noise) 0.842
poi_calc_centroids 0.95 ±0.02 0.92 ±0.01 -2.6% (noise) 0.054
nii_extract_label 0.38 ±0.01 0.37 ±0.02 -2.1% (noise) 0.075
poi_resample_from_to 0.64 ±0.03 0.63 ±0.02 -1.7% (noise) 0.574
poi_to_global 0.25 ±0.01 0.25 ±0.01 -1.6% (noise) 0.094
poi_local_to_global_arr 0.24 ±0.00 0.25 ±0.01 +1.4% (noise) 0.119
nii_reorient 0.69 ±0.02 0.68 ±0.02 -1.3% (noise) 0.323
nii_compute_crop 0.13 ±0.01 0.13 ±0.01 +0.9% (noise) 0.615
nii_load_seg 1.34 ±0.05 1.35 ±0.03 +0.8% (noise) 0.444
nii_get_connected_components 0.58 ±0.03 0.58 ±0.02 -0.7% (noise) 0.459
poi_rescale 0.26 ±0.02 0.26 ±0.02 -0.7% (noise) 0.823
nii_filter_connected_components 0.75 ±0.01 0.75 ±0.01 +0.3% (noise) 0.967
nii_center_of_masses 0.34 ±0.01 0.33 ±0.01 -0.1% (noise) 0.825

Gate: a measurement fails when the baseline is ≥ 1 ms, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

Memory (peak RSS growth per call)

baseline ab4d843 vs head ab4d843 · python 3.11.16 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.90 MiB

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 MiB are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_fill_holes 6.41 ±0.00 6.45 ±0.00 +0.7% —
nii_load_img 3.56 ±0.00 3.57 ±0.00 +0.1% —
nii_save 3.84 ±0.00 3.84 ±0.00 +0.1% —
nii_load_seg 6.07 ±0.00 6.07 ±0.00 +0.1% —
poi_calc_poi_from_subreg_vert 7.30 ±0.00 7.30 ±0.00 -0.1% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_set_dtype 5.37 ±0.00 5.37 ±0.00 +0.0% —
nii_reorient 5.97 ±0.00 5.97 ±0.00 +0.0% —
nii_rescale 6.42 ±0.00 6.42 ±0.00 +0.0% —
nii_rescale_seg 6.18 ±0.00 6.18 ±0.00 +0.0% —
nii_resample_from_to 6.55 ±0.00 6.55 ±0.00 +0.0% —
nii_apply_crop 5.93 ±0.00 5.93 ±0.00 +0.0% —
nii_pad_to 5.49 ±0.00 5.49 ±0.00 +0.0% —
nii_volumes 3.52 ±0.00 3.52 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
nii_extract_label 5.49 ±0.00 5.49 ±0.00 +0.0% —
nii_map_labels 5.55 ±0.00 5.55 ±0.00 +0.0% —
nii_dilate_msk 6.05 ±0.00 6.05 ±0.00 +0.0% —
nii_erode_msk 6.07 ±0.00 6.07 ±0.00 +0.0% —
nii_get_connected_components 6.68 ±0.00 6.68 ±0.00 +0.0% —
nii_filter_connected_components 6.99 ±0.00 6.99 ±0.00 +0.0% —
poi_calc_centroids 6.18 ±0.00 6.18 ±0.00 +0.0% —
poi_calc_centroids_nocrop 6.05 ±0.00 6.05 ±0.00 +0.0% —
poi_reorient 3.89 ±0.00 3.89 ±0.00 +0.0% —
poi_to_global 3.14 ±0.00 3.14 ±0.00 +0.0% —
poi_local_to_global_arr 3.02 ±0.00 3.02 ±0.00 +0.0% —
poi_resample_from_to 5.53 ±0.00 5.53 ±0.00 +0.0% —
metric_voxels 250463.00 ±0.00 250463.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 14.51 ±0.00 14.51 ±0.00 +0.0% —
nii_get_array 1.65 ±0.00 1.65 ±0.00 +0.0% (noise) —
nii_compute_crop 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.61 ±0.00 2.61 ±0.00 +0.0% (noise) —
poi_save 1.46 ±0.00 1.46 ±0.00 +0.0% (noise) —
poi_map_labels 1.77 ±0.00 1.77 ±0.00 +0.0% (noise) —
poi_load 1.61 ±0.00 1.61 ±0.00 +0.0% (noise) —

ct_2d — shape (73, 47, 1)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_fill_holes 6.35 ±0.00 6.39 ±0.00 +0.7% —
nii_load_img 3.50 ±0.00 3.50 ±0.00 +0.1% —
nii_save 3.77 ±0.00 3.78 ±0.00 +0.1% —
nii_load_seg 6.01 ±0.00 6.01 ±0.00 +0.1% —
nii_set_dtype 5.30 ±0.00 5.30 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_reorient 5.91 ±0.00 5.91 ±0.00 +0.0% —
nii_rescale 6.36 ±0.00 6.36 ±0.00 +0.0% —
nii_rescale_seg 6.12 ±0.00 6.12 ±0.00 +0.0% —
nii_resample_from_to 6.48 ±0.00 6.48 ±0.00 +0.0% —
nii_apply_crop 5.87 ±0.00 5.87 ±0.00 +0.0% —
nii_pad_to 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.15 ±0.00 3.15 ±0.00 +0.0% —
nii_extract_label 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_map_labels 5.49 ±0.00 5.49 ±0.00 +0.0% —
nii_dilate_msk 5.99 ±0.00 5.99 ±0.00 +0.0% —
nii_erode_msk 6.01 ±0.00 6.01 ±0.00 +0.0% —
nii_get_connected_components 6.62 ±0.00 6.62 ±0.00 +0.0% —
nii_filter_connected_components 6.93 ±0.00 6.93 ±0.00 +0.0% —
poi_calc_centroids 6.12 ±0.00 6.12 ±0.00 +0.0% —
poi_calc_centroids_nocrop 6.05 ±0.00 6.05 ±0.00 +0.0% —
poi_reorient 3.83 ±0.00 3.83 ±0.00 +0.0% —
poi_to_global 3.08 ±0.00 3.08 ±0.00 +0.0% —
poi_resample_from_to 5.46 ±0.00 5.46 ±0.00 +0.0% —
metric_voxels 3431.00 ±0.00 3431.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 37.60 ±0.00 37.60 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
nii_unique 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_save 1.40 ±0.00 1.40 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

mri_3d — shape (68, 52, 67)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_fill_holes 6.35 ±0.00 6.39 ±0.00 +0.7% —
poi_calc_centroids 6.12 ±0.00 6.12 ±0.00 -0.1% —
nii_volumes 3.47 ±0.00 3.46 ±0.00 -0.1% —
nii_load_img 3.56 ±0.00 3.57 ±0.00 +0.1% —
nii_save 3.77 ±0.00 3.78 ±0.00 +0.1% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_load_seg 6.01 ±0.00 6.01 ±0.00 +0.1% —
nii_set_dtype 5.37 ±0.00 5.37 ±0.00 +0.0% —
nii_reorient 5.91 ±0.00 5.91 ±0.00 +0.0% —
nii_rescale 6.36 ±0.00 6.36 ±0.00 +0.0% —
nii_rescale_seg 6.12 ±0.00 6.12 ±0.00 +0.0% —
nii_resample_from_to 6.48 ±0.00 6.48 ±0.00 +0.0% —
nii_apply_crop 5.87 ±0.00 5.87 ±0.00 +0.0% —
nii_pad_to 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_center_of_masses 3.15 ±0.00 3.15 ±0.00 +0.0% —
nii_extract_label 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_map_labels 5.49 ±0.00 5.49 ±0.00 +0.0% —
nii_dilate_msk 5.99 ±0.00 5.99 ±0.00 +0.0% —
nii_erode_msk 6.01 ±0.00 6.01 ±0.00 +0.0% —
nii_get_connected_components 6.62 ±0.00 6.62 ±0.00 +0.0% —
nii_filter_connected_components 6.93 ±0.00 6.93 ±0.00 +0.0% —
poi_calc_centroids_nocrop 5.99 ±0.00 5.99 ±0.00 +0.0% —
poi_reorient 3.83 ±0.00 3.83 ±0.00 +0.0% —
poi_to_global 3.08 ±0.00 3.08 ±0.00 +0.0% —
poi_resample_from_to 5.46 ±0.00 5.46 ±0.00 +0.0% —
poi_calc_poi_from_subreg_vert 7.30 ±0.00 7.30 ±0.00 +0.0% —
metric_voxels 236912.00 ±0.00 236912.00 ±0.00 +0.0% —
metric_labels 8.00 ±0.00 8.00 ±0.00 +0.0% —
metric_foreground_pct 18.21 ±0.00 18.21 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
nii_unique 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_save 1.46 ±0.00 1.46 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

mri_2d — shape (68, 52, 1)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_fill_holes 6.35 ±0.00 6.39 ±0.00 +0.7% —
nii_load_img 3.56 ±0.00 3.57 ±0.00 +0.1% —
nii_save 3.77 ±0.00 3.78 ±0.00 +0.1% —
nii_load_seg 6.01 ±0.00 6.01 ±0.00 +0.1% —
nii_set_dtype 5.37 ±0.00 5.37 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_reorient 5.91 ±0.00 5.91 ±0.00 +0.0% —
nii_rescale 6.36 ±0.00 6.36 ±0.00 +0.0% —
nii_rescale_seg 6.12 ±0.00 6.12 ±0.00 +0.0% —
nii_resample_from_to 6.48 ±0.00 6.48 ±0.00 +0.0% —
nii_apply_crop 5.87 ±0.00 5.87 ±0.00 +0.0% —
nii_pad_to 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.15 ±0.00 3.15 ±0.00 +0.0% —
nii_extract_label 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_map_labels 5.49 ±0.00 5.49 ±0.00 +0.0% —
nii_dilate_msk 5.99 ±0.00 5.99 ±0.00 +0.0% —
nii_erode_msk 6.01 ±0.00 6.01 ±0.00 +0.0% —
nii_get_connected_components 6.62 ±0.00 6.62 ±0.00 +0.0% —
nii_filter_connected_components 6.93 ±0.00 6.93 ±0.00 +0.0% —
poi_calc_centroids 6.12 ±0.00 6.12 ±0.00 +0.0% —
poi_calc_centroids_nocrop 6.05 ±0.00 6.05 ±0.00 +0.0% —
poi_reorient 3.83 ±0.00 3.83 ±0.00 +0.0% —
poi_to_global 3.08 ±0.00 3.08 ±0.00 +0.0% —
poi_resample_from_to 5.46 ±0.00 5.46 ±0.00 +0.0% —
metric_voxels 3536.00 ±0.00 3536.00 ±0.00 +0.0% —
metric_labels 7.00 ±0.00 7.00 ±0.00 +0.0% —
metric_foreground_pct 50.17 ±0.00 50.17 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
nii_unique 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_save 1.46 ±0.00 1.46 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

Gate: a measurement fails when the baseline is ≥ 1 MiB, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

@robert-graf robert-graf self-assigned this Aug 28, 2026
@robert-graf robert-graf added the enhancement New feature or request label Aug 28, 2026
This was referenced Sep 1, 2026
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@Hendrik-code
Hendrik-code merged commit 80e9de9 into main Sep 2, 2026
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@Hendrik-code
Hendrik-code deleted the Point-Reg branch September 2, 2026 07:55
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