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feat(np_utils): add non-convex ray marching and label interface thickness - #145

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feat/np-raymarch-thickness
Aug 28, 2026
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feat(np_utils): add non-convex ray marching and label interface thickness#145
Hendrik-code merged 2 commits into
mainfrom
feat/np-raymarch-thickness

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@Hendrik-code Hendrik-code commented Aug 27, 2026

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Upstreams B3 from the cross-repo survey.

⚠️ Stacked on #141 — np_label_interface_thickness builds on np_compute_boundary_normals from that PR, so this targets feat/upstream-point-and-normal-helpers rather than main. Retarget to main once #141 merges; the diff shown here is only this PR's changes.

What

np_utils

  • np_raymarch_until_background(arr, start, direction, …) — fixed-step, trilinear-interpolated march until the mask drops below a threshold, with max_steps / max_distance guards. Accepts a prebuilt interpolator for marching many rays through one mask.
  • np_label_interface_thickness(arr, label, other_label, zoom=…) — how thick label is where it meets other_label, measured by marching inward along the surface normal from every interface voxel.

poi_fun/ray_casting

  • max_distance_ray_cast_non_convex(region: NII, …) — NII wrapper, default step min(zoom)/16.

NII

  • label_interface_thickness(label, other_label, …) — returns millimetres via zoom.

Why this is a real gap

max_distance_ray_cast_convex bisects, which silently assumes convexity. On a mask with an interior gap it reports the far outer wall rather than the near edge of the gap:

mask [5,35) with a hole at [15,20), ray from x=6 along +x result
max_distance_ray_cast_convex (existing) 34.5 — skipped the gap
max_distance_ray_cast_non_convex (new) 14.5 — correct

Both numbers are asserted in the tests, so the distinction stays pinned.

Changes from the source implementation

  • The interpolator is built once and reused. The original constructed a RegularGridInterpolator over the whole volume inside the per-boundary-voxel function, so cost scaled as O(n_boundary × volume). It is now built once in np_label_interface_thickness and passed in.
  • Distances are in mm when zoom is given, rather than voxels.
  • max_count_component is a parameter instead of hardcoded to 2.
  • Fixed a crash: when max_steps=None and only max_distance was set, the fallback assigned 1e8 (a float) to range(), raising TypeError. Now covered by a test.

A note on what the number means

Thickness is measured from the interface voxel's center to the 0.5 isosurface, so an 8-voxel slab reads ≈8.5, not 8.0. The half-voxel is inherent to interpolating a binary mask, and the tests assert the value with that offset rather than papering over it.

Verification

  • 13 new tests across unit_tests/test_nputils.py and unit_tests/test_nii_extended.py: exit point on a slab; stopping at an interior gap; the convex-bisection contrast; None on step and distance limits; missing-limit assertion; leaving the volume; known slab thickness and its zero variance; zoom scaling; no-contact empty result; max_count_component filtering (with a fixture where the second component genuinely touches the reference, so the parameter is actually exercised); and NII/array-level agreement.
  • Full suite: 491 passed, 4 skipped. ruff check clean.

🤖 Generated with Claude Code

@Hendrik-code @claude
feat(np_utils): add non-convex ray marching and label interface thick…
ae2e926 
…ness

Adds np_raymarch_until_background and np_label_interface_thickness to np_utils,
max_distance_ray_cast_non_convex to poi_fun/ray_casting, and
NII.label_interface_thickness as the mm-aware wrapper.

The existing max_distance_ray_cast_convex bisects, which assumes the region is
convex: on a mask with an interior gap it reports the far outer wall instead of
the near edge of the gap. The new marcher takes fixed trilinear-interpolated
steps, so concave and multi-lobed structures are handled correctly. A test
pins the difference - on the same mask the bisection returns 34.5 where the
marcher correctly stops at 14.5.

np_label_interface_thickness measures how thick one structure is where it meets
another, by marching inward along the surface normal from every interface
voxel.

Changes from the source implementation:
- the RegularGridInterpolator is built once and reused across rays, instead of
  being rebuilt over the whole volume for every boundary voxel
- distances are returned in mm when a zoom is given, rather than voxels
- max_count_component is a parameter instead of being hardcoded to 2
- fixed a crash when max_steps was None and only max_distance was set: the
  fallback assigned a float to range()

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@robert-graf
robert-graf self-requested a review August 28, 2026 09:55
Base automatically changed from feat/upstream-point-and-normal-helpers to main August 28, 2026 10:39
@Hendrik-code Hendrik-code self-assigned this Aug 28, 2026
@Hendrik-code Hendrik-code added the enhancement New feature or request label Aug 28, 2026
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github-actions Bot commented Aug 28, 2026

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Benchmark comparison

Speed (wall time per call)

baseline 0171e70 vs head 0171e70 · 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_dilate_msk 121.81 ±0.54 120.22 ±0.27 -1.3% 0.001
poi_calc_centroids_nocrop 4.30 ±0.03 4.34 ±0.03 +0.9% 0.027
nii_erode_msk 6.05 ±0.12 6.01 ±0.04 -0.7% 0.236
nii_fill_holes 4.56 ±0.03 4.59 ±0.03 +0.7% 0.053
nii_load_img 11.62 ±0.09 11.69 ±1.85 +0.6% 0.249
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_save 11.40 ±0.08 11.46 ±0.04 +0.5% 0.261
nii_filter_connected_components 4.19 ±0.02 4.17 ±0.03 -0.5% 0.087
nii_rescale_seg 3.02 ±0.01 3.04 ±0.03 +0.4% 0.412
nii_resample_from_to 41.48 ±0.10 41.62 ±0.27 +0.3% 0.276
nii_rescale 39.74 ±0.16 39.83 ±0.13 +0.2% 0.148
poi_calc_poi_from_subreg_vert 11.35 ±0.10 11.33 ±0.08 -0.1% 0.964
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 0.03 ±0.00 0.04 ±0.00 +19.5% (noise) 0.003
nii_pad_to 0.49 ±0.02 0.53 ±0.03 +7.6% (noise) 0.150
nii_set_dtype 0.35 ±0.02 0.37 ±0.03 +6.3% (noise) 0.201
poi_to_global 0.15 ±0.02 0.16 ±0.01 +5.1% (noise) 0.980
poi_save 0.36 ±0.02 0.34 ±0.01 -5.0% (noise) 0.519
nii_apply_crop 0.49 ±0.03 0.51 ±0.03 +3.5% (noise) 0.763
poi_rescale 0.17 ±0.01 0.17 ±0.01 +2.8% (noise) 0.637
poi_local_to_global_arr 0.24 ±0.00 0.23 ±0.00 -2.7% (noise) 0.005
nii_reorient 0.62 ±0.03 0.64 ±0.03 +2.4% (noise) 0.348
nii_compute_crop 0.27 ±0.02 0.28 ±0.02 +2.1% (noise) 0.658
nii_map_labels 0.77 ±0.02 0.78 ±0.02 +2.0% (noise) 0.208
poi_calc_centroids 2.41 ±0.42 2.36 ±0.03 -2.0% (noise) 0.184
poi_resample_from_to 0.53 ±0.01 0.53 ±0.02 -1.3% (noise) 0.902
poi_reorient 0.32 ±0.01 0.32 ±0.03 +1.2% (noise) 0.593
nii_extract_label 0.29 ±0.01 0.30 ±0.01 +1.1% (noise) 0.932
nii_get_connected_components 1.97 ±0.04 1.95 ±0.02 -0.9% (noise) 0.215
nii_unique 0.57 ±0.00 0.57 ±0.01 +0.9% (noise) 0.326
nii_volumes 1.90 ±0.01 1.88 ±0.02 -0.8% (noise) 0.079
poi_load 0.86 ±0.02 0.86 ±0.02 -0.5% (noise) 0.551
nii_center_of_masses 1.79 ±0.01 1.78 ±0.01 -0.4% (noise) 0.420
nii_load_seg 2.60 ±0.03 2.61 ±0.02 +0.4% (noise) 0.796
poi_map_labels 0.14 ±0.01 0.14 ±0.01 -0.0% (noise) 0.799

ct_2d — shape (73, 47, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_dilate_msk 14.08 ±0.10 13.81 ±0.04 -1.9% 0.001
nii_resample_from_to 7.06 ±0.03 7.07 ±0.12 +0.2% 0.714
nii_rescale 5.34 ±0.04 5.35 ±0.05 +0.1% 0.303
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% —
nii_get_array 0.02 ±0.00 0.01 ±0.00 -17.8% (noise) 0.227
nii_center_of_masses 0.21 ±0.02 0.18 ±0.01 -12.6% (noise) 0.026
nii_unique 0.12 ±0.01 0.11 ±0.01 -7.8% (noise) 0.234
poi_to_global 0.23 ±0.01 0.22 ±0.01 -5.9% (noise) 0.313
poi_save 0.46 ±0.02 0.48 ±0.03 +5.0% (noise) 0.560
nii_map_labels 0.46 ±0.01 0.44 ±0.02 -3.9% (noise) 0.520
nii_get_connected_components 0.61 ±0.03 0.59 ±0.01 -2.9% (noise) 0.410
nii_apply_crop 0.63 ±0.03 0.61 ±0.01 -2.7% (noise) 0.121
nii_extract_label 0.40 ±0.02 0.39 ±0.02 -2.2% (noise) 0.726
nii_volumes 0.26 ±0.01 0.27 ±0.01 +2.1% (noise) 0.724
nii_set_dtype 0.38 ±0.02 0.37 ±0.01 -1.9% (noise) 0.132
poi_map_labels 0.19 ±0.01 0.19 ±0.01 +1.8% (noise) 0.879
nii_load_img 1.40 ±0.02 1.37 ±0.01 -1.8% (noise) 0.118
poi_local_to_global_arr 0.27 ±0.01 0.27 ±0.00 -1.7% (noise) 0.575
poi_resample_from_to 0.69 ±0.02 0.68 ±0.01 -1.5% (noise) 0.092
poi_reorient 0.43 ±0.02 0.42 ±0.01 -1.3% (noise) 0.300
nii_rescale_seg 0.72 ±0.02 0.71 ±0.01 -1.3% (noise) 0.518
poi_calc_centroids_nocrop 1.03 ±0.01 1.02 ±0.03 -1.2% (noise) 0.699
nii_fill_holes 0.77 ±0.02 0.76 ±0.02 -1.1% (noise) 0.446
poi_rescale 0.24 ±0.01 0.24 ±0.01 -1.0% (noise) 0.658
poi_load 0.97 ±0.01 0.97 ±0.01 -0.9% (noise) 0.229
nii_save 1.28 ±0.02 1.27 ±0.02 -0.7% (noise) 0.998
nii_erode_msk 0.89 ±0.04 0.88 ±0.02 -0.6% (noise) 0.584
nii_reorient 0.74 ±0.02 0.73 ±0.02 -0.4% (noise) 0.502
poi_calc_centroids 0.84 ±0.02 0.83 ±0.02 -0.3% (noise) 0.444
nii_pad_to 0.52 ±0.04 0.52 ±0.01 +0.3% (noise) 0.392
nii_filter_connected_components 0.77 ±0.02 0.77 ±0.00 +0.2% (noise) 0.455
nii_load_seg 1.51 ±0.01 1.52 ±0.02 +0.2% (noise) 0.721
nii_compute_crop 0.13 ±0.01 0.13 ±0.00 -0.1% (noise) 0.875

mri_3d — shape (68, 52, 67)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_dilate_msk 158.45 ±0.74 154.88 ±0.32 -2.3% 0.000
poi_calc_centroids_nocrop 9.01 ±0.04 8.92 ±0.05 -1.1% 0.024
nii_filter_connected_components 4.55 ±0.02 4.51 ±0.04 -0.8% 0.082
nii_erode_msk 7.54 ±0.09 7.49 ±0.04 -0.6% 0.168
nii_save 9.42 ±0.03 9.45 ±0.08 +0.4% 0.810
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
poi_calc_poi_from_subreg_vert 10.73 ±0.08 10.69 ±0.06 -0.4% 0.909
nii_rescale 37.48 ±0.28 37.56 ±0.13 +0.2% 0.671
nii_resample_from_to 39.27 ±0.27 39.19 ±0.07 -0.2% 0.723
nii_rescale_seg 3.03 ±0.02 3.03 ±0.03 +0.0% 0.971
nii_load_img 9.40 ±0.05 9.40 ±0.03 -0.0% 0.493
nii_fill_holes 5.45 ±0.07 5.45 ±0.01 +0.0% 0.637
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 0.04 ±0.00 0.05 ±0.01 +37.1% (noise) 0.003
poi_to_global 0.26 ±0.01 0.25 ±0.01 -4.2% (noise) 0.468
poi_rescale 0.28 ±0.00 0.28 ±0.01 +3.2% (noise) 0.156
poi_map_labels 0.24 ±0.01 0.23 ±0.00 -3.0% (noise) 0.042
nii_pad_to 0.66 ±0.01 0.68 ±0.02 +2.6% (noise) 0.375
poi_save 0.53 ±0.01 0.54 ±0.02 +2.5% (noise) 0.506
nii_set_dtype 0.47 ±0.01 0.46 ±0.01 -1.9% (noise) 0.124
nii_load_seg 2.77 ±0.05 2.72 ±0.06 -1.7% (noise) 0.235
nii_compute_crop 0.33 ±0.01 0.34 ±0.01 +1.7% (noise) 0.880
nii_extract_label 0.42 ±0.01 0.41 ±0.02 -1.3% (noise) 0.726
poi_load 2.07 ±0.02 2.10 ±0.01 +1.2% (noise) 0.033
nii_apply_crop 0.66 ±0.01 0.66 ±0.01 -1.0% (noise) 0.295
poi_local_to_global_arr 0.28 ±0.01 0.28 ±0.01 -0.5% (noise) 0.712
nii_reorient 0.78 ±0.02 0.78 ±0.02 +0.4% (noise) 0.453
poi_resample_from_to 0.71 ±0.02 0.71 ±0.01 +0.3% (noise) 0.541
nii_unique 0.59 ±0.02 0.59 ±0.01 +0.2% (noise) 0.589
poi_calc_centroids 2.76 ±0.02 2.77 ±0.02 +0.2% (noise) 0.630
poi_reorient 0.44 ±0.01 0.44 ±0.02 -0.2% (noise) 0.590
nii_center_of_masses 2.05 ±0.01 2.05 ±0.03 +0.2% (noise) 0.669
nii_volumes 2.00 ±0.01 2.00 ±0.01 +0.1% (noise) 0.658
nii_get_connected_components 2.01 ±0.01 2.01 ±0.02 +0.1% (noise) 0.733
nii_map_labels 0.96 ±0.01 0.96 ±0.02 +0.0% (noise) 0.935

mri_2d — shape (68, 52, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_dilate_msk 18.72 ±0.09 18.19 ±0.05 -2.8% 0.000
nii_rescale 5.44 ±0.11 5.36 ±0.03 -1.6% 0.395
nii_resample_from_to 7.16 ±0.11 7.12 ±0.05 -0.5% 0.195
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_set_dtype 0.38 ±0.01 0.41 ±0.02 +8.7% (noise) 0.011
nii_get_array 0.01 ±0.00 0.02 ±0.00 +6.4% (noise) 0.340
poi_rescale 0.28 ±0.01 0.26 ±0.02 -4.7% (noise) 0.325
poi_resample_from_to 0.69 ±0.01 0.72 ±0.13 +3.6% (noise) 0.189
nii_get_connected_components 0.60 ±0.02 0.58 ±0.03 -3.4% (noise) 0.938
poi_load 1.84 ±0.02 1.90 ±0.03 +3.2% (noise) 0.002
poi_map_labels 0.23 ±0.01 0.23 ±0.01 -3.0% (noise) 0.477
poi_reorient 0.46 ±0.01 0.44 ±0.02 -3.0% (noise) 0.064
nii_erode_msk 1.14 ±0.02 1.11 ±0.01 -2.8% (noise) 0.072
nii_unique 0.12 ±0.00 0.12 ±0.01 +2.4% (noise) 0.658
nii_compute_crop 0.13 ±0.01 0.13 ±0.01 +2.2% (noise) 0.547
nii_filter_connected_components 0.81 ±0.03 0.80 ±0.02 -2.0% (noise) 0.738
nii_load_seg 1.54 ±0.02 1.51 ±0.01 -1.9% (noise) 0.036
poi_calc_centroids 1.05 ±0.02 1.07 ±0.05 +1.7% (noise) 0.134
nii_pad_to 0.51 ±0.02 0.52 ±0.02 +1.4% (noise) 0.944
poi_calc_centroids_nocrop 1.27 ±0.02 1.25 ±0.01 -1.4% (noise) 0.158
nii_apply_crop 0.62 ±0.02 0.61 ±0.01 -1.3% (noise) 0.389
nii_fill_holes 0.97 ±0.02 0.96 ±0.02 -1.3% (noise) 0.320
nii_extract_label 0.38 ±0.01 0.38 ±0.02 -1.2% (noise) 0.758
nii_rescale_seg 0.70 ±0.02 0.70 ±0.02 -1.2% (noise) 0.928
nii_load_img 1.40 ±0.04 1.38 ±0.03 -1.1% (noise) 0.423
poi_save 0.51 ±0.02 0.52 ±0.01 +1.1% (noise) 0.598
nii_volumes 0.44 ±0.01 0.43 ±0.01 -1.1% (noise) 0.298
nii_map_labels 0.45 ±0.03 0.45 ±0.02 +0.9% (noise) 0.423
nii_reorient 0.74 ±0.01 0.75 ±0.02 +0.8% (noise) 0.302
poi_local_to_global_arr 0.27 ±0.01 0.27 ±0.01 +0.6% (noise) 0.502
nii_save 1.28 ±0.01 1.27 ±0.02 -0.5% (noise) 0.890
nii_center_of_masses 0.37 ±0.01 0.37 ±0.01 +0.1% (noise) 0.571
poi_to_global 0.26 ±0.02 0.26 ±0.01 +0.0% (noise) 0.414

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 0171e70 vs head 0171e70 · 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_load_img 3.53 ±0.00 3.58 ±0.00 +1.4% —
nii_rescale_seg 5.95 ±0.00 5.88 ±0.00 -1.1% —
nii_rescale 6.13 ±0.00 6.07 ±0.00 -1.0% —
nii_resample_from_to 6.26 ±0.00 6.20 ±0.00 -1.0% —
nii_load_seg 5.91 ±0.00 5.96 ±0.00 +0.9% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_dilate_msk 5.85 ±0.00 5.87 ±0.00 +0.3% —
nii_erode_msk 5.87 ±0.00 5.88 ±0.00 +0.3% —
nii_save 3.71 ±0.00 3.71 ±0.00 +0.0% —
nii_set_dtype 5.18 ±0.00 5.18 ±0.00 +0.0% —
nii_reorient 5.80 ±0.00 5.80 ±0.00 +0.0% —
nii_apply_crop 5.80 ±0.00 5.80 ±0.00 +0.0% —
nii_pad_to 5.36 ±0.00 5.36 ±0.00 +0.0% —
nii_volumes 3.52 ±0.00 3.52 ±0.00 +0.0% —
nii_center_of_masses 3.27 ±0.00 3.27 ±0.00 +0.0% —
nii_extract_label 5.30 ±0.00 5.30 ±0.00 +0.0% —
nii_map_labels 5.43 ±0.00 5.43 ±0.00 +0.0% —
nii_fill_holes 6.22 ±0.00 6.22 ±0.00 +0.0% —
nii_get_connected_components 6.55 ±0.00 6.55 ±0.00 +0.0% —
nii_filter_connected_components 6.80 ±0.00 6.80 ±0.00 +0.0% —
poi_calc_centroids 5.99 ±0.00 5.99 ±0.00 +0.0% —
poi_calc_centroids_nocrop 5.86 ±0.00 5.86 ±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 5.18 ±0.00 5.18 ±0.00 +0.0% —
poi_calc_poi_from_subreg_vert 7.05 ±0.00 7.05 ±0.00 +0.0% 0.178
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 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
nii_unique 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_rescale 2.61 ±0.00 2.61 ±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 1.77 ±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_load_img 3.46 ±0.00 3.52 ±0.00 +1.5% —
nii_rescale_seg 5.88 ±0.00 5.82 ±0.00 -1.1% —
nii_rescale 6.07 ±0.00 6.01 ±0.00 -1.0% —
nii_resample_from_to 6.20 ±0.00 6.13 ±0.00 -1.0% —
nii_load_seg 5.85 ±0.00 5.90 ±0.00 +0.9% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_dilate_msk 5.79 ±0.00 5.80 ±0.00 +0.3% —
nii_erode_msk 5.80 ±0.00 5.82 ±0.00 +0.3% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_set_dtype 5.12 ±0.00 5.12 ±0.00 +0.0% —
nii_reorient 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_apply_crop 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_pad_to 5.30 ±0.00 5.30 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
nii_extract_label 5.24 ±0.00 5.24 ±0.00 +0.0% —
nii_map_labels 5.37 ±0.00 5.37 ±0.00 +0.0% —
nii_fill_holes 6.16 ±0.00 6.16 ±0.00 +0.0% —
nii_get_connected_components 6.49 ±0.00 6.49 ±0.00 +0.0% —
nii_filter_connected_components 6.74 ±0.00 6.74 ±0.00 +0.0% —
poi_calc_centroids 5.93 ±0.00 5.93 ±0.00 +0.0% 0.374
poi_calc_centroids_nocrop 5.86 ±0.00 5.86 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
poi_resample_from_to 5.11 ±0.00 5.11 ±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 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±0.00 +0.0% (noise) —
poi_save 1.34 ±0.00 1.34 ±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_load_img 3.53 ±0.00 3.58 ±0.00 +1.4% —
nii_rescale_seg 5.88 ±0.00 5.82 ±0.00 -1.1% —
nii_rescale 6.07 ±0.00 6.01 ±0.00 -1.0% —
nii_resample_from_to 6.20 ±0.00 6.13 ±0.00 -1.0% —
nii_load_seg 5.85 ±0.00 5.90 ±0.00 +0.9% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_dilate_msk 5.79 ±0.00 5.80 ±0.00 +0.3% —
nii_erode_msk 5.80 ±0.00 5.82 ±0.00 +0.3% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_set_dtype 5.18 ±0.00 5.18 ±0.00 +0.0% —
nii_reorient 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_apply_crop 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_pad_to 5.30 ±0.00 5.30 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
nii_extract_label 5.24 ±0.00 5.24 ±0.00 +0.0% —
nii_map_labels 5.37 ±0.00 5.37 ±0.00 +0.0% —
nii_fill_holes 6.16 ±0.00 6.16 ±0.00 +0.0% —
nii_get_connected_components 6.49 ±0.00 6.49 ±0.00 +0.0% —
nii_filter_connected_components 6.74 ±0.00 6.74 ±0.00 +0.0% —
poi_calc_centroids 5.93 ±0.00 5.93 ±0.00 +0.0% —
poi_calc_centroids_nocrop 5.80 ±0.00 5.80 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
poi_resample_from_to 5.11 ±0.00 5.11 ±0.00 +0.0% —
poi_calc_poi_from_subreg_vert 7.05 ±0.00 7.05 ±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 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±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_2d — shape (68, 52, 1)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_load_img 3.53 ±0.00 3.58 ±0.00 +1.4% —
nii_rescale_seg 5.88 ±0.00 5.82 ±0.00 -1.1% —
nii_rescale 6.07 ±0.00 6.01 ±0.00 -1.0% —
nii_resample_from_to 6.20 ±0.00 6.13 ±0.00 -1.0% —
nii_load_seg 5.85 ±0.00 5.90 ±0.00 +0.9% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_dilate_msk 5.79 ±0.00 5.80 ±0.00 +0.3% —
nii_erode_msk 5.80 ±0.00 5.82 ±0.00 +0.3% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_set_dtype 5.18 ±0.00 5.18 ±0.00 +0.0% —
nii_reorient 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_apply_crop 5.74 ±0.00 5.74 ±0.00 +0.0% —
nii_pad_to 5.30 ±0.00 5.30 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
nii_extract_label 5.24 ±0.00 5.24 ±0.00 +0.0% —
nii_map_labels 5.37 ±0.00 5.37 ±0.00 +0.0% —
nii_fill_holes 6.16 ±0.00 6.16 ±0.00 +0.0% —
nii_get_connected_components 6.49 ±0.00 6.49 ±0.00 +0.0% —
nii_filter_connected_components 6.74 ±0.00 6.74 ±0.00 +0.0% —
poi_calc_centroids 5.93 ±0.00 5.93 ±0.00 +0.0% —
poi_calc_centroids_nocrop 5.86 ±0.00 5.86 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
poi_resample_from_to 5.11 ±0.00 5.11 ±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 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±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) —

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.

@Hendrik-code
Hendrik-code merged commit 718144e into main Aug 28, 2026
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@Hendrik-code
Hendrik-code deleted the feat/np-raymarch-thickness branch August 28, 2026 13:01
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