Documentation by robert-graf · Pull Request #132 · Hendrik-code/TPTBox

robert-graf · 2026-08-17T10:05:35Z

No description provided.

…nto development_robert

- Fix 24 ghost args (docstring names not in signature) and 53 undocumented params (in signature but missing from Args block) across core, spine, registration, segmentation, mesh3D, stitching, and logger modules - Refresh stale summaries/Returns/Notes where behavior had drifted (NII.apply_crop, extract_label, map_labels, ravel; POI.apply_crop had a dead second docstring; POI.to_global; several spinestats helpers; General_Registration class docstring) - Rename verbos -> verbose param on NII.load_nrrd / load_slicer_nrrd - Enrich docs/api pages for logger, mesh3d, stitching Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

github-actions · 2026-08-17T10:08:48Z

Benchmark comparison

Speed (wall time per call)

baseline 71d52bb vs head 71d52bb · python 3.11.15 · 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`	3.20 ±0.03	3.48 ±0.02	+9.0%	0.000
`nii_dilate_msk`	122.70 ±4.43	130.54 ±6.24	+6.4%	0.090
`poi_calc_centroids_nocrop`	4.62 ±0.05	4.89 ±0.07	+5.9%	0.000
`poi_calc_poi_from_subreg_vert`	11.93 ±0.22	12.44 ±0.18	+4.2%	0.005
`nii_save`	11.82 ±0.09	12.32 ±0.05	+4.2%	0.000

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_fill_holes`	4.78 ±0.03	4.95 ±0.14	+3.6%	0.039
`nii_filter_connected_components`	4.46 ±0.06	4.61 ±0.07	+3.5%	0.004
`nii_erode_msk`	6.24 ±0.13	6.43 ±0.60	+3.1%	0.233
`nii_resample_from_to`	41.95 ±0.20	43.13 ±0.27	+2.8%	0.000
`nii_rescale`	40.00 ±0.11	41.06 ±0.32	+2.7%	0.002
`nii_load_img`	12.40 ±0.04	12.39 ±0.06	-0.1%	0.665
`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_reorient`	0.80 ±0.02	1.07 ±0.02	+33.1% (noise)	0.000
`nii_set_dtype`	0.53 ±0.02	0.66 ±0.01	+25.5% (noise)	0.000
`poi_map_labels`	0.18 ±0.02	0.23 ±0.01	+24.4% (noise)	0.010
`nii_apply_crop`	0.71 ±0.04	0.88 ±0.01	+23.0% (noise)	0.000
`poi_resample_from_to`	0.67 ±0.02	0.82 ±0.04	+22.1% (noise)	0.000
`poi_to_global`	0.23 ±0.01	0.28 ±0.01	+19.9% (noise)	0.001
`nii_pad_to`	0.76 ±0.03	0.90 ±0.03	+18.6% (noise)	0.000
`nii_extract_label`	0.50 ±0.03	0.58 ±0.02	+18.0% (noise)	0.001
`nii_map_labels`	0.96 ±0.02	1.10 ±0.04	+14.8% (noise)	0.001
`nii_get_array`	0.06 ±0.01	0.06 ±0.00	+14.2% (noise)	0.118
`nii_compute_crop`	0.35 ±0.02	0.40 ±0.00	+13.5% (noise)	0.002
`poi_load`	0.96 ±0.03	1.07 ±0.03	+11.3% (noise)	0.000
`nii_load_seg`	2.92 ±0.05	3.20 ±0.03	+9.7% (noise)	0.000
`poi_save`	0.51 ±0.03	0.55 ±0.02	+8.6% (noise)	0.006
`poi_rescale`	0.26 ±0.02	0.28 ±0.02	+8.5% (noise)	0.051
`poi_calc_centroids`	2.65 ±0.01	2.86 ±0.02	+8.1% (noise)	0.000
`nii_unique`	0.66 ±0.01	0.71 ±0.01	+7.8% (noise)	0.000
`poi_local_to_global_arr`	0.27 ±0.01	0.29 ±0.01	+7.8% (noise)	0.003
`nii_get_connected_components`	2.15 ±0.03	2.32 ±0.03	+7.5% (noise)	0.000
`poi_reorient`	0.47 ±0.02	0.50 ±0.01	+5.2% (noise)	0.014
`nii_volumes`	1.97 ±0.03	2.06 ±0.01	+4.3% (noise)	0.005
`nii_center_of_masses`	1.86 ±0.01	1.93 ±0.02	+3.5% (noise)	0.000

`ct_2d` — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	5.73 ±0.18	5.97 ±0.06	+4.2%	0.094
`nii_resample_from_to`	7.65 ±1.18	7.53 ±0.49	-1.6%	0.490
`nii_dilate_msk`	14.02 ±0.13	13.97 ±0.08	-0.4%	0.689
`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 ±0.01	0.02 ±0.00	+18.3% (noise)	0.302
`poi_map_labels`	0.23 ±0.01	0.26 ±0.01	+12.3% (noise)	0.032
`nii_rescale_seg`	0.86 ±0.03	0.96 ±0.02	+11.7% (noise)	0.000
`poi_reorient`	0.50 ±0.02	0.56 ±0.02	+11.6% (noise)	0.001
`nii_reorient`	0.87 ±0.04	0.97 ±0.23	+11.1% (noise)	0.237
`nii_set_dtype`	0.46 ±0.01	0.51 ±0.01	+11.0% (noise)	0.000
`poi_to_global`	0.29 ±0.02	0.32 ±0.04	+10.7% (noise)	0.100
`nii_unique`	0.16 ±0.01	0.17 ±0.03	+10.7% (noise)	0.077
`nii_get_connected_components`	0.73 ±0.03	0.78 ±0.03	+7.7% (noise)	0.039
`poi_resample_from_to`	0.80 ±0.02	0.85 ±0.01	+7.3% (noise)	0.001
`nii_center_of_masses`	0.25 ±0.01	0.27 ±0.01	+7.1% (noise)	0.006
`nii_load_img`	1.56 ±0.05	1.66 ±0.07	+6.5% (noise)	0.019
`nii_compute_crop`	0.18 ±0.01	0.19 ±0.00	+6.4% (noise)	0.021
`nii_pad_to`	0.65 ±0.02	0.70 ±0.02	+6.2% (noise)	0.007
`nii_load_seg`	1.71 ±0.04	1.82 ±0.02	+6.2% (noise)	0.002
`nii_save`	1.46 ±0.03	1.55 ±0.02	+5.9% (noise)	0.001
`nii_filter_connected_components`	0.93 ±0.02	0.98 ±0.03	+5.7% (noise)	0.006
`poi_rescale`	0.31 ±0.01	0.33 ±0.01	+5.6% (noise)	0.012
`poi_load`	1.07 ±0.02	1.13 ±0.02	+5.5% (noise)	0.001
`poi_calc_centroids`	1.03 ±0.03	1.09 ±0.02	+5.4% (noise)	0.005
`nii_fill_holes`	0.92 ±0.02	0.96 ±0.02	+4.3% (noise)	0.007
`poi_calc_centroids_nocrop`	1.22 ±0.01	1.27 ±0.01	+4.3% (noise)	0.000
`nii_map_labels`	0.58 ±0.02	0.60 ±0.01	+4.3% (noise)	0.019
`nii_apply_crop`	0.79 ±0.01	0.82 ±0.01	+3.9% (noise)	0.001
`nii_erode_msk`	1.05 ±0.01	1.08 ±0.03	+3.2% (noise)	0.010
`poi_save`	0.59 ±0.04	0.60 ±0.01	+2.1% (noise)	0.433
`nii_volumes`	0.34 ±0.01	0.35 ±0.01	+1.7% (noise)	0.048
`nii_extract_label`	0.52 ±0.02	0.53 ±0.02	+1.0% (noise)	0.346
`poi_local_to_global_arr`	0.32 ±0.02	0.32 ±0.01	-0.3% (noise)	0.817

`mri_3d` — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale_seg`	3.15 ±0.03	3.29 ±0.02	+4.5%	0.000
`poi_calc_poi_from_subreg_vert`	11.16 ±0.08	11.58 ±0.32	+3.8%	0.016
`nii_erode_msk`	7.81 ±0.09	8.09 ±0.50	+3.5%	0.137
`nii_load_img`	9.81 ±0.10	10.12 ±0.06	+3.1%	0.004
`nii_resample_from_to`	39.36 ±0.30	40.58 ±0.10	+3.1%	0.001

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	37.71 ±0.23	38.74 ±0.63	+2.8%	0.013
`nii_fill_holes`	5.62 ±0.05	5.73 ±0.05	+1.9%	0.006
`poi_calc_centroids_nocrop`	9.14 ±0.06	9.31 ±0.01	+1.8%	0.017
`nii_save`	9.77 ±0.29	9.91 ±0.10	+1.4%	0.833
`nii_load_seg`	3.08 ±0.30	3.12 ±0.04	+1.2%	0.471
`nii_filter_connected_components`	4.74 ±0.07	4.79 ±0.07	+1.1%	0.100
`nii_dilate_msk`	155.06 ±2.45	156.21 ±0.56	+0.7%	0.911
`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_reorient`	0.52 ±0.02	0.59 ±0.01	+13.7% (noise)	0.000
`poi_save`	0.60 ±0.02	0.68 ±0.03	+13.6% (noise)	0.005
`nii_get_array`	0.06 ±0.02	0.05 ±0.02	-13.4% (noise)	0.555
`poi_resample_from_to`	0.82 ±0.03	0.91 ±0.01	+10.9% (noise)	0.001
`nii_apply_crop`	0.79 ±0.03	0.87 ±0.01	+10.5% (noise)	0.000
`nii_extract_label`	0.53 ±0.02	0.58 ±0.02	+10.0% (noise)	0.000
`poi_rescale`	0.34 ±0.01	0.37 ±0.02	+9.6% (noise)	0.012
`nii_reorient`	0.94 ±0.03	1.01 ±0.02	+8.0% (noise)	0.017
`poi_map_labels`	0.28 ±0.01	0.30 ±0.01	+8.0% (noise)	0.010
`nii_set_dtype`	0.59 ±0.01	0.63 ±0.03	+7.7% (noise)	0.009
`poi_to_global`	0.32 ±0.02	0.34 ±0.01	+7.5% (noise)	0.089
`nii_map_labels`	1.06 ±0.02	1.14 ±0.02	+7.2% (noise)	0.002
`nii_compute_crop`	0.37 ±0.00	0.39 ±0.02	+6.0% (noise)	0.019
`poi_local_to_global_arr`	0.31 ±0.01	0.33 ±0.01	+5.6% (noise)	0.011
`poi_calc_centroids`	2.90 ±0.05	3.06 ±0.02	+5.6% (noise)	0.005
`poi_load`	2.16 ±0.05	2.27 ±0.02	+5.3% (noise)	0.023
`nii_get_connected_components`	2.13 ±0.03	2.23 ±0.02	+5.1% (noise)	0.000
`nii_unique`	0.66 ±0.02	0.68 ±0.01	+3.7% (noise)	0.009
`nii_pad_to`	0.85 ±0.01	0.87 ±0.02	+2.3% (noise)	0.152
`nii_center_of_masses`	2.11 ±0.03	2.15 ±0.01	+2.0% (noise)	0.014
`nii_volumes`	2.07 ±0.03	2.11 ±0.00	+1.6% (noise)	0.068

`mri_2d` — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	5.81 ±0.22	5.88 ±0.05	+1.3%	0.216
`nii_dilate_msk`	18.24 ±0.06	18.36 ±0.15	+0.7%	0.051
`nii_resample_from_to`	7.71 ±0.06	7.75 ±0.12	+0.6%	0.382
`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_unique`	0.14 ±0.01	0.17 ±0.00	+21.0% (noise)	0.000
`nii_get_array`	0.02 ±0.00	0.03 ±0.00	+20.9% (noise)	0.051
`nii_map_labels`	0.53 ±0.02	0.61 ±0.02	+13.9% (noise)	0.000
`nii_compute_crop`	0.17 ±0.01	0.20 ±0.02	+13.4% (noise)	0.026
`nii_set_dtype`	0.45 ±0.02	0.50 ±0.01	+12.7% (noise)	0.000
`nii_pad_to`	0.61 ±0.02	0.68 ±0.01	+11.8% (noise)	0.000
`nii_rescale_seg`	0.85 ±0.02	0.93 ±0.01	+9.5% (noise)	0.000
`poi_calc_centroids`	1.18 ±0.04	1.29 ±0.16	+9.1% (noise)	0.083
`nii_filter_connected_components`	0.91 ±0.02	0.98 ±0.01	+8.5% (noise)	0.000
`poi_reorient`	0.55 ±0.02	0.59 ±0.02	+8.4% (noise)	0.002
`poi_local_to_global_arr`	0.30 ±0.01	0.33 ±0.01	+8.1% (noise)	0.141
`nii_reorient`	0.88 ±0.02	0.95 ±0.02	+8.0% (noise)	0.000
`nii_get_connected_components`	0.71 ±0.02	0.76 ±0.01	+7.2% (noise)	0.001
`poi_save`	0.63 ±0.03	0.67 ±0.02	+6.7% (noise)	0.260
`nii_extract_label`	0.50 ±0.03	0.53 ±0.24	+6.5% (noise)	0.290
`nii_volumes`	0.49 ±0.02	0.52 ±0.02	+6.4% (noise)	0.022
`nii_apply_crop`	0.77 ±0.04	0.82 ±0.01	+6.3% (noise)	0.069
`nii_fill_holes`	1.08 ±0.03	1.14 ±0.03	+5.9% (noise)	0.004
`nii_erode_msk`	1.24 ±0.01	1.31 ±0.03	+5.7% (noise)	0.001
`nii_save`	1.50 ±0.03	1.59 ±0.03	+5.4% (noise)	0.006
`poi_calc_centroids_nocrop`	1.44 ±0.05	1.49 ±0.02	+3.9% (noise)	0.015
`poi_load`	1.92 ±0.01	2.00 ±0.02	+3.8% (noise)	0.000
`nii_load_img`	1.59 ±0.02	1.65 ±0.01	+3.7% (noise)	0.000
`poi_to_global`	0.32 ±0.02	0.33 ±0.01	+3.5% (noise)	0.799
`poi_rescale`	0.35 ±0.01	0.36 ±0.01	+3.5% (noise)	0.068
`poi_resample_from_to`	0.88 ±0.02	0.90 ±0.01	+1.7% (noise)	0.257
`nii_center_of_masses`	0.44 ±0.01	0.45 ±0.02	+1.3% (noise)	0.347
`nii_load_seg`	1.81 ±0.02	1.83 ±0.02	+1.0% (noise)	0.193
`poi_map_labels`	0.30 ±0.01	0.30 ±0.01	-0.3% (noise)	0.279

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 71d52bb vs head 71d52bb · python 3.11.15 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.89 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_seg`	6.01 ±0.00	5.92 ±0.00	-1.4%	—
`nii_load_img`	3.57 ±0.00	3.53 ±0.00	-1.2%	—
`nii_dilate_msk`	5.93 ±0.00	5.87 ±0.00	-1.0%	—
`nii_erode_msk`	5.94 ±0.00	5.88 ±0.00	-1.0%	—
`nii_set_dtype`	5.24 ±0.00	5.19 ±0.00	-0.9%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_extract_label`	5.43 ±0.00	5.38 ±0.00	-0.9%	—
`nii_map_labels`	5.49 ±0.00	5.44 ±0.00	-0.9%	—
`nii_apply_crop`	5.86 ±0.00	5.82 ±0.00	-0.8%	—
`poi_calc_centroids`	6.05 ±0.00	6.00 ±0.00	-0.8%	—
`poi_resample_from_to`	5.22 ±0.00	5.18 ±0.00	-0.7%	—
`nii_fill_holes`	6.28 ±0.00	6.23 ±0.00	-0.7%	—
`nii_get_connected_components`	6.61 ±0.00	6.57 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.86 ±0.00	6.82 ±0.00	-0.7%	—
`nii_reorient`	5.86 ±0.00	5.82 ±0.00	-0.7%	—
`nii_rescale_seg`	5.93 ±0.00	5.89 ±0.00	-0.7%	—
`nii_pad_to`	5.41 ±0.00	5.38 ±0.00	-0.6%	—
`nii_rescale`	6.12 ±0.00	6.08 ±0.00	-0.6%	—
`nii_resample_from_to`	6.25 ±0.00	6.21 ±0.00	-0.6%	—
`poi_calc_poi_from_subreg_vert`	7.11 ±0.00	7.06 ±0.00	-0.6%	—
`poi_calc_centroids_nocrop`	5.91 ±0.00	5.88 ±0.00	-0.6%	—
`poi_to_global`	3.09 ±0.00	3.08 ±0.00	-0.1%	—
`nii_center_of_masses`	3.28 ±0.00	3.27 ±0.00	-0.1%	—
`nii_volumes`	3.53 ±0.00	3.52 ±0.00	-0.1%	—
`nii_save`	3.71 ±0.00	3.71 ±0.00	-0.1%	—
`poi_reorient`	3.84 ±0.00	3.83 ±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	1.40 ±0.00	-0.3% (noise)	—
`poi_load`	1.61 ±0.00	1.61 ±0.00	-0.2% (noise)	—
`nii_get_array`	1.65 ±0.00	1.65 ±0.00	-0.2% (noise)	—
`poi_map_labels`	1.77 ±0.00	1.77 ±0.00	-0.2% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	-0.1% (noise)	—
`nii_compute_crop`	2.90 ±0.00	2.90 ±0.00	-0.1% (noise)	—
`poi_local_to_global_arr`	2.96 ±0.00	2.96 ±0.00	-0.1% (noise)	—
`nii_unique`	2.96 ±0.00	2.96 ±0.00	-0.1% (noise)	—

`ct_2d` — shape (73, 47, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_load_seg`	5.94 ±0.00	5.85 ±0.00	-1.4%	—
`nii_load_img`	3.50 ±0.00	3.46 ±0.00	-1.2%	—
`nii_dilate_msk`	5.86 ±0.00	5.80 ±0.00	-1.0%	—
`nii_erode_msk`	5.87 ±0.00	5.81 ±0.00	-1.0%	—
`nii_set_dtype`	5.17 ±0.00	5.12 ±0.00	-0.9%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_extract_label`	5.36 ±0.00	5.31 ±0.00	-0.9%	—
`nii_map_labels`	5.42 ±0.00	5.37 ±0.00	-0.9%	—
`nii_apply_crop`	5.79 ±0.00	5.75 ±0.00	-0.8%	—
`poi_calc_centroids`	5.98 ±0.00	5.93 ±0.00	-0.8%	—
`poi_resample_from_to`	5.16 ±0.00	5.12 ±0.00	-0.8%	—
`nii_fill_holes`	6.21 ±0.00	6.16 ±0.00	-0.8%	—
`nii_get_connected_components`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.79 ±0.00	6.75 ±0.00	-0.7%	—
`nii_reorient`	5.79 ±0.00	5.75 ±0.00	-0.7%	—
`nii_rescale_seg`	5.86 ±0.00	5.82 ±0.00	-0.7%	—
`nii_pad_to`	5.34 ±0.00	5.30 ±0.00	-0.7%	—
`nii_rescale`	6.05 ±0.00	6.01 ±0.00	-0.6%	—
`nii_resample_from_to`	6.18 ±0.00	6.14 ±0.00	-0.6%	—
`poi_calc_centroids_nocrop`	5.90 ±0.00	5.87 ±0.00	-0.6%	—
`poi_to_global`	3.02 ±0.00	3.01 ±0.00	-0.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.20 ±0.00	-0.1%	—
`nii_volumes`	3.46 ±0.00	3.45 ±0.00	-0.1%	—
`nii_save`	3.64 ±0.00	3.64 ±0.00	-0.1%	—
`poi_reorient`	3.77 ±0.00	3.76 ±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	1.33 ±0.00	-0.3% (noise)	—
`poi_load`	1.55 ±0.00	1.54 ±0.00	-0.3% (noise)	—
`nii_get_array`	1.58 ±0.00	1.58 ±0.00	-0.2% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.70 ±0.00	-0.2% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	-0.2% (noise)	—
`nii_compute_crop`	2.83 ±0.00	2.83 ±0.00	-0.1% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	-0.1% (noise)	—
`nii_unique`	2.89 ±0.00	2.89 ±0.00	-0.1% (noise)	—

`mri_3d` — shape (68, 52, 67)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_load_seg`	5.94 ±0.00	5.85 ±0.00	-1.4%	—
`nii_load_img`	3.56 ±0.00	3.52 ±0.00	-1.2%	—
`nii_dilate_msk`	5.86 ±0.00	5.80 ±0.00	-1.0%	—
`nii_erode_msk`	5.87 ±0.00	5.81 ±0.00	-1.0%	—
`nii_set_dtype`	5.23 ±0.00	5.18 ±0.00	-0.9%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_extract_label`	5.36 ±0.00	5.31 ±0.00	-0.9%	—
`nii_map_labels`	5.42 ±0.00	5.37 ±0.00	-0.9%	—
`nii_apply_crop`	5.79 ±0.00	5.75 ±0.00	-0.8%	—
`poi_calc_centroids`	5.98 ±0.00	5.93 ±0.00	-0.8%	—
`poi_resample_from_to`	5.16 ±0.00	5.12 ±0.00	-0.8%	—
`nii_fill_holes`	6.21 ±0.00	6.16 ±0.00	-0.8%	—
`nii_get_connected_components`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.79 ±0.00	6.75 ±0.00	-0.7%	—
`nii_reorient`	5.79 ±0.00	5.75 ±0.00	-0.7%	—
`nii_rescale_seg`	5.86 ±0.00	5.82 ±0.00	-0.7%	—
`poi_calc_poi_from_subreg_vert`	7.10 ±0.00	7.05 ±0.00	-0.7%	—
`nii_pad_to`	5.34 ±0.00	5.30 ±0.00	-0.7%	—
`nii_rescale`	6.05 ±0.00	6.01 ±0.00	-0.6%	—
`nii_resample_from_to`	6.18 ±0.00	6.14 ±0.00	-0.6%	—
`poi_calc_centroids_nocrop`	5.84 ±0.00	5.80 ±0.00	-0.6%	—
`poi_to_global`	3.02 ±0.00	3.01 ±0.00	-0.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.20 ±0.00	-0.1%	—
`nii_volumes`	3.46 ±0.00	3.45 ±0.00	-0.1%	—
`nii_save`	3.64 ±0.00	3.64 ±0.00	-0.1%	—
`poi_reorient`	3.77 ±0.00	3.76 ±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	1.39 ±0.00	-0.3% (noise)	—
`poi_load`	1.55 ±0.00	1.54 ±0.00	-0.3% (noise)	—
`nii_get_array`	1.58 ±0.00	1.58 ±0.00	-0.2% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.70 ±0.00	-0.2% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	-0.2% (noise)	—
`nii_compute_crop`	2.83 ±0.00	2.83 ±0.00	-0.1% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	-0.1% (noise)	—
`nii_unique`	2.89 ±0.00	2.89 ±0.00	-0.1% (noise)	—

`mri_2d` — shape (68, 52, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_load_seg`	5.94 ±0.00	5.85 ±0.00	-1.4%	—
`nii_load_img`	3.56 ±0.00	3.52 ±0.00	-1.2%	—
`nii_dilate_msk`	5.86 ±0.00	5.80 ±0.00	-1.0%	—
`nii_erode_msk`	5.87 ±0.00	5.81 ±0.00	-1.0%	—
`nii_set_dtype`	5.23 ±0.00	5.18 ±0.00	-0.9%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_extract_label`	5.36 ±0.00	5.31 ±0.00	-0.9%	—
`nii_map_labels`	5.42 ±0.00	5.37 ±0.00	-0.9%	—
`nii_apply_crop`	5.79 ±0.00	5.75 ±0.00	-0.8%	—
`poi_calc_centroids`	5.98 ±0.00	5.93 ±0.00	-0.8%	—
`poi_resample_from_to`	5.16 ±0.00	5.12 ±0.00	-0.8%	—
`nii_fill_holes`	6.21 ±0.00	6.16 ±0.00	-0.8%	—
`nii_get_connected_components`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.79 ±0.00	6.75 ±0.00	-0.7%	—
`nii_reorient`	5.79 ±0.00	5.75 ±0.00	-0.7%	—
`nii_rescale_seg`	5.86 ±0.00	5.82 ±0.00	-0.7%	—
`nii_pad_to`	5.34 ±0.00	5.30 ±0.00	-0.7%	—
`nii_rescale`	6.05 ±0.00	6.01 ±0.00	-0.6%	—
`nii_resample_from_to`	6.18 ±0.00	6.14 ±0.00	-0.6%	—
`poi_calc_centroids_nocrop`	5.90 ±0.00	5.87 ±0.00	-0.6%	—
`poi_to_global`	3.02 ±0.00	3.01 ±0.00	-0.1%	—
`nii_center_of_masses`	3.21 ±0.00	3.20 ±0.00	-0.1%	—
`nii_volumes`	3.46 ±0.00	3.45 ±0.00	-0.1%	—
`nii_save`	3.64 ±0.00	3.64 ±0.00	-0.1%	—
`poi_reorient`	3.77 ±0.00	3.76 ±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	1.39 ±0.00	-0.3% (noise)	—
`poi_load`	1.55 ±0.00	1.54 ±0.00	-0.3% (noise)	—
`nii_get_array`	1.58 ±0.00	1.58 ±0.00	-0.2% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.70 ±0.00	-0.2% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	-0.2% (noise)	—
`nii_compute_crop`	2.83 ±0.00	2.83 ±0.00	-0.1% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	-0.1% (noise)	—
`nii_unique`	2.89 ±0.00	2.89 ±0.00	-0.1% (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 and others added 3 commits August 17, 2026 10:55

Merge branch 'development_robert' of github.com:Hendrik-code/TPTBox i…

9131b53

…nto development_robert

style fixes by ruff

1ebc26f

robert-graf changed the title ~~Development robert~~ Documentation Aug 17, 2026

Hendrik-code assigned robert-graf Aug 17, 2026

Hendrik-code added the documentation Improvements or additions to documentation label Aug 17, 2026

robert-graf merged commit 445fbc3 into main Aug 17, 2026
6 checks passed

robert-graf deleted the development_robert branch August 17, 2026 11:27

Navigation Menu

Documentation - #132

Documentation#132
robert-graf merged 3 commits into
mainfrom
development_robert

robert-graf commented Aug 17, 2026

Uh oh!

github-actions Bot commented Aug 17, 2026 •

edited

Loading

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

robert-graf commented Aug 17, 2026

Uh oh!

github-actions Bot commented Aug 17, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

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)

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

github-actions Bot commented Aug 17, 2026 •

edited

Loading

`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)