docs(tutorials): update notebooks and atlas example to current API by robert-graf · Pull Request #149 · Hendrik-code/TPTBox

robert-graf · 2026-09-01T15:07:22Z

Summary

Aligns the tutorial notebooks and the atlas-POI-transfer example with the current TPTBox API — no functional code changes outside the notebooks / example script.

tutorial_Nifty.ipynb: compute_crop_slice / apply_crop_slice (removed) → compute_crop / apply_crop
tutorial_POI.ipynb: renamed markdown docs to calc_poi_from_subreg_vert, calc_centroids(first_stage=, second_stage=), calc_poi_labeled_buffered; fixed removed method names in the class overview (crop_centroids → apply_crop, shift_all_centroid_coordinates → shift_all_coordinates, dropped non-existent reorient_centroids_to)
tutorial_Dataset_processing.ipynb: dropped deprecated c_val=0 from ridged_points_from_poi in the three registration cells
examples/registration/atlas_poi_transfer_leg/example.{ipynb,py}: use run_vibeseg (was non-existent run_totalvibeseg), import prep_Atlas / Register_Point_Atlas from atlas_poi_transfer_leg_ct, adapt prep_Atlas call to the current 5-arg signature (seg, ct, out_atlas, ct_atlas, atlas_centroids, atlas_left=…)

Sample-data paths in tutorial_BIDS_files.ipynb / tutorial_pointregistation.ipynb still point at user-local NAS mounts (unchanged — existing TODO markers cover that).

Depends on

Debug #148 (base branch — Debug)
feat(registration): DeepALI closed-form point reg + template pre-registration hook #139 (Point-Reg / DeepALI closed-form point reg)

Test plan

Run each updated notebook end-to-end where sample data is available
Verify calc_poi_from_subreg_vert, calc_centroids(first_stage=…, second_stage=…), calc_poi_labeled_buffered all import cleanly
Verify atlas_poi_transfer_leg_ct.prep_Atlas runs against a real seg + ct pair

🤖 Generated with Claude Code

- tutorial_Nifty: compute_crop_slice/apply_crop_slice → compute_crop/apply_crop - tutorial_POI: rename calc_centroids_from_subreg_vert → calc_poi_from_subreg_vert, calc_centroids params vert_id/subreg_id → first_stage/second_stage, calc_centroids_labeled_buffered → calc_poi_labeled_buffered - tutorial_Dataset_processing: drop deprecated c_val=0 from ridged_points_from_poi - atlas_poi_transfer_leg example.ipynb/example.py: use run_vibeseg (was run_totalvibeseg), import prep_Atlas/Register_Point_Atlas from atlas_poi_transfer_leg_ct, adapt prep_Atlas to new (seg, ct, out_atlas, ct_atlas, atlas_centroids, atlas_left) signature Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012aiNSCPxTnizYuyTJVScLV

github-actions · 2026-09-02T08:07:02Z

Benchmark comparison

Speed (wall time per call)

baseline 004e994 vs head 004e994 · 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_rescale_seg`	3.09 ±0.07	3.53 ±0.13	+14.0%	0.001
`nii_load_img`	11.92 ±0.48	11.01 ±0.13	-7.6%	0.013
`nii_save`	12.47 ±0.28	11.94 ±0.22	-4.2%	0.028
`nii_load_seg`	3.14 ±0.09	3.03 ±0.16	-3.4%	0.274
`nii_filter_connected_components`	4.39 ±0.06	4.53 ±0.14	+3.1%	0.115

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`poi_calc_centroids_nocrop`	4.53 ±0.14	4.40 ±0.05	-2.8%	0.088
`nii_rescale`	40.69 ±0.36	41.65 ±0.17	+2.3%	0.004
`nii_resample_from_to`	42.85 ±0.70	43.67 ±0.55	+1.9%	0.078
`nii_erode_msk`	6.38 ±0.21	6.46 ±0.26	+1.3%	0.539
`nii_dilate_msk`	124.09 ±0.53	125.53 ±0.24	+1.2%	0.000
`poi_calc_poi_from_subreg_vert`	12.91 ±0.15	13.01 ±0.45	+0.8%	0.393
`nii_fill_holes`	4.49 ±0.04	4.52 ±0.13	+0.7%	0.458
`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_apply_crop`	0.57 ±0.03	0.84 ±0.05	+47.6% (noise)	0.000
`nii_get_array`	0.04 ±0.00	0.06 ±0.01	+37.1% (noise)	0.011
`poi_to_global`	0.20 ±0.02	0.26 ±0.02	+29.9% (noise)	0.001
`nii_map_labels`	1.02 ±0.08	1.32 ±0.07	+29.2% (noise)	0.000
`nii_extract_label`	0.35 ±0.02	0.45 ±0.05	+26.6% (noise)	0.005
`nii_pad_to`	0.64 ±0.03	0.80 ±0.07	+24.8% (noise)	0.006
`nii_compute_crop`	0.32 ±0.03	0.39 ±0.01	+22.8% (noise)	0.000
`poi_reorient`	0.38 ±0.03	0.45 ±0.02	+19.3% (noise)	0.019
`nii_reorient`	0.74 ±0.04	0.86 ±0.04	+17.2% (noise)	0.001
`poi_rescale`	0.22 ±0.02	0.25 ±0.03	+17.1% (noise)	0.019
`poi_load`	1.25 ±0.05	1.07 ±0.03	-14.8% (noise)	0.001
`nii_volumes`	1.81 ±0.02	2.08 ±0.05	+14.8% (noise)	0.000
`nii_unique`	0.65 ±0.01	0.73 ±0.05	+12.9% (noise)	0.012
`poi_local_to_global_arr`	0.33 ±0.01	0.36 ±0.04	+8.0% (noise)	0.531
`nii_center_of_masses`	1.68 ±0.02	1.82 ±0.06	+7.8% (noise)	0.002
`nii_get_connected_components`	2.29 ±0.06	2.41 ±0.03	+5.5% (noise)	0.012
`poi_map_labels`	0.19 ±0.02	0.18 ±0.02	-5.3% (noise)	0.085
`poi_save`	0.45 ±0.03	0.43 ±0.05	-3.7% (noise)	0.469
`poi_resample_from_to`	0.71 ±0.03	0.69 ±0.02	-3.1% (noise)	0.103
`poi_calc_centroids`	2.46 ±0.06	2.40 ±0.05	-2.4% (noise)	0.096
`nii_set_dtype`	0.51 ±0.06	0.51 ±0.03	+0.5% (noise)	0.850

`ct_2d` — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	5.61 ±0.09	5.69 ±0.09	+1.4%	0.282
`nii_resample_from_to`	7.70 ±0.12	7.80 ±0.20	+1.3%	0.815
`nii_dilate_msk`	15.16 ±0.17	14.99 ±0.11	-1.2%	0.267
`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_map_labels`	0.21 ±0.00	0.25 ±0.01	+19.5% (noise)	0.001
`nii_erode_msk`	1.22 ±0.05	1.06 ±0.02	-13.1% (noise)	0.000
`nii_map_labels`	0.61 ±0.02	0.53 ±0.01	-12.5% (noise)	0.000
`nii_load_img`	1.87 ±0.10	1.67 ±0.04	-10.4% (noise)	0.006
`poi_save`	0.51 ±0.03	0.56 ±0.04	+9.2% (noise)	0.039
`nii_apply_crop`	0.72 ±0.02	0.67 ±0.02	-7.0% (noise)	0.001
`nii_set_dtype`	0.46 ±0.04	0.43 ±0.01	-7.0% (noise)	0.129
`poi_reorient`	0.47 ±0.02	0.50 ±0.02	+6.9% (noise)	0.065
`nii_fill_holes`	1.04 ±0.02	0.97 ±0.05	-6.9% (noise)	0.012
`nii_unique`	0.13 ±0.01	0.12 ±0.01	-6.8% (noise)	0.108
`nii_compute_crop`	0.16 ±0.01	0.15 ±0.01	-5.7% (noise)	0.102
`nii_filter_connected_components`	0.95 ±0.11	1.00 ±0.04	+4.9% (noise)	0.589
`poi_resample_from_to`	0.80 ±0.02	0.83 ±0.03	+3.6% (noise)	0.022
`poi_rescale`	0.28 ±0.01	0.29 ±0.02	+3.3% (noise)	0.281
`poi_calc_centroids_nocrop`	1.31 ±0.08	1.27 ±0.08	-2.9% (noise)	0.978
`nii_load_seg`	1.85 ±0.11	1.90 ±0.07	+2.8% (noise)	0.513
`poi_load`	1.49 ±0.09	1.53 ±0.10	+2.6% (noise)	0.131
`poi_local_to_global_arr`	0.37 ±0.01	0.37 ±0.01	+2.4% (noise)	0.357
`nii_volumes`	0.31 ±0.02	0.31 ±0.01	-2.1% (noise)	0.841
`nii_center_of_masses`	0.22 ±0.02	0.23 ±0.02	+2.0% (noise)	0.684
`poi_calc_centroids`	1.09 ±0.05	1.07 ±0.03	-1.9% (noise)	0.316
`nii_pad_to`	0.58 ±0.03	0.57 ±0.03	-1.8% (noise)	0.389
`nii_extract_label`	0.47 ±0.03	0.46 ±0.02	-1.6% (noise)	0.921
`nii_reorient`	0.87 ±0.06	0.88 ±0.03	+1.5% (noise)	0.344
`nii_save`	1.53 ±0.09	1.52 ±0.06	-0.8% (noise)	0.697
`poi_to_global`	0.26 ±0.01	0.26 ±0.01	+0.5% (noise)	0.262
`nii_rescale_seg`	0.83 ±0.04	0.84 ±0.03	+0.4% (noise)	0.468
`nii_get_connected_components`	0.73 ±0.02	0.74 ±0.05	+0.3% (noise)	0.899
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	+0.2% (noise)	0.507

`mri_3d` — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`poi_calc_poi_from_subreg_vert`	12.29 ±0.27	13.58 ±0.92	+10.5%	0.102
`nii_rescale_seg`	3.69 ±0.22	3.45 ±0.07	-6.6%	0.036
`nii_save`	10.38 ±0.17	9.76 ±0.25	-6.0%	0.005
`nii_load_img`	9.84 ±0.22	9.48 ±0.37	-3.7%	0.020
`nii_load_seg`	3.43 ±0.07	3.35 ±0.09	-2.2%	0.209

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_filter_connected_components`	4.84 ±0.12	4.92 ±0.08	+1.6%	0.493
`nii_dilate_msk`	160.79 ±0.26	163.13 ±0.69	+1.5%	0.000
`nii_rescale`	39.15 ±0.39	38.65 ±0.60	-1.3%	0.074
`nii_resample_from_to`	40.66 ±0.30	40.39 ±0.30	-0.7%	0.043
`nii_erode_msk`	8.09 ±0.14	8.04 ±0.14	-0.6%	0.225
`nii_fill_holes`	5.58 ±0.10	5.56 ±0.05	-0.4%	0.197
`poi_calc_centroids_nocrop`	8.91 ±0.18	8.92 ±0.22	+0.0%	0.781
`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_rescale`	0.31 ±0.04	0.36 ±0.02	+17.3% (noise)	0.145
`poi_map_labels`	0.28 ±0.02	0.32 ±0.03	+12.6% (noise)	0.022
`poi_save`	0.57 ±0.03	0.64 ±0.01	+12.1% (noise)	0.012
`poi_load`	2.87 ±0.22	3.17 ±0.36	+10.2% (noise)	0.420
`nii_unique`	0.69 ±0.01	0.76 ±0.04	+9.3% (noise)	0.027
`nii_get_array`	0.07 ±0.00	0.07 ±0.01	-9.3% (noise)	0.687
`poi_local_to_global_arr`	0.38 ±0.02	0.41 ±0.02	+7.6% (noise)	0.009
`nii_get_connected_components`	2.53 ±0.12	2.34 ±0.06	-7.4% (noise)	0.044
`nii_set_dtype`	0.63 ±0.03	0.58 ±0.02	-7.3% (noise)	0.032
`nii_extract_label`	0.49 ±0.02	0.52 ±0.05	+5.9% (noise)	0.093
`nii_reorient`	0.98 ±0.02	0.93 ±0.02	-5.9% (noise)	0.005
`nii_volumes`	1.97 ±0.08	2.09 ±0.03	+5.8% (noise)	0.059
`poi_calc_centroids`	2.80 ±0.04	2.84 ±0.05	+1.2% (noise)	0.348
`nii_center_of_masses`	2.12 ±0.04	2.10 ±0.03	-0.9% (noise)	0.941
`poi_resample_from_to`	0.97 ±0.05	0.97 ±0.05	-0.9% (noise)	0.779
`poi_reorient`	0.49 ±0.01	0.49 ±0.02	+0.8% (noise)	0.329
`nii_compute_crop`	0.36 ±0.01	0.36 ±0.02	-0.7% (noise)	0.315
`nii_apply_crop`	0.77 ±0.06	0.77 ±0.02	-0.7% (noise)	0.289
`nii_map_labels`	1.25 ±0.07	1.24 ±0.04	-0.5% (noise)	0.723
`nii_pad_to`	0.81 ±0.01	0.81 ±0.03	+0.1% (noise)	0.721
`poi_to_global`	0.31 ±0.01	0.31 ±0.01	-0.0% (noise)	0.155

`mri_2d` — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	5.79 ±0.19	5.60 ±0.06	-3.2%	0.036
`nii_resample_from_to`	7.61 ±0.13	7.84 ±0.11	+3.1%	0.008
`nii_dilate_msk`	20.15 ±0.33	20.04 ±0.26	-0.5%	0.273
`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_center_of_masses`	0.44 ±0.02	0.54 ±0.03	+22.7% (noise)	0.000
`nii_volumes`	0.49 ±0.02	0.58 ±0.01	+18.4% (noise)	0.000
`nii_unique`	0.12 ±0.01	0.14 ±0.01	+18.3% (noise)	0.005
`nii_extract_label`	0.42 ±0.05	0.49 ±0.03	+16.5% (noise)	0.066
`nii_apply_crop`	0.65 ±0.02	0.75 ±0.06	+15.5% (noise)	0.004
`nii_pad_to`	0.54 ±0.05	0.60 ±0.03	+12.7% (noise)	0.126
`nii_compute_crop`	0.14 ±0.01	0.16 ±0.00	+12.4% (noise)	0.023
`nii_set_dtype`	0.49 ±0.02	0.43 ±0.03	-11.8% (noise)	0.019
`nii_save`	1.63 ±0.06	1.45 ±0.53	-11.3% (noise)	0.708
`nii_filter_connected_components`	0.99 ±0.05	0.89 ±0.04	-10.4% (noise)	0.010
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	-9.3% (noise)	0.046
`poi_calc_centroids`	1.33 ±0.04	1.21 ±0.02	-9.0% (noise)	0.001
`poi_load`	2.21 ±0.07	2.40 ±0.07	+8.2% (noise)	0.010
`nii_rescale_seg`	0.87 ±0.04	0.80 ±0.02	-8.1% (noise)	0.008
`nii_map_labels`	0.50 ±0.03	0.53 ±0.01	+6.8% (noise)	0.016
`poi_rescale`	0.31 ±0.03	0.29 ±0.01	-6.4% (noise)	0.288
`nii_load_img`	1.78 ±0.13	1.68 ±0.11	-5.8% (noise)	0.055
`poi_save`	0.58 ±0.01	0.61 ±0.04	+5.7% (noise)	0.141
`nii_get_connected_components`	0.72 ±0.05	0.68 ±0.03	-5.4% (noise)	0.365
`nii_erode_msk`	1.42 ±0.05	1.49 ±0.05	+5.0% (noise)	0.317
`poi_resample_from_to`	0.82 ±0.04	0.78 ±0.03	-4.5% (noise)	0.126
`poi_to_global`	0.28 ±0.02	0.27 ±0.00	-3.1% (noise)	0.277
`poi_local_to_global_arr`	0.37 ±0.02	0.38 ±0.02	+2.8% (noise)	0.914
`poi_map_labels`	0.26 ±0.04	0.27 ±0.01	+2.5% (noise)	0.785
`nii_reorient`	0.90 ±0.03	0.88 ±0.04	-2.0% (noise)	0.424
`poi_calc_centroids_nocrop`	1.58 ±0.03	1.55 ±0.05	-1.7% (noise)	0.269
`poi_reorient`	0.50 ±0.03	0.49 ±0.06	-1.4% (noise)	0.552
`nii_load_seg`	1.86 ±0.03	1.84 ±0.13	-1.1% (noise)	0.782
`nii_fill_holes`	1.25 ±0.05	1.26 ±0.16	+1.1% (noise)	0.284

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 004e994 vs head 004e994 · python 3.11.16 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.96 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
`poi_to_global`	3.08 ±0.00	3.14 ±0.00	+2.0%	—
`nii_center_of_masses`	3.27 ±0.00	3.34 ±0.00	+1.9%	—
`nii_save`	3.71 ±0.00	3.78 ±0.00	+1.8%	—
`nii_volumes`	3.52 ±0.00	3.59 ±0.00	+1.8%	—
`poi_reorient`	3.83 ±0.00	3.89 ±0.00	+1.6%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.28 ±0.00	5.23 ±0.00	-1.0%	—
`nii_reorient`	5.91 ±0.00	5.86 ±0.00	-0.9%	—
`nii_load_img`	3.57 ±0.00	3.59 ±0.00	+0.8%	—
`nii_load_seg`	6.01 ±0.00	5.96 ±0.00	-0.7%	—
`nii_dilate_msk`	5.93 ±0.00	5.90 ±0.00	-0.5%	—
`nii_erode_msk`	5.95 ±0.00	5.91 ±0.00	-0.5%	—
`nii_rescale_seg`	5.95 ±0.00	5.96 ±0.00	+0.3%	—
`nii_rescale`	6.17 ±0.00	6.15 ±0.00	-0.3%	—
`nii_resample_from_to`	6.30 ±0.00	6.28 ±0.00	-0.3%	—
`nii_set_dtype`	5.24 ±0.00	5.23 ±0.00	-0.2%	—
`poi_calc_poi_from_subreg_vert`	7.12 ±0.00	7.10 ±0.00	-0.2%	—
`nii_extract_label`	5.37 ±0.00	5.36 ±0.00	-0.2%	—
`nii_pad_to`	5.43 ±0.00	5.41 ±0.00	-0.2%	—
`nii_map_labels`	5.49 ±0.00	5.48 ±0.00	-0.2%	—
`nii_apply_crop`	5.87 ±0.00	5.86 ±0.00	-0.2%	—
`poi_calc_centroids_nocrop`	5.93 ±0.00	5.91 ±0.00	-0.2%	—
`poi_calc_centroids`	6.05 ±0.00	6.04 ±0.00	-0.2%	—
`nii_get_connected_components`	6.62 ±0.00	6.61 ±0.00	-0.2%	—
`nii_filter_connected_components`	6.87 ±0.00	6.86 ±0.00	-0.2%	—
`nii_fill_holes`	6.28 ±0.00	6.27 ±0.00	-0.1%	—
`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%	—
`poi_save`	1.40 ±0.00	1.46 ±0.00	+4.5% (noise)	—
`poi_load`	1.61 ±0.00	1.68 ±0.00	+3.9% (noise)	—
`nii_get_array`	1.65 ±0.00	1.71 ±0.00	+3.8% (noise)	—
`poi_map_labels`	1.77 ±0.00	1.84 ±0.00	+3.5% (noise)	—
`poi_rescale`	2.61 ±0.00	2.67 ±0.00	+2.4% (noise)	—
`nii_compute_crop`	2.90 ±0.00	2.96 ±0.00	+2.2% (noise)	—
`poi_local_to_global_arr`	2.96 ±0.00	3.02 ±0.00	+2.1% (noise)	—
`nii_unique`	2.96 ±0.00	3.02 ±0.00	+2.1% (noise)	—

`ct_2d` — shape (73, 47, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_to_global`	3.02 ±0.00	3.08 ±0.00	+2.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.27 ±0.00	+1.9%	—
`nii_save`	3.65 ±0.00	3.71 ±0.00	+1.8%	—
`nii_volumes`	3.46 ±0.00	3.52 ±0.00	+1.8%	—
`poi_reorient`	3.77 ±0.00	3.83 ±0.00	+1.7%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.21 ±0.00	5.16 ±0.00	-1.0%	—
`nii_load_img`	3.50 ±0.00	3.53 ±0.00	+0.9%	—
`nii_reorient`	5.84 ±0.00	5.79 ±0.00	-0.9%	—
`nii_load_seg`	5.95 ±0.00	5.90 ±0.00	-0.7%	—
`nii_dilate_msk`	5.87 ±0.00	5.84 ±0.00	-0.5%	—
`nii_erode_msk`	5.88 ±0.00	5.85 ±0.00	-0.5%	—
`nii_rescale_seg`	5.88 ±0.00	5.90 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_set_dtype`	5.18 ±0.00	5.17 ±0.00	-0.2%	—
`nii_extract_label`	5.30 ±0.00	5.29 ±0.00	-0.2%	—
`nii_pad_to`	5.36 ±0.00	5.35 ±0.00	-0.2%	—
`nii_map_labels`	5.43 ±0.00	5.42 ±0.00	-0.2%	—
`nii_apply_crop`	5.80 ±0.00	5.79 ±0.00	-0.2%	—
`poi_calc_centroids_nocrop`	5.93 ±0.00	5.91 ±0.00	-0.2%	—
`poi_calc_centroids`	5.99 ±0.00	5.98 ±0.00	-0.2%	—
`nii_get_connected_components`	6.55 ±0.00	6.54 ±0.00	-0.2%	—
`nii_filter_connected_components`	6.80 ±0.00	6.79 ±0.00	-0.2%	—
`nii_fill_holes`	6.22 ±0.00	6.21 ±0.00	-0.1%	—
`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%	—
`poi_save`	1.34 ±0.00	1.40 ±0.00	+4.7% (noise)	—
`poi_load`	1.55 ±0.00	1.61 ±0.00	+4.0% (noise)	—
`nii_get_array`	1.59 ±0.00	1.65 ±0.00	+3.9% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.77 ±0.00	+3.7% (noise)	—
`poi_rescale`	2.54 ±0.00	2.61 ±0.00	+2.5% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.90 ±0.00	+2.2% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.96 ±0.00	+2.2% (noise)	—
`nii_unique`	2.90 ±0.00	2.96 ±0.00	+2.2% (noise)	—

`mri_3d` — shape (68, 52, 67)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_to_global`	3.02 ±0.00	3.08 ±0.00	+2.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.27 ±0.00	+1.9%	—
`nii_save`	3.65 ±0.00	3.71 ±0.00	+1.8%	—
`nii_volumes`	3.46 ±0.00	3.53 ±0.00	+1.8%	—
`poi_reorient`	3.77 ±0.00	3.83 ±0.00	+1.7%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.21 ±0.00	5.16 ±0.00	-1.0%	—
`nii_load_img`	3.56 ±0.00	3.59 ±0.00	+0.9%	—
`nii_reorient`	5.84 ±0.00	5.79 ±0.00	-0.9%	—
`nii_load_seg`	5.95 ±0.00	5.90 ±0.00	-0.7%	—
`nii_dilate_msk`	5.87 ±0.00	5.84 ±0.00	-0.5%	—
`nii_erode_msk`	5.88 ±0.00	5.85 ±0.00	-0.5%	—
`nii_rescale_seg`	5.88 ±0.00	5.90 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_set_dtype`	5.24 ±0.00	5.23 ±0.00	-0.2%	—
`nii_extract_label`	5.30 ±0.00	5.29 ±0.00	-0.2%	—
`nii_pad_to`	5.36 ±0.00	5.35 ±0.00	-0.2%	—
`nii_map_labels`	5.43 ±0.00	5.42 ±0.00	-0.2%	—
`nii_apply_crop`	5.80 ±0.00	5.79 ±0.00	-0.2%	—
`poi_calc_centroids_nocrop`	5.86 ±0.00	5.85 ±0.00	-0.2%	—
`poi_calc_centroids`	5.99 ±0.00	5.98 ±0.00	-0.2%	—
`nii_get_connected_components`	6.55 ±0.00	6.54 ±0.00	-0.2%	—
`nii_filter_connected_components`	6.80 ±0.00	6.79 ±0.00	-0.2%	—
`poi_calc_poi_from_subreg_vert`	7.11 ±0.00	7.10 ±0.00	-0.2%	—
`nii_fill_holes`	6.22 ±0.00	6.21 ±0.00	-0.1%	—
`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`	1.40 ±0.00	1.46 ±0.00	+4.5% (noise)	—
`poi_load`	1.55 ±0.00	1.61 ±0.00	+4.0% (noise)	—
`nii_get_array`	1.59 ±0.00	1.65 ±0.00	+3.9% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.77 ±0.00	+3.7% (noise)	—
`poi_rescale`	2.54 ±0.00	2.61 ±0.00	+2.5% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.90 ±0.00	+2.2% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.96 ±0.00	+2.2% (noise)	—
`nii_unique`	2.90 ±0.00	2.96 ±0.00	+2.2% (noise)	—

`mri_2d` — shape (68, 52, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_to_global`	3.02 ±0.00	3.08 ±0.00	+2.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.27 ±0.00	+1.9%	—
`nii_save`	3.65 ±0.00	3.71 ±0.00	+1.8%	—
`nii_volumes`	3.46 ±0.00	3.52 ±0.12	+1.8%	0.801
`poi_reorient`	3.77 ±0.00	3.83 ±0.00	+1.7%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.21 ±0.00	5.16 ±0.00	-1.0%	—
`nii_load_img`	3.56 ±0.00	3.59 ±0.00	+0.9%	—
`nii_reorient`	5.84 ±0.00	5.79 ±0.00	-0.9%	—
`nii_load_seg`	5.95 ±0.00	5.90 ±0.00	-0.7%	—
`nii_dilate_msk`	5.87 ±0.00	5.84 ±0.00	-0.5%	—
`nii_erode_msk`	5.88 ±0.00	5.85 ±0.00	-0.5%	—
`nii_rescale_seg`	5.88 ±0.00	5.90 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_set_dtype`	5.24 ±0.00	5.23 ±0.00	-0.2%	—
`nii_extract_label`	5.30 ±0.00	5.29 ±0.00	-0.2%	—
`nii_pad_to`	5.36 ±0.00	5.35 ±0.00	-0.2%	—
`nii_map_labels`	5.43 ±0.00	5.42 ±0.00	-0.2%	—
`nii_apply_crop`	5.80 ±0.00	5.79 ±0.00	-0.2%	—
`poi_calc_centroids_nocrop`	5.93 ±0.00	5.91 ±0.00	-0.2%	—
`poi_calc_centroids`	5.99 ±0.00	5.98 ±0.00	-0.2%	—
`nii_get_connected_components`	6.55 ±0.00	6.54 ±0.00	-0.2%	—
`nii_filter_connected_components`	6.80 ±0.00	6.79 ±0.00	-0.2%	—
`nii_fill_holes`	6.22 ±0.00	6.21 ±0.00	-0.1%	—
`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%	—
`poi_save`	1.40 ±0.00	1.46 ±0.00	+4.5% (noise)	—
`poi_load`	1.55 ±0.00	1.61 ±0.00	+4.0% (noise)	—
`nii_get_array`	1.59 ±0.00	1.65 ±0.00	+3.9% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.77 ±0.00	+3.7% (noise)	—
`poi_rescale`	2.54 ±0.00	2.61 ±0.00	+2.5% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.90 ±0.00	+2.2% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.96 ±0.00	+2.2% (noise)	—
`nii_unique`	2.90 ±0.00	2.96 ±0.00	+2.2% (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 requested a review from Hendrik-code September 1, 2026 15:08

robert-graf self-assigned this Sep 1, 2026

robert-graf added the bug Something isn't working label Sep 1, 2026

Base automatically changed from debug to main September 2, 2026 08:02

Merge branch 'main' into tutorial

46f4c7f

Hendrik-code approved these changes Sep 2, 2026

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Hendrik-code merged commit 257340a into main Sep 2, 2026
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Hendrik-code deleted the tutorial branch September 2, 2026 08:07

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docs(tutorials): update notebooks and atlas example to current API - #149

docs(tutorials): update notebooks and atlas example to current API#149
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robert-graf commented Sep 1, 2026

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Benchmark comparison

Speed (wall time per call)

ct_3d — shape (73, 47, 73)

ct_2d — shape (73, 47, 1)

mri_3d — shape (68, 52, 67)

mri_2d — shape (68, 52, 1)

Memory (peak RSS growth per call)

ct_3d — shape (73, 47, 73)

ct_2d — shape (73, 47, 1)

mri_3d — shape (68, 52, 67)

mri_2d — shape (68, 52, 1)

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`ct_3d` — shape (73, 47, 73)

`ct_2d` — shape (73, 47, 1)

`mri_3d` — shape (68, 52, 67)

`mri_2d` — shape (68, 52, 1)

`ct_3d` — shape (73, 47, 73)

`ct_2d` — shape (73, 47, 1)

`mri_3d` — shape (68, 52, 67)

`mri_2d` — shape (68, 52, 1)